NNNNNN.p NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNONNNNNNNNNNNNNNNNNNNNNNo  @`! #@%`')+-/1 3@579;=?A C@E`GIKMOQ S@U`W[]_a c@e`gikmoq s@u`wy{} @` @ ` @ ` @ ` @ ` ǀ ɠ @ ` ׀ ٠  @` @`!Aa   !Aa!!#A%a')+-/1!3A5a79;=?A!CAEaGIKMOQ!SAUaWY[]_a!cAeagkmoq!sAuawy}!Aa!Aa!Aa!Aa!Aaǁɡ!Aaׁ١!Oo!Aa " B b  !"!B!b!!!!!"!""#B"%b"'")"+"-"/#1"#35b#o  @`! #@%`')+-/1 3@579;=?A C@E`GIKMOQ S@U`W[]_a c@e`gikmoq s@u`wy{} @` @ ` @ ` @ ` @ ` ǀ ɠ @ ` ׀ ٠  @` @`!Aa   !Aa!!#A%a')+-/1!3A5a79;=?A!CAEaGIKMOQ!SAUaWY[]_a!cAeagkmoq!sAuawy}!Aa!Aa!Aa!Aa!Aaǁɡ!Aaׁ١!Oo!Aa " B b  !"!B!b!!!!!"!""#B"%b"'")"+"-"/#1"#35b#A462  CD_LONG CUS ]1CD_SHORTCUS ^1READ ME f;CC31HELPPRG wi2KEYWORDSPRG Oi6REFBASE PRG iYl=REFSPLITPRG ؆eiLESAMPLE REF ji{~FLOW_ASCTXT ׮fJLEES DIT +. `FLOW_IBMTXT f[REFBASE2TXT ɽi:UPDATE TXT 6f4Y   AONPxNEN:N`NNZNN7A탖amEalNak`aTpd~A탖NPp avpa`4pa`.p a`(x"mNƦE paux"mNƦE>paux"mNƦp$m($$m( aJayFx$m(ؒ"mNƦ$m(R$m( ]oE\pauvx "mNƦEcpau`x "mNƦEypauJx "mNƦEpau4x "mNƦEpaux"mNƦEp aux"mNƦEp atx"mNƦEpatx"mNƦEpatx"mNƦEp 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Multiple Comma-Delimited files ... ------------------------------------- Issue extraction--reserved Help ... Discipline abbreviations ... Quit ...Issues Extract single REF-file ... Extract multiple REF-files ... Load issues ... Show issues ...Profiles Load profile ... Show profile ... Save profile ... Print profile ... --Journal profiles------ Sort and shrink ... Sort and expand ... Printer--Port selection--------------- Parallel (printer) Serial (modem)--Printer selection------------ Matrix printer HP DeskJet - Courier 6pt HP DeskJet - Prestige 7pt HP LaserJet4 - Courier 16 cpi HP LaserJet4 - Gothic 21 cpiWritten in GFA-Basic V3.6 by|J.M. de Boer, Dept. Nematology,|Agricultural Univ, POBox 8123,|Wageningen, THE NETHERLANDSConverting export-files from Current Contents on Diskette (V. 3.1/3.2) into data files for REF_BASE. ----------------------------Export your records in the Comma-Delimited File Format using one or bothof the following Custom Record Formats:SHORT FORMAT (*.CDS): | LONG FORMAT (*.CDL):1. Authors | 1. Authors 10. Abstract2. Title | 2. Title 11. Full Source3. Abbr source | 3. Abbr source 12. Publisher4. Author Keywords | 4. Author Keywords 13. Book Editor5. KeyWords Plus | 5. KeyWords Plus 14. ISBN/ISSN6. Discipline | 6. Discipline7. Document Type | 7. Document Type8. Language | 8. Language9. Addresses | 9. AddressesIf you use the long format abstracts will be placed in the REMARKS field,and full information of Current Book references (Full Source, Publisher,Book Editor, ISBN/ISSN number) will be placed in the TITLE field.Use left 5 characters of file name to code CC edition, volume, and issue,e.g.: L9404 .CDS = Life Sciences, 1994, Issue 04. A9215PIC.CDL = Agriculture & Biology, 1992, Issue 15.Convert the *.CD? export file into a REF_BASE file. The information aboutthe CC edition will then be placed in the FILE-field in the formatL94/04A92/15 respectively.Disciplines are abbreviated to 8 characters, using internal tables.Volume numbers of less than 3 digits are provided with leading zeros, andpage numbers of less than 4 digits are provided with leading spaces. Theissues are placed in parenthesis at the end of the journal field. All thisshould ensure a correct sort on the journal field in most cases.EXCEPTIONS: Page numbers of J Biol ChemProc Natl Acad Sci USAare stretched to 5 positions with leading spaces. All vertical tabs (ASCII11) occurring in the abstracts are replaced by single spaces.By selecting , all *.CD?-files withina folder are converted, and written a user-specified path. By selecting a list of all journal issues present in each *.CD?-fileis also saved, with extension *.ISS. This list can be read into REF_BASE. Extracting Journal issues from REF_BASE files. --------------------This option loads a *.REF file, extracts a single copy of each differentjournal issue in this file, and saves this list in a REF_BASE compatibleformat (extension *.ISS) using the following fields:Year - (Unchanged)Read/Document - Number of articles in this issueFile - (Unchanged)Journal - Journal, volume, and issueDate - (Unchanged)For correct extraction the journal field should have the formatJ Examples 012: 12-15 (1) which is converted to J Examples 012 (1)To show an issue list you must always load the *.ISS file from disk, sinceafter each extraction any loaded *.ISS files are erased from memory. Give name of CCOD export file: Enter path for saving *.REF and *.ISS files: File not found..., back to menu .... Enter path for loading *.CD?-files: Enter path for saving REF and ISS files: Loading file: Converting ... unmatched disciplines! Issue extraction ... Give name of REF_BASE file: Enter path for saving ISS file: Enter path for loading REF-files: Enter path for saving ISS files: Give name of issue file: Give name of profile: *.PRO Save profile: Set_No. (s16.67h6v3T(s16.67h7v8T(s0p16h4099T(s0p21h3b4102T*Current Book Contents*Animal & Plant SciencesBiochemistry & BiophysicsChemistryClinical MedicineExperimental Biology & MedicineImmunologyMicrobiology & Cell BiologyMolecular Biology & GeneticsMultidisciplinaryNeurosciences & BehaviorPharmacologyPhysiologyAgricultural ChemistryAgriculture / AgronomyAnimal SciencesAquatic SciencesBiotechnology & Applied MicrobiologyEntomology / Pest ControlEnvironment / EcologyFood / NutritionVeterinary Medicine / Animal HealthAnalytical, Inorganic & Nuclear ChemistryApplied Physics / Condensed MatterComputer Engineering, Technology & Applicat.Earth SciencesMathematicsOrganic Chemistry / Polymer SciencePhysical Chemistry / Chemical PhysicsSpace ScienceAerospaceCommunication / Information / DPElectric & ElectronicEnvironmental / CivilGeneral / ManagementGeo / Petro / MiningInstrumentation / ControlMaterialsMechanicsMetallurgyOptics & AcousticsAnesthesia & Intensive CareCardiovascular & Respiratory SystemsClinical Immunology & Infectious DiseaseClinical Psychology & PsychiatryDentistryDermatologyEndocrinology, Metabolism & NutritionEnvironmental & Social MedicineGastroenterology And HepatologyGeneral MedicineHematologyMedical Technology & Laboratory MedicineNeurologyOncologyOphthalmologyOrthopedics & Sports MedicineOtolaryngologyPediatricsPharmacology / ToxicologyRadiology & Nuclear MedicineReproductive MedicineRheumatologySurgeryUrologyFood Science / Nutrition*CurBookAniPlaScCliniMedExpBioMeMicrCellMolBiGenAgriChemAgriAgroAnimaSciAquatSciEntoPestEnviEcolFoodNutrPlantSciVeterMedAnalChemApplPhysComputEnEarthSciOrgaChemPhysChemSpaceSciAeroSpacCommInfoEnvirCivGenManagGeoPetroInstrConOptiAcouCardRespClinImmuClinPsycEnvirSocGastHepaGenerMedMedTechnRadioNuc references loaded.Maximum number of|records is reached!This file does not|fit in memory! Cancel Incomplete record at|end of file! issues loaded.J BIOL CHEM PROC NATL ACAD SCI USA --- already|exists! What to do?Replace|New Name|Cancel Enter new name for saving your REF-file: Saving issues ...(Press [ESC] to return to main menu) Number of issues: linesPrint profile? Yes | No Did you select the|correct printer-port|and printer-type? Yes | Check (Life Sciences)(All editions)(Ag, Bio & Env Sci)(Phys, Chem & Earth)(Eng, Tech & Ap Sci)PRESS ANY KEY OR MOUSE TO CONTINUE .........(Clinical Medicine)PRESS ANY KEY OR MOUSE TO RETURN TO THE MENU ...... Maximum # records in CD?-files for data-conversion: Maximum # records in REF-files for issue extraction: Maximum # issues in ISS-files for display: Maximum # lines in profiles: 200 Free memory: (Use this as an indicator bytes of the maximum size of files to be converted!) This program works only in|ST-high, TT-medium & TT-high|screen resolution!, size Record # has charac-|ters and is too large for|REFBASE! It will be reduced|to an acceptable size! --- In: , pp. . Editor(s): . ISBN/ISSN ?  LL$$$< *B.$$2 " 6 z $. 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JEf0DH2HgR@?=n~jDnL8v@aa<z Ndz* I0`  fEQNdS|$Ne Jn~j|- nj XnRnn0nnc|.g8 _g>.g@ +gN -gR $f ,fHQ!aRnn"_p$RHQa"_`Rnn`)  g *fp `Jn~jp-`Jn~kp `=_nSnnRnNuHLv=B~jDBNG,LxC*E0RJCfRCR@r2HAARACd ` Efr0Sb Eg4 5e.!A*e0R 9c0`R1R@0c JEr+J@jr-D@UEoJYEc0SEnHJEf0SEH@HdREf0SEH@H 0 0REfH@C* nj XnRnn0nncJ.g _g .g +g -g HQa\L`Rnn`Jn~jp-`Jn~kp `=_nSnnRnNu؄*؄؅CH` ؅X`$_  Ia.YHR"H @`ʘ؄*؄؅AHNu؅X`$_ IaYHR"H`$IaL Z0AcA`QS@ QNuHd0Hd0Hd` QNu$Ia Z0Ac4ASB Q`QNup`p-@Nu`Bm`Bn Bf ` Bf ` Bf ` Bf ` Bf ` Bf `~ Bf `n Bf `^ Bf `N Bf `> Bf `. Bf ` Bf ` BfRLQ Nu There is memory space for (key)words. Choose text file(s) for extraction: Number of words: Calculating distribution of word lengths ... Convert to lowercase ... Main sort by ASCII-code ... Removing duplicates ... Number of keywords: Quick second sort by alphabet ... RAM shortage: slow final alphabetical sort ... Free memory: End of extraction. Keyword list ready for saving or printing. KEYWORDS.PRG ... -------------------- Extract text file ... Save keyword list ... Print keyword list ...------------------------- Quit...Extraction Remove punctuation marks & numbers Count keyword frequencies Convert to lower case--keyword separator:----------------- Space Semicolon + space (--------------------------------------reserved Help ...Printer Matrix printer 11 inch paper 12 inch paper Condensed 17 cpi Elite condensed 20 cpi Superscript HP DeskJet (A4 paper) Prestige 7 pt 17 cpi Courier 6 pt 20 cpi Gothic 6 pt 24 cpi HP LaserJet-4 (A4 paper) Courier scalable 17 cpi Courier scalable 20 cpi Gothic scalable 18 cpi Gothic scalable 21 cpi Margin for perforator Left & right pages--Printer connection:- Parallel (printer) Serial (modem)Statistics Longest word: Distribution of word lengths ... Line longer than 4767|characters!. Loading|is cancelled.Error in last line:|No termination by|CR + LF Skip Extract another file? No | Yes No more space !|Loading is stopped !Enter file name for saving keywords:\*.KWDPrint Keywords? Yes | No Pause between pages? stops printing.Page Pause for paper change!|Continue printing?(s16.67h7v8T(s20h6v3TWhich style of Gothic|font do you wish? Bold | Normal (s17h4099T(s20h4099T(s18h3b4102T(s18h1b4102T(s21h3b4102T(s21h0b4102TThe longest word is characters.Available number of characters per line: This is columns of wide.REMOVE PUNCTUATION MARKS AND NUMBERSThis option strips the start and end of each word from characters withan ASCII-code of less than 65. This includes all numbers and punctuationmarks. Use this for instance for extracting word processor files.COUNT WORD FREQUENCIESWith this option the number of times that a keyword occurs in the fileis counted. This number is 'attached' to the end of the keyword, and willbe sent with the keywords to the printer or to disk.CONVERT TO LOWER CASEThis ensures that during extraction of normal texts, words which aresituated at the beginning of a sentence, and which therefore begin inupper case, will not be put separately in the keyword list.KEYWORD SEPARATORIndicate by which character(s) the keywords in the text file are separated.NOTES: Above mentioned options only work DURING the extraction procedure.Select them in advance, and then choose to makethe keyword list. After every succesful extraction the start of the new listis shown in the window. Text files containing lines longer than 4767characters may be refused for extraction.MATRIX PRINTERUse 11 INCH /12 INCH to select the length of the paperUse CONDENSED/ELITE CONDENSED to select the number of characters per inch.With SUPERSCRIPT the number of lines per page is increased.HP DESKJETChoose the desired font. Courier 6/20 is always present. For Prestige 7/17you must install the cartridge. (Gothic is not yet operational)PRINTINGTo make perforations possible, a margin of about 1 cm can be selected.By selecting LEFT & RIGHT PAGES the even pages are printed i.e. withthe header reversed and (if selected) the margin on the right side.The keyword list is printed in three columns per page, and words that aretoo long will be truncated. If the keywords are relatively short,automatically more than three columns per page will be printed. K E Y W O R D S A program for extracting sorted lists of (key)words from text files. TT-Version, 9 November 1994 Written in GFA-Basic V. 3.60 Public Domain - Not for sale Author: Jan M. de Boer / Department of Nematology / Wageningen Agricul- tural University / P.O. Box 8123 / Wageningen / THE NETHERLANDS.Enter (optional) header text:Average word length: ###.#Most frequent word length: characters ( words)This program works only in|ST-High, TT-Medium, and|TT-High screen resolution! $6&  t  ( 6l$0$8$ &x :6  |R2RpDFTVf Rz|*2&*"2&nR2,^**> * f((@44"&Xb0L$| x`HyQ 24`@H` @HHyQaݞa"Hav`HyQ`HyQ 24`aX`$aR@ApDrAeA`?a0J@g*?CJap0g?C2paxSWfTNuB.@=|DNuB.@a=GDgNup`Xa`aCF"E p`4Jg$_a: HN$_a: HN$_aBHN$_a؄BpHN$_aB0HN$_axBpHN$_alN$_ab؄N$_aXN$_aPN$_aF 0HN$_a:؄00HHN$_a,p`PyAONEpANNLNNNNGbNzN"NhN.NNFN(NLNX NcNgNZrNbNN2N;NApJ-[gpJfNpJ-gpJfND"m N`QA"m N&g pJ--gpJfN&` pE m NNx"mNN"m N,gNj m 0(gNvrA "m N&gN€pJ-KgpRf QKNR pJ-gpJWHH/pJ--gpJWHHgNa`$NHy NMXrN$m\$$m\ oPr`QrNup~A^NbHx?<#NN\+@A풠/x m^AH "@p _Nx m^p0H+@x m^p0H+@+m+mp+@p +@NuQ[ANANACN0-J@^HH/pANE3pNgAN0-HSANCNp\N~CN($m$$m op N~CN($m$$m op\N~$m CN$m$$`p\N~CN$m$$$m $m$l$$m$ $mr$mҒANC`NpANCNNANNxrA+@A`CNN\CN`|p\N~CN($m$p\N~CN$m$$$m $m$l$$m$ $mr$mҒANC`NpANCNNANNxrA+@p Эr/ҭNANNfNBNV$m8Bp$m`$p N~$m` CN,$m$$m g>$m8R$m 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JEf0DH2HgR@?=n~jDnL8v@aa<z Ndz* I0`  fEQNdS|$Ne Jn~j|- nj XnRnn0nnc|.g8 _g>.g@ +gN -gR $f ,fHQ!aۘRnn"_p$RHQaۈ"_`Rnn`)  g *fp `Jn~jp-`Jn~kp `=_nSnnRnNuHLv=B~jDBN\LxC*E0RJCfRCR@r2HAARACd ` Efr0Sb Eg4 5e.!A*e0R 9c0`R1R@0c JEr+J@jr-D@UEoJYEc0SEnHJEf0SEH@HdREf0SEH@H 0 0REfH@C* nj XnRnn0nncJ.g _g .g +g -g HQaL`Rnn`Jn~jp-`Jn~kp `=_nSnnRnNu   AgSA ANua@`H"a`BaB@(` aBC(@HAC&21i0d R@`aBHP?< NN\Nu0^ M / hawFAN`RAD0C?0FA0A ff fA"H"2"2"2`B؄*؄؅CH`Ұ؅X`$_  Ia~YHR"H @`ʘ؄*؄؅AHNu؅X`$_ IaHYHR"H`$Ia Z0AcA`QS@ QNuHd0Hd0Hd` QNu$Ia| Z0Ac4ASB Q`QNuHPa _@f  "002Nup@` .,NuA`A` A`A@00HNuA `A`A`A `A `p`p-@NuH.gZ <r4<?k"SWga`TL8Haaa`6a`.a`&Bg?/Bg<k B<?HNuDBB?HNu'h4Tk6RBkB<kZ Bb 26k NupNp`RAeNuRjNuPRBNuRBgBDBj" Be 26kNuRAeNuRjNuPSBNuPprtNur$o  BNugDk  BDBNu4 Bf `. Bf ` Bf ` BfRLQ Nu`@rb003ffRd2g4kڱcKc Nu`TrbD0n3fnfRd n2g4kƱcKc Nu`.<?FQNu`.<FQNu`,.<',<\DD]Q.<'QNu`,.<',<\DD]Q.<'QNu` 7o;=|>?` ??7?o?????o?7? ?`|>=;o7 `??_o/7  ?`?@|>|>;\:l6/7 `` 7o 2e2e2e22 2}2}}}o7 `)U @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ ' @@@@@@@@@@@@@@@@@@@@@@@@@@@@?@@@@@ ? @@@@@@@@@@@@@@@@@@@@@@<<@x@@~@@>  @~@@@@@@@@@@@<??<<<<<<@xxxxxx@xxxxx?@? @@  @A@@@@<~<@x@@~@@'' @AG|@@@~?@~@|@?????@<<<<<<<<@ # !xxxxxxxx @@@@@Axxxxxx@@?@@@@|@ ~ @@@@@@@@@@@@@@@@@@_@@@~}@@@@@ ? @@@@@@@@@@@@@@@@@@@_@@@@@@@ @?@ # @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@` 7o;=|>?` ??7?o?????o?7? ?`|>=;o7 `??_o/7  ?`?@|>|>;\:l6/7 `` 7o 2e2e2e22 2}2}}}o7 `REFBASE 2.10 - 9 November 1994 GFA UNABLE TO LOAD!File(s) won't fit in memory!Bytes allowed: Bytes in file(s): Sorry Repeat Select Save current directory? Yes *.DIRSAVE directory to file:------------------------------------Print current directory?Do you want to quit? Quit By Jan M. de Boer, Departmentof Nematology, Wageningen Agri-cultural University, POB 8123,6701 PD Wageningen, HollandFloat Acc/CpxDisplaySort Input Amend Goto View Expand Accept Titles Open Save KeywrdsPrint Alpha RecordsFields Mode TagSel ClrTagsFile Search HitlistLoad Find Exit Erase Help Add... Clear Done Fetch Lookup MissingOrderLbReprintRun Edit Enter New Help! Insert Set #TagSet Authors Year Subject Read/Document File Title Journal Date Keywords Remarks BASIC Set_No. Begins with (=) Does not begin with (!=) Ends with Does not end with Before (<) After (>) Up to and including (<=) Including and after (>=) Includes ([]) Does not include (][) Untag selected records ... Invert tags ... Tag all records ... Delete selected records ... Delete tagged records ... Undo record deletions ... Find duplicates ... Case conversion ... Garbage removal ... Export field ... Search and replace ... Erase field ... Paste block ... Remove marks { } ... Remove abstracts ... Remove issues ( ) ... Import field ... Decapitalize journals ... Cursor blink Use wildcards ('*' and '?') Recall previous sorts Sort/Goto/FindDupl by ASCII Partial equation (=,<=,>,>=) Use Quickfind algorithm Mouse delay time: Soft scroll pause units: Use VDI 8*16 font Select field Select a relation Select a sort key Choose records Choose target field Select a function Set preferences Print Continuous print Select report layout Select reference layout Chain search Copy field to block Select a paste option Select a font Pages + formfeeds Print header(s) No header(s) No margins Print margins 11 inch paper 12 inch paper Pica 10 cpi Elite 12 cpi Condensed 17 cpi Condensed 20 cpi Cour 10 cpi- 6 lpi Pres 12 cpi- 6 lpi Pres 12 cpi- 7 lpi Pres 16 cpi- 8 lpi Pres 16 cpi-10 lpi Cour 20 cpi-12 lpi Cour 16 cpi- 6 lpi Cour 16 cpi- 8 lpi Cour 16 cpi-10 lpi Goth 12 cpi- 6 lpi Goth 16 cpi- 8 lpi Cour 11 cpi- 6 lpi Cour 13 cpi- 7 lpi Cour 15 cpi- 8 lpi Line Printer 8 lpi Goth 14 cpi- 6 lpi Goth 17 cpi- 7 lpi Goth 21 cpi- 8 lpi Goth 23 cpi-10 lpi 7 lines / inch 12 lines / inch Draft quality Letter quality All records Selected records Tagged records Reference Card Author table Title table Journal table Parallel port Serial port Disk Screen Show header... Matrix printer HP DeskJet HP LaserJet-4 Awaken printer ... JANFEBMARAPRMAYJUNJULAUGSEPOCTNOVDECJanuaryFebruaryMarchAprilMayAugustSeptemberOctoberDecember to main menu... [ESC] \REFBASE.MODWrong version ofmode file! Is (=) Is not (!=) OFF\REFBASE.PRN Memory shortage! Chain Search ... [C] Display all records ... [F3] [A] Display selected records ... [S] Display tagged records ... [D] Show selection rule ... [R] Profile Search ... [P] Save MODE preferences ... [M] Exit chain search ... [Esc] [E] Fetch limits: hits / k RAM buffer: Save overflow as Loaded: recordsDeleted: recordsSpace: recordsRead drive: Write drive: <<<< EXIT >>>>Disk space _ : kFile size... : kFree memory : k * Database for scientific references * - bytes#####keywords[return] to paste Record of (^D Duplicate record; ^M Mark Menu; ^P Print record) (^M Mark Menu; ^P Print record)######CHAIN SEARCH RESULTS (NOT YET SAVED)NO SEARCH RESULTSMerging file Loading file Field too long!|Cannot load from floppy!|Use harddisk instead!. STOP Error in last line:|No termination by|CR + LF Skip No more record space!Loading is stopped!Keywords are overwritten due tomemory shortage! The keyword-file(s) must be reloaded for use!Incomplete record|at end of file!Cancel loadingof more files?NEW FILEErasing previous file(s) from memory... Erasing previous file(s) from memory... UNABLE TO MERGE! NEW Erase current file(s)from memory and startnew file?This file won't fit in memory!File selection is cancelled.*.*Too many folders!Directory incomplete! # Too many files! * REF ISS ??? LOAD CHAIN MERGE ALL UNDO DEL ATTR RENAME EXIT ESC=EXIT * ^P=PRINT DIR * ^S=SAVE DIR * PRESS LETTER TO SELECT PARTITIONIs drive B reallyswitched ON ?#########Erase file(s) from drive Rename file(s)? files arewrite protected! Modify file attributes Read Only ( Read/Write ... Hidden (#) ... Visible ... Error duringdisk access ... Menu Rename file - [Return] to skip File not found!Another file with thisname already exists! Retry Fix All Selectd(^D=Duplicate record; ^M=Mark Menu)Erase keywords?SaveSelSaveTagTag selected records? Yes Clear tags? All Selected Tagged Print this record? Copy to block... Paste block to START Paste block to END Fill with block... Erase field... Lower case... Field has been copiedand is ready for PASTEReplaceby block?No block to PASTE!Untag selected records?No tags found amongselected records!Tag all records?Invert tags? Delete record ?Delete selected records?Error in PROC|delete_selected!No selected recordsto delete!Delete tagged records?Smax&<0 in PROC|delete-tagged!No tagged recordsRestore deleted record(s)?(They will be placed at thebottom of the file, and areaccessible with Display All) Last Cancel There are nodeleted records! OK Edit Block[CLRHOME] Erase block [INSERT] Accept block [ESC] Exit / Reject blockShow BlockPress ESC to exit Double space detectedat position Not enough memoryfor sorting!Issues Save All Records:Save Selected Records:Save Tagged Records:Export <> Field:*.OUTis write protected!AppendThere are no recordsfor this operation!No block to paste!Enter a value for mouse delay (0-9):Enter # units for soft scroll pause (0-9): DIRECTORY: Fetch selected records... Count selected records... File Bytes | Hits Records | Total Bytes | Searched | RAMMaximum file size for searchresults is reached! - Chainsearch is stopped! Hits in file are discarded!Search failed! records found!Would you like toSee them?Time: Writing records to RAM buffer... Reading records from RAM buffer... Saving records from RAM buffer...Repeat search withcurrent selectionrule? records found.Would you like themto be displayed? Ready No rule to repeat!And Or Select a value Select a value - Wildcards: '*' and '?' Press F10 to accept a selection. Press F3/F4 to combine multiple selections.ESC returns the main menu.No more selectionsallowed! Value: Cancel Accept (^K Keywords; ^B Block; ^P Paste; ^= CharSet)Stop AMEND and leaverecord unchanged?Reject this recordand stop INPUT?Shrink_detect Kick HP Deskjet awake? CANCEL Print report No selected records!No tagged records!Save Print Defaults Choose 16, 17 or 20 charactersper inch for printing tables!Print file to diskEnter labelfor field 4:Give number of blank linesbetween references: 0 1 2 Indent references?Pause between pages.Continue with next page? PRESS ANY KEY TO PAUSE, PRESS [ESC] TO STOP THE PRINTING Printing finished. Press mouse button or any key to continue.ENTER/MODIFY PAGE HEADER AND PRESS [RETURN] TO ACCEPT] Page #AUTHORSSUBJECTJOURNALREAD/DOCREC #TITLE As To Print control Printer type Printer options Exit P R I N T M E N U Most functions will need no explanation. The default setting is to print the records as 'references' to the matrix printer: simply choose the desired records and click on 'print report' to print them. If you use sheets of paper, click on 'continuous print' to select 'page print'. ----------------------------- Printing to disk exactly follows the settings of the printers with respect to headers, margins, page-length, and page-width. If you want to export references for 1ST Word Plus, it is best to choose 10 cpi with a right margin: the references will then be one screen wide.NOTE: search & replace usesASCII-character mode.Alphabetical search is not(yet) available.Replace in in field Select search value with Select replace valuePress F10 to start the replace operation or ESC to return to the main menu. occurrences replaced records !Paste Fill with block Erase in Paste in Fill in to start of field to end of field the text: with the text:Press F10 to start the Paste operation or ESC to return to the main menu.Press F10 to start the Erase operation or ESC to return to the main menu.Fill/Paste text toolong for this field!Continue? fields erased! fields filled! fields pasted!Select import fileImport file won't fit in memory!Bytes in file: Not enough fields inToo many fields inimport file!Import is cancelled!ExpoSelExpoTagClear marks inRemarks field?Remove marking labels {..}in Remarks field? marks removedRemove abstracts fromremarks field? Enter start of abstract: abstracts removed!Remove issue numbers (..)at end of journal field? issues removed! SUMMARY OF KEY FUNCTIONS (^ = CONTROL-KEY) Use ESC to exit (most of) the sub-menus and return to the previous menu. Youcan also use ESC to quit from the main menu. I = invert screen; K = keywordsmenu; B = edit block. Press ^F2 to repeat a selection. ^X = quit.When entering (F5) or editing (F6) records: ESC = reject modifications; INSERT= add/replace record; TAB = go to next field; CLRHOME = erase field; ^B =show block; ^P = paste block; ^K = enter keywords menu (RETURN to paste key-word at cursor position); # = insert current date (READ and DATE field only);SHIFT = start/end of line/field; CONTROL = word left/right^DELETE = delete word; Shift-DELETE = delete line; UNDO = restore field.During record display: ^ cursor up/down = scroll by page (table view)or by 20 records (card view); SHIFT cursor up/down = scroll by 1/10 filelength; SPACEBAR = 1 page forward; BACKSPACE = 1 page backward; ^ CLRHOME =top of file; ^Z = bottom of file; HELP = full display of remarks (HELP, ESC,UNDO to exit); INSERT or V = switch between card/table view (same as F8);Cursor left/right: (1) switch between columns in expanded table view (F9), or(2) backward/forward auto-scroll in title view (F10); DELETE = delete record;^M = enter/exit mark menu; I, K, and B as above; ^D = copy record to bottom offile (card view only); ^P = Print record (card view only); Alt-U = F7 = Goto; Numeric keypad has scroll functions similar to those on an MS-DOS PC.Press F to switch between 8*16 and 8*8 font during table view or keywords view.was written in GFA-BASIC V 3.6 by Jan M. de Boer, Department of Nematology, WageningenAgricultural University, P.O. Box 8123, 6700 ES Wageningen, HOLLAND - Public Domain / Not for sale. Keywords search options: F2 - Select : Collect all keywords matching a given selection rule and display them as a subset (= equivalent to Select in the main menu). F5 - Find : Search for the first keyword that includes a given search term, starting from the cursor position, and move to this position in the keywords file (= equivalent to Find or Search in a word processor or text editor). F6 - Repeat : Repeat a previous Find operation, starting from the current cursor position. F7 - Goto : Jump to the keyword that begins with a given search term. This (binary) search operation will only work correctly if the keywords in the file are sorted by alphabet or ASCII. Note: to start a new Find operation, first place the cursor at the start of the file by pressing CONTROL + CLR-HOME., position Remove?in position ST-High (640 x 400) |TT-Medium (640 x 480) |TT-High (1280 x 960) |resolutions only! begins with ... (ASCII) First sort your recordson the desired field!Search for duplicate recordsin JOURNAL field ?NOTE: This operation will eraseall current record tags !No duplicates found!Duplicate records.Duplos For duplicate searchfirst sort by JOURNAL!Select case conversionField: UpperPause between pages? Normal (= even + uneven) Uneven pages only Even pages only Normal with left margins Normal with right margins Uneven pages only/left margins Even pages only/right margins without margins? with left margin with right margin Record # + TITLE Auth + Year + Subj + TITLE + Jour + File Short Medium (+ File & Subject) Large (+ Keywords & Marks) Full (+ Remarks) Do you want uni-directional print?&d@(s10h12v3T(s12h10v8T(s16.67h7v8T(s20h6v3T(s16.67h12v3T(s16.67h6v3T(s12h12v6T(s16.67h9.5v6T(s0p11h0s0b4099T(s0p13h0s0b4099T(s0p15h0s0b4099T(s0p20h0s0b4099T(s0p16.67h8.5v0s0b0T(s0p14h0s0b4102T(s0p17h0s0b4102T(s0p21h0s3b4102T(s0p23h0s3b4102T998999EVEN PAGES ONLYUNEVEN PAGES ONLYNORMAL PAGE PRINTFirst page: Last page: GARBAGE COLLECTIONRemove deleted recordsirreversibly from memory?Records | Bytes | AverageAll | Selected | Tagged | Enter label to add (without brackets) dummy{Done{Done {Fetch}{LookUp}{Missing{Missing {Order library}{Reprint}Keywords won't fit in memory!Not enough space!(one AND/OR/NOT allowed) Select :Too many keywords found!Storage buffer is full!Select operation is stopped! NOT Find the following word: Erasing keywords ...PROFILE SEARCH[INSERT] = insert line[DELETE] = delete line [TAB] next field [INSERT] accept record [CLRHOME] erase field [TAB] prev field [ESC] reject record [UNDO] restore fieldCAPS LOCKBOTP=0SFT < > REMINVFNTKWD*.SELLOAD Selection Profile:Change field? YES Set Numbers notyet operational! SORRY [ empty line ! ]Before you can EDIT aprofile you must firstENTER some lines or LOADa profile from disk!Delete this line?Remove this profile?SAVE Selection Profile:No profile to save![ Empty line ! ]~>fl~r:XNH44444PXdx8T*T&h@T@^x6 :j4<0|"D0 FV 4> \ L~D6808BR@ >,B^ *8022 hl0n F ".4&  T4D&NhN*n:2:D 8:0  x"**&&Ĭ***&DDf8z"^ZB$p62*&bR:"p&>6:`R:j` FЌ$*L8&  $&$&$&$& *vn8(JZ$8L:, \&,>(D&@ ,Tn: T:& 6t002H" >@*h4\v>2 0 "F,4 2vP"$*h`,t : 4X@@@bD@@x8 ^((&PL\L&0<(8$v,.8480""&&JDFRV2:h@0B(( *( **062:&******0.  : 6D8:0:RPPPRR : 2::.8:| B8: 8j:hNФX(l    X@  .4 T B& 08>:<  84:.8( :&& & 000400088282 6(*(",V(fdvj`|4b&Xb  *  $"$&(&::lfZl $H4d:&.fR< $"D j2Fj & &@:>^ &P$,0N$2L@$NlJ >Nz@T"b^8"4"""$:$:R4 $$:":8 ^*xp000@L ^880"&&,@ Lt^&r"&t $8*""&H $...****L$L(< <88 0:0 j(* >F><fp 2*8 ^J*RB(Hx20n"r2``6&PD44X""h**&.::.h&P6$4X$$Pn&&"*8<ZF&>n&8,*RJ8TR8>6&HL,<bD|L4<2\ $&0fDZ8^lddb6\Ĵ\~RHlb(464,T& .>2Lv2D$2T8, &Ln, .4&:>2666n,&8v8$$$&*F.$P"*,&. (:. $nl:&:: &::(&&::x&v &$.*B""""""""""""""RP*@8(,R.(,28о28:V$$:&8 :& &62.&<"8 &"F8 """v8@@@^^^@^^B@@@^b@b`.6&4,`Rb,HZdd @(n0((T &h*,0  *"*,D8L2V"bdf2BB2B..Tf$0rb:402" :,* ؊Z@2V$> :l*n Ƣ"@zb((N  \4$&(ZvZ *|@@"R2& >0@NTDbh  "@ ` >^,\F*&,,:rfF@ *F f((@4n"&Xb0L$B 8~N|  Begins with (=) Does not begin with (!=) Ends with Does not end with Before (<) After (>) Up to and including (<=) Including and after (>=) Includes ([]) Does not include (][) Untag selected records ... Invert tags ... Tag all records ... Delete selected records ... Delete tagged records ... Undo record deletions ... Find duplicates ... Case conversion ... Garbage removal ... Export field ... Search and replace ... Erase field ... 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@CJH~8:E#P&<2 `b$bYEf`"RAf rЁЀ`&Ѐe "ЀeЁdp`ҎJAkfgRer?DDЁaAa8$HX :CJE` YEjT"_$P"2trDDd0d d d` QjNu`aDa DNu na^ K"ng42 $`gk2&Hg Af deђ$`ebѐXf&n Nu AgebѐA``-K x$ n($n$"HgD" &Akc(bѐ S`g(" k#&Ac(bё2+SAI3 Q&f-I$&n Nu-K x$&ր n($n$"Hg^" k&Ac(b b S` S`g:" k#&Ac(bbrkX`ؑ2+SAI3 Q&f-I$&n NuaT n4L6(ndnfHHHNua4 n40(ndHNua" n40(nfHNua n40(HNu`aFNu؄*؄؅CH`؅X`$_  IanYHR"H @`ʘ؄*؄؅AHNu؅X`$_ Ia8YHR"H` REFSPLIT 5 Nov 1993 ... --------------------------- Split ... Help ... Quit ...By JM de Boer, Dept Nematology,|Agricultural Univ, POBox 8123,|Wageningen, THE NETHERLANDS.|File memory: bytes. R E F S P L I T A program for recovering files which have become too large to load with REFBASE, e.g. due to an unwanted APPEND operation. The REFBASE file is split in two or more files named PARTXX.REF, which are saved to disk again. If these split files are still too large, give each file a new name, and repeat the splitting procedure. NOTE: If you want to read a file from drive A (or B) and save the splitted parts to drive A (or B) again, there must be enough space on your floppy disk to hold both the source file and the destination files. If you do not have a harddisk, and you want to split a file which occupies more than half the space of the floppy disk, you will need two diskdrives: one to read from, and one to write to.Give name of file to split:*.*Give path for saving split files:Save path: File size: Number of input blocks: Block size: Tail size: Not enough disk space for | saving the split files!CancelFile not found! Menu Loading block #Scanning block #Saving part #A very large record (size |over bytes) has been|detected.|Unable to continue!Loading tail segment ... Ready!pSplitting is cancelled!Original file (1) is corrupted (2) or contains records that are too large (3) or is not a REFBASE file  BVr :*T"   Z44P 8lJ  * f((@4"&Xb0L$| iHNufnpNupNu"lDaDNuJnDaDNuzxeҁ؄d`ef Nup`*f"_KBMDI O:HQ <-H*,`N,7d d3 d# d# # d# # # # d ALH dAL H LH Ford, T.; Graham, J.; Rickwood, D. 1994 Biochemi Artic/En L94/35 Iodixanol: A nonionic iso-osmotic centrifugation medium for the formation of self-generated gradients Anal Biochem 220: 360-366 (2) AUG 1 RAT-LIVER; LYSOSOMAL MEMBRANES; NYCODENZ GRADIENTS; PERCOLL; PROTEIN; CELLS; ORGANELLES J Graham/Univ Essex/Dept Biol/Wivenhoe Pk/Colchester CO4 3SQ/Essex, England| --- The physical and biological properties of Iodixanol, a new nonionic density gradient medium, are described in this paper. It is effectively a dimer of Nycodenz and it exhibits two significant advantages over previous iodinated density gradient media-its aqueous solutions are iso-osmotic up to a density of 1.32 g/ml and it is capable of forming self-generating gradients in 1 to 3 h. It has a very low toxicity toward biological material and enzyme assays can be carried out in its presence. (C) 1994 Academic Press, Inc. Graham, J.; Ford, T.; Rickwood, D. 1994 Biochemi Artic/En L94/35 The preparation of subcellular organelles from mouse liver in self-generated gradients of iodixanol Anal Biochem 220: 367-373 (2) AUG 1 RAT-LIVER; LYSOSOMAL MEMBRANES; NYCODENZ GRADIENTS; BETA-OXIDATION; PEROXISOMES; MITOCHONDRIA; CHOLESTEROL; PERCOLL; ENZYMES J Graham/Merseyside Innovat Ctr/131 Mt Pleasant/Liverpool L3 5TF/Merseyside, England| --- This paper reports the use of a new density gradient compound, Iodixanol, for the resolution of the major organelles from mouse liver. A major advantage of Iodixanol over other iodinated density gradient media is its ready ability to form self-generated gradients. Gradient-forming conditions have been modulated to provide optimal recoveries of Golgi membranes, lysosomes, mitochondria, and peroxisomes. The organelles were isolated in high yield (80-90% of gradient input) and high purity. Nycodenz and Iodixanol were compared using preformed gradients. Iodixanol provided resolution superior to that of Nycodenz, notably of peroxisomes and mitochondria and the separation of lysosomes from endoplasmic reticulum. Because Iodixanol does not interfere significantly with marker enzyme activities, gradient fractions can be analyzed without removal of the gradient medium. (C) 1994 Academic Press, Inc. Fleischer, B. 1994 MicrCell Revie/En L94/41 Superantigens APMIS 102: 3-12 (1) JAN superantigen; exotoxin; T lymphocyte; T-cell receptor; STAPHYLOCOCCAL ENTEROTOXIN-B; SHOCK SYNDROME TOXIN-1; CLASS-II MOLECULES; MAMMARY-TUMOR VIRUS; HUMAN T-CELLS; RECEPTOR BETA-CHAIN; STREPTOCOCCAL PYROGENIC EXOTOXINS; MYCOPLASMA-ARTHRITIDIS MITOGEN; HLA-DR; MONOCLONAL-ANTIBODY B Fleischer/Bernhard Nocht Inst Trop Med/Bernhard Nocht Str 74/D-20359 Hamburg, Germany| --- ''Superantigens'' is the term for a group of molecules that have in common an extremely potent stimulatory activity for T lymphocytes of several species. They stimulate CD4(+), CD8(+) and gamma delta(+) T cells by a unique mechanism: they cross-link variable parts of the T-cell receptor (TCR) with MHC class II molecules on accessory or target cells. The interaction site on the class II molecule and on the TCR is different from the peptide binding site; on the TCR it is the variable part of the beta chain (V-beta) The prototype superantigen is the staphylococcal enterotoxin B (SEB), member of a family of genetically related proteins produced by Staphylococcus aureus and Streptococcus pyogenes. These are soluble exotoxins of approximately 27 kd molecular mass. It is intriguing that this molecular mechanism of T-cell stimulation has been independently produced at least three times in evolution. Other pathogens producing superantigens are retroviruses (the Mouse Mammary Tumor Viruses) and a mycoplasma (Mycoplasma arthritidis). Many additional candidate superantigens have been proposed, but in most cases unequivocal evidence for superantigen activity is still missing. There are several reasons why these molecules have aroused such tremendous interest in recent years. First, they have provided key information on tolerance mechanisms, both on the deletion of T cells in the thymus and on the induction of peripheral tolerance by anergy and apoptosis. Second, of all polyclonal T-cell stimulators they are the ones that most closely mimic the recognition of specific antigen. Finally, they have been recognized as important factors in the pathogenicity of the producing pathogens, inducing shock and immunosuppression. Whilst there is evidence that superantigens could be involved in the pathogenesis of certain human diseases, in most cases this is still very preliminary and indirect. Ferreira, C.; Capella, A.N.; Sitnik, R.; Terra, W.R. 1994 Biochemi Artic/En L94/35 Digestive enzymes in midgut cells, endo- and ectoperitrophic contents, and peritrophic membranes of Spodoptera frugiperda (Lepidoptera) larvae Arch Insect Biochem Physiol 026: 299-313 (4) microapocrine secretion; immobilized enzymes; peritrophic membrane; membrane-bound enzymes; ERINNYIS-ELLO; CASSAVA HORNWORM; SECRETORY MECHANISMS; ORGANIZATION; INFERENCES; INSECTS C Ferreira/Univ Sao Paulo/Inst Quim/Dept Bioquim/CP 20780/BR-01498970 Sao Paulo, Brazil| --- In the midgut of Spodoptera frugiperda larvae, subcellular fractionation data suggest that am in opeptidase and part of amylase, carboxypeptidase A, dipeptidase, and trypsin are bound to the microvillar membranes; that major amounts of soluble dipeptidase, cellobiase, and maltase are trapped in the cell glycocalyx; and finally that soluble carboxypeptidase, amylase, and trypsin occur in intracellular vesicles. Most luminal acetylglucosaminidase is soluble and restricted to the ectoperitrophic contents. Aminopeptidase occurs in minor amounts bound to membranes both in the ectoperitrophic contents and incorporated in the peritrophic membrane. Amylase, carboxypeptidase A, and trypsin are found in minor amounts in the ectoperitrophic contents (both soluble and membrane-bound) and in major amounts in the peritrophic membrane with contents. Part of the activities recovered in the last mentioned contents corresponds to enzyme molecules incorporated in the peritrophic membrane. The results suggest that initial digestion is carried out in major amounts by enzymes in the endoperitrophic space and, in minor amounts, by enzymes immobilized in the peritrophic membrane. Intermediate and final digestion occur at the ectoperitrophic space or at the surface of midgut cells. The results also lend support to the hypothesis that amylase and trypsin are derived from membrane-bound forms, are released in soluble form by a microapocrine mechanism, and are partly incorporated into the peritrophic membrane. (C) 1994 Wiley-Liss, Inc. Escriche, B.; Martinezramirez, A.C.; Real, M.D.; Silva, F.J.; Ferre, J. 1994 Biochemi Artic/En L94/35 Occurrence of three different binding sites for Bacillus thuringiensis delta-endotoxins in the midgut brush border membrane of the potato tuber moth, Phthorimaea operculella (Zeller) Arch Insect Biochem Physiol 026: 315-327 (4) Bacillus thuringiensis; Phthorimaea operculella; insecticidal crystal protein; receptors; INSECTICIDAL CRYSTAL PROTEINS; BUTTERFLY PIERIS-BRASSICAE; PLUTELLA-XYLOSTELLA; DIAMONDBACK MOTH; RESISTANCE; SPECIFICITY; RECEPTORS; SPECTRUM; VESICLES; AFFINITY B Escriche/Univ Valencia/Fac CC Biol/Dept Genet/E-46100 Burjassot, Spain| --- The potato tuber moth is susceptible to at least three insecticidal crystal proteins (ICPs) from Bacillus thuringiensis: CrylA(b), CrylB, and CrylC. To design useful combinations of toxin genes either in transgenic plants or in new genetically modified B. thuringiensis strains, it is necessary to determine the binding characteristics of the different ICPs so as not to combine a pair sharing the same binding site. This has been accomplished using two different techniques: I-125-labeling of the ICPs with further measurement of the radioactivity bound to brush border membrane vesicles, and microscopic visualization of the bound ICPs by enzyme-linked reagents such as antibodies or streptavidin using biotinylated ICPs. Our results st-cow that CrylA(b), CrylB, and CrylC bind to different sites in the brush border membrane of midgut epithelial cells. Also, the affinity of the binding sites for the ICPs and their concentration in brush border membrane vesicles has been determined in a laboratory strain and a storage collected population. No significant differences were found between these two strains. (C) 1994 Wiley-iiss, Inc. Dua, H.S.; Gomes, J.A.P.; Singh, A.; Eagle, R.C.; Donoso, L.A.; Laibson, P.R. 1994 CliniMed Lette/En L94/42 Fresh-frozen cucumber as a mount for conjunctival and corneal tissue in cryomicrotomy Arch Ophthalmol 112:1139-1141 (9) SEP HS Dua/Univ Nottingham Hosp/Queens Med Ctr/Dept Ophthalmol/Nottingham NG7 2UH, England| Hirayama, B.; Hazama, A.; Loo, D.F.; Wright, E.M.; Kisby, G.E. 1994 Biochemi Artic/En L94/35 Transport of cycasin by the intestinal Na+/glucose cotransporter Bba-Biomembranes 1193: 151-154 (1) JUL 13 cycasin transport; sodium-dependent glucose transport; glucose transporter; methylazoxymethanol; (kidney); (intestine); NA+ GLUCOSE COTRANSPORTER; RABBIT SMALL-INTESTINE; BRUSH-BORDER VESICLES; VOLTAGE-CLAMP; KINETICS GE Kisby/Oregon Hlth Sci Univ/Ctr Res Occupat & Environm Toxicol/3181 SW San Jackson Pk Rd/L606/Portland, OR 97201 USA| --- The medicinal and food use of seed from the cycad plant (Cycas spp.), which contains the neurotoxin cycasin, is a proposed etiological factor for amyotrophic lateral sclerosis/Parkinsonism dementia complex (ALS/PDC), a prototypical neurodegenerative disease found in the western Pacific. Cycasin, the beta-D-glucoside of methylazoxymethanol might enter neurons and other cells via a glucose transporter. Since the intestinal brush-border Na+/glucose cotransporter plays a major role in the absorption of monosaccharides, the following studies were conducted to determine if cycasin, the beta-D-glucoside of methylazoxymethanol, is a substrate for the transporter. We measured the ability of cycasin to (i) inhibit Na+/glucose uptake into rabbit intestinal brush-border membrane vesicles, and (ii) to generate current by the cloned Na+/glucose cotransporter (SGLT1) expressed in Xenopus laevis oocytes. The results show that cycasin inhibits Na+-dependent sugar transport in the vesicles, and cycasin generates phlorizin-sensitive currents in oocytes. We conclude that cycasin is a substrate for the intestinal brush-border Na+/glucose cotransporter, albeit with a lower affinity than D-glucose. This suggests that cycasin may be absorbed from the gut lumen by the cotransporter, and as a result either cycasin or the aglycone is presented to the blood-brain barrier for uptake into the brain. Draehmpaehl, D. 1994 VeterMed Artic/Ge A94/35 Observation About the Titer of Antisperm Antibodies from Guinea Pigs After Immunization Against Their Own Sperms and After Induce of Unilateral Cryptorchism Berl Mun Tierarztl Wochenschr 107: 157-162 (5) MAY MONOCLONAL-ANTIBODIES; AUTO-ANTIGENS; INFERTILITY; FERTILIZATION; REPRODUCTION; SPERMATOZOA; INHIBITION; INVITRO D Draehmpaehl/Freien Univ Berlin/Fak Vet Med/Inst Anat/Heidekampweg 100/D-12437 Berlin, Germany| --- Four guinea pigs were immunized against sperms from their own epididymis. The titers of autoantibodies against the sperms in the tubuli of the parenchyma testis increased after 4 weeks. The heads of sperms were also gummed up. The left testis of another 7 guinea pigs were shifted into the abdominal cavity. These animals showed also increasing autoantibody-titer. The observations demonstrated. that the blood-testis-barrier is a physiological one for the autoantibodies. At higher temperatures, as with kryptorchid testes, this barrier becomes permeable for antibodies so that infertility can result. Golding, D.W. 1994 MolBiGen Revie/En L94/35 A pattern confirmed and refined - Synaptic, nonsynaptic and parasynaptic exocytosis Bioessays 016: 503-508 (7) JUL CENTRAL-NERVOUS-SYSTEM; DENSE-CORED VESICLES; MOSSY FIBER SYNAPSES; LYMNAEA-STAGNALIS; TANNIC-ACID; ULTRASTRUCTURAL DEMONSTRATION; RELEASE SITES; NEUROPEPTIDE RELEASE; ENDOCRINE PANCREAS; CAUDODORSAL CELLS DW Golding/Univ Newcastle upon Tyne/Biomed Em Unit/Ridley Bldg/Newcastle Tyne NE1 7RU/Tyne & Wear, England| --- Neurons are now known to produce a variety of types of chemical transmitters. Classical transmitters are stored within synaptic vesicles which undergo synaptic exocytosis in association with presynaptic thickenings. The larger, dense-cored secretory granules present in most neurons contain neuropeptides and mainly discharge their contents at morphologically undifferentiated (i.e. nonsynaptic) sites. The synaptic character of vesicle discharge enables transmitters to exercise a highly focal action, whereas nonsynaptic release probably relates to the slow rate of degradation of many neuropeptides and their consequent widespread diffusion and sphere of action. However, one variant of the basic pattern, involving the restriction of granule discharge to areas of the terminal plasmalemma situated adjacent to the postsynaptic cells (i.e. a parasynaptic configuration), enables a degree of targeted peptide discharge to be achieved, The diversity of patterns of neural exocytosis adds a further dimension to the complexity of nervous function. Earnshaw, W.C.; Pluta, A.F. 1994 MolBiGen Artic/En L94/42 Mitosis Bioessays 016: 639-643 (9) SEP MATURATION-PROMOTING FACTOR; DNA TOPOISOMERASE-II; METAPHASE CHROMOSOME STRUCTURE; NUCLEAR-ENVELOPE; SACCHAROMYCES-CEREVISIAE; PROTEIN-KINASE; BUDDING YEAST; PHOSPHORYLATION SITES; MICROTUBULE DYNAMICS; MITOTIC CHROMOSOMES WC Earnshaw/Johns Hopkins Univ/Sch Med/Dept Cell Biol & Anat/725 N Wolfe St/Baltimore, MD 21205 USA| --- Within the last decade, the study of mitosis has evolved into a multidisciplinary science in which findings from fields as diverse as chromosome biology and cytoskeletal architecture have converged to present a more cohesive understanding of the complex events that occur when cells divide. The largest strides have been made in the identification and characterization of regulatory enzymes (kinases and phosphatases) that modulate mitotic activity, as well as a number of the proteins and structural components (spindle, chromosomes, nuclear envelope) which carry out the mitotic instructions. One emerging theme appears to be that molecular signalling, which can involve modification of components (such as phosphorylation) or even their specific destruction, monitors the state of the mitotic cell at all stages. One of the major challenges for the future will be the identification of addititonal targets of the signalling machinery, as well as new regulatory components and their targets on the chromosomes, on the spindle, and at the cleavage furrow. Gilroy, S.; Trewavas, T. 1994 MolBiGen Artic/En L94/42 A decade of plant signals Bioessays 016: 677-682 (9) SEP DEPENDENT PROTEIN-KINASE; AUXIN-BINDING PROTEINS; CYTOSOLIC FREE CALCIUM; LOCUS RECEPTOR KINASE; AVENA-FATUA ALEURONE; PLASMA-MEMBRANE; GUARD-CELLS; ABSCISIC-ACID; CYTOPLASMIC CALCIUM; GIBBERELLIN PERCEPTION S Gilroy/Penn State Univ/Dept Biol/208 Mueller Lab/University Pk, PA 16802 USA| Anderson, J.P.; Cappello, J.; Martin, D.C. 1994 Biochemi Artic/En L94/35 Morphology and primary crystal structure of a silk-like protein polymer synthesized by genetically engineered Escherichia coli bacteria Biopolymers 034:1049-1058 (8) AUG MODEL; FIBROIN DC Martin/Univ Michigan/Coll Engn/Ctr Macromolec Sci & Engn/Hh Dow Bldg/Ann Arbor, MI 48109 USA| --- The morphology and primary crystal structure of SLPF, a protein polymer produced by genetically engineered Escherichia coli bacteria, were characterized. SLPF is a segmented copolymer consisting of amino acid sequence blocks modeled on the crystalline segments of silk fibroin and the cell attachment domain of human fibronectin. Wide angle x-ray scattering (WAXS), transmission electron microscopy (TEM), selected area electron diffraction (SAED), and molecular simulations were used to analyze the primary crystal structure of SLPF. TEM experiments conducted on SLPF droplets cast from formic acid on amorphous carbon film demonstrated that these protein films have a microstructure formed of woven sheaves. The sheaves are composed of well-defined whisker crystallites. The width of the whiskers, 11.8 +/- 2.2 nm, may be correlated to the length of the silk-like segment in SLPF as predicted by molecular simulations. WAXS data, TEM images, SAED, patterns, molecular simulations, and theoretical diffraction patterns all were consistent with the crankshaft model proposed for Silk I by Lotz and Keith. (C) 1994 John Wiley & Sons, Inc. Akhtar, M.; Mahmood, I. 1994 Biotechn Revie/En A94/40 Potentiality of Phytochemicals in Nematode Control - A Review Bioresource Technol 048: 189-201 (3) Cultural Practice; Phytochemical; Nematode Control; Waste Management; Waste by-Products; Waste Utilization; Review; PLANT PARASITIC NEMATODES; MELOIDOGYNE-ARENARIA; CHITIN AMENDMENTS; SOIL; INCOGNITA; TOXICITY; WASTES; ROOTS M Akhtar/Aligarh Muslim Univ/Dept Bot/Ctr Agr/Aligarh 202002, India| --- In the search for alternatives to chemical control of nematodes and with consideration for resource-poor farmers, the potential nematicidal value of a number of plant parts, by-products, and residues, and plant interculture with other crop plants, have been studied. In order to find out their nematicidal properties, the plant materials have been tested by in-vitro, pot and field trials by extracting or incorporating the materials as soil amendments, seed treatments and/or bare-root dip treatments. Root exudates of certain plants have also exhibited nematicidal activity. However, the mode of action of the materials on nematodes is not understood. The beneficial effects of natural phytochemicals reveals a promising area of non-chemical nematode management, but further work on the plant-based nematicides is needed. Fukuoka, S.I. 1994 Biochemi Artic/En L94/35 Analysis of ZAPs, zymogen granule membrane associated proteins, in the regulated exocytosis of the pancreas Biosci Biotechnol Biochem 058:1282-1285 (7) JUL AMINO-ACID SEQUENCE; BINDING PROTEINS; RAT PANCREAS; GENE ENCODES; PROTEASE; FAMILY SI Fukuoka/Kyoto Univ/Food Sci Res Inst/Uji/Kyoto 611, Japan| --- To characterize molecules involved in the intracellular sorting and regulated exocytosis of digestive enzymes in the pancreas, proteins that are specificially associated with the zymogen granule membranes were analyzed. Zymogen granules, the major secretory organelles in the pancreas, were highly purified. SDS-PAGE analysis found at least 7 protein components in the zymogen granule membranes including ZAP (zymogen granule membrane associated protein) 75, 54, 47, 36, 32, 29, 25 (numbers refer to their apparent kDas). ZAP75 is identical to the glycophosphatidylinositol (GPI)-anchored protein, GP2. Partial amino acid sequencing of ZAP47 and ZAP36 found similarities to a preprocarboxypeptidase B and annexins, respectively. The method we used was a useful tool for structural analysis of the members of ZAPs. Bright, J.; Khar, A. 1994 Biochemi Revie/En L94/35 Apoptosis: Programmed cell death in health and disease Biosci Rep 014: 67-81 (2) APR apoptosis; programmed cell death; ADENOVIRUS E1A PROTEINS; NATURAL-KILLER CELLS; C-MYC; DNA FRAGMENTATION; CAENORHABDITIS-ELEGANS; T-CELLS; THYMOCYTE APOPTOSIS; MURINE THYMOCYTES; SIGNAL DELIVERY; IMMUNE-SYSTEM A Khar/Ctr Cellular & Molec Biol/Uppal Rd/Hyderabad 500007, India| --- Apoptosis is a normal physiological cell death process of eliminating unwanted cells from living organisms during embryonic and adult development. Apoptotic cells are characterised by fragmentation of nuclear DNA and formation of apoptotic bodies. Genetic analysis revealed the involvement of many death and survival genes in apoptosis which are regulated by extracellular factors. There are multiple inducers and inhibitors of apoptosis which interact with target cell specific surface receptors and transduce the signal by second messengers to programme cell death. The regulation of apoptosis is elusive, but defective regulation leads to aetiology of various ailments. Understanding the molecular mechanism of apoptosis including death genes. death signals. surface receptors and signal pathways will provide new insights in developing strategies to regulate the cell survival/death. The current knowledge on the molecular events of apoptotic cell death and their significance in health and disease is reviewed. Altschuler, M.; Heddens, D.K.; Diveley, R.R.; Kresheck, G.C. 1994 Biochemi Note/En L94/40 Plasmid DNA isolation utilizing a novel nonionic detergent Biotechniques 017: 434-436 (3) SEP SEQUENCING METHOD M Altschuler/No Illinois Univ/Ctr Plant Molec Biol/de Kalb, IL 60115 USA| Allen, M.; Saldeen, T.; Gyllensten, U. 1994 Biochemi Artic/En L94/40 PCR-based DNA typing of saliva on stamps and envelopes Biotechniques 017: 546-552 (3) SEP POLYMERASE CHAIN-REACTION; OLIGONUCLEOTIDE PROBES; BETA-GLOBIN; HLA; SEQUENCES; AMPLIFICATION; FINGERPRINTS; POLYMORPHISM; SAMPLES; GENES U Gyllensten/Univ Uppsala/Ctr Biomed/Dept Med Genet/Box 589/S-75123 Uppsala, Sweden| --- In forensic cases involving mail bombs, extortion, kidnapping or threatening letters, biological evidence such as the saliva used to attach the stamp and seal the envelope could be used for genetic analysis. We have developed a highly sensitive semi-nested PCR method for the HLA-DRBI focus, suitable for the analyses of very limited amounts of DNA. When applied to a set of stamps and envelopes with saliva from control individuals, typing results we, e consistent with those obtained rising hairs drawn from the same individuals. No interference was found due to DNA from the fingerprints of people handling the letters. The system was applied to three forensic cases with threatening letters. The first case resulted in an exclusion of the suspect. In the second case, the suspect could not be excluded (probability of identical genotype by chance >0.01). These results demonstrate that biological evidence in cases with threatening fetters is amenable to genetic typing. Bolger, R.; Checovich, W. 1994 Biochemi Note/En L94/40 A new protease activity assay using fluorescence polarization Biotechniques 017: 585-589 (3) SEP PROTEOLYTIC-ENZYMES; LABELED CASEIN; SUBSTRATE; PROTEINS W Checovich/Panvera Corp/565 Sci Dr/Madison, WI 53711 USA| --- Fluorescence polarization (FP) technology was used to develop an assay for protease activity that is more sensitive than other nonradioactive protease assays and requires no separations, precipitations or transfers of the reaction mixture. FP measures changes in the molecular volume of fluorescently labeled molecules. In the assay described in the present studies, changes in molecular volume due to the cleavage of intact fluorescein thiocarbamoyl (FTC)-casein molecules to smaller FTC peptides were measured. The sensitivity of the FP protease assay was compared with a non-FP fluorescent assay. The FP-based assay was twofold to twentyfold more sensitive than the non-FP assay, depending on the protease tested. Because measurements were taken in real time, the progress of the reaction was followed both kinetically and at a single time point. This assay provided a sensitive measure of activity for the three common protease classes: serine proteases, sulfhydryl proteases and acid proteases. Dorai, H.; Mccartney, J.E.; Hudziak, R.M.; Tai, M.S.; Laminet, A.A.; Houston, L.L.; Huston, J.S.; Oppermann, H. 1994 MicrCell Artic/En L94/40 Mammalian cell expression of single-chain Fv (sFv) antibody proteins and their C-terminal fusions with interleukin-2 and other effector domains Biotechnology 012: 890-897 (9) SEP ESCHERICHIA-COLI; INFECTED-CELLS; BINDING SITES; IMMUNOGLOBULIN; ANTIGEN; FORMS; GENE; AMPLIFICATION; SECRETION; FRAGMENTS H Oppermann/Creat Biomolecules Inc/45 South St/Hopkinton, MA 01748 USA| --- The production of several single-chain Fv (sFv) antibody proteins was examined by three modes of mammalian cell expression. Our primary model was the 741F8 anti-c-erbB-2 sFv, assembled as either the V-H-V-L or V-L-V-H, and expressed alone, with C-terminal cysteine for dimerization, or as fusion proteins with carboxyl-terminal effector domains, including interleukin-2, the B domain of staphylococcal protein A, the S-peptide of ribonuclease S, or hexa-histidine metal chelate peptide. Constructs were expressed and secreted transiently in 293 cells and stably in CHO or Sp2/0 cell lines, the latter yielding up to 10 mg per liter. Single-chain constructs of MOPC 315 myeloma and 26-10 monoclonal antibodies were also expressed, as were hybrids comprising unrelated V-H and V-L regions. Our results suggest that mammalian expression is a practical and valuable complement to the bacterial expression of single-chain antibodies. Boerma, H.R.; Hussey, R.S.; Phillips, D.V.; Wood, E.D.; Finnerty, S.L. 1994 AgriAgro Note/En A94/41 Registration of 'Doles' soybean Crop Sci 034:1411-1412 (5) SEP-OCT HR Boerma/Univ Georgia/Dept Crop & Soil Sci/Athens, GA 30602 USA| Anand, S.C.; Buss, G.R.; Gibson, P. 1994 AgriAgro Note/En A94/41 Registration of soybean cyst nematode resistant germplasms: S88-1608 and S89-2122 Crop Sci 034:1428-1429 (5) SEP-OCT SC Anand/Univ Missouri/Portageville, MO 63873 USA| Chow, K.L.; Emmons, S.W. 1994 ExpBioMe Artic/En L94/40 HOM-C/Hox genes and tour interacting loci determine the morphogenetic properties of single cells in the nematode male tail Development 120:2579-2592 (9) SEP C-elegans; morphogenesis; homeobox; HOM-C/Hox; genes; neurogenesis; CAENORHABDITIS-ELEGANS MALE; POST-EMBRYONIC DEVELOPMENT; C-ELEGANS; PATTERN-FORMATION; NERVOUS-SYSTEM; BODY REGION; DROSOPHILA; FATES; GENETICS; EXPRESSION SW Emmons/Yeshiva Univ Albert Einstein Coll Med/Dept Molec Genet/1300 Morris Pk Ave/Bronx, NY 10461 USA| --- The copulatory structure of the C. elegans male tail includes a set of nine bilaterally symmetrical pairs of sense organs known as rays. Each ray comprises three cells, which are generated by a stereotyped cell sublineage expressed by 18 epidermal ray precursor cells. A pattern formation mechanism in the epidermis guides the specification of morphogenetic differences between the rays necessary for correct organelle assembly at specific positions within the epidermis. Expression of these ray differences was altered in mutations we described previously, resulting in displaced and fused rays. Here we show that two genes of the C. elegans HOM-C/Hox gene complex play a role in the pattern formation mechanism. Increasing or decreasing the gene dosage of mab-5, an Antennapedia homolog, and egl-5, an Abdominal B homolog, results in displacement and fusion of specific rays. These changes are interpreted as anterior or posterior transformations in ray identities. Mutations in the genes previously described are dominant modifiers of these effects. This suggests that these genes act in the same morphogenetic pathway as mab-5 and egl-5. Several lines of evidence, including cell ablation experiments, argue that the identity of each ray is specified cell-autonomously in the terminal cells of the ray lineages. mab-5 and egl-5, therefore, specify the morphogenetic properties of differentiating cells, without change in cell lineage or apparent cell type. Modifier genes may act upstream of mab-5 and egl-5 to regulate their expression. Alternatively, they may act at the same step in the pathway, as cofactors, or they may be target genes. Target genes could include genes specifying cell recognition and adhesion molecules governing ray organelle assembly. Hutton, J.C. 1994 ?Endocri Artic/En L94/41 Insulin secretory granule biogenesis and the proinsulin-processing endopeptidases Diabetologia 037:S48-S56 ( Suppl. 2) SEP proinsulin; convertases; biosynthesis; MICROINJECTED XENOPUS OOCYTES; PANCREATIC B-CELLS; FUNCTIONAL EXPRESSION; SUBTILISIN FAMILY; ATT20 CELLS; KEX2-LIKE ENDOPROTEASE; PROPROTEIN CONVERTASE; CHROMAFFIN GRANULES; MEMBRANE-PROTEINS; STORAGE GRANULES JC Hutton/Univ Cambridge/Addenbrookes Hosp/Dept Clin Biochem/Hills Rd/Cambridge CB2 2QR, England| --- The insulin storage granule of the pancreatic beta cell is assembled within the trans Golgi network from around 50 or so gene products many of which are synthesized coordinately with the major component, proinsulin. An important contribution to our understanding of the regulation of this process has come from studies of the post-translational processing of proinsulin and of other proteins which are stored in the granule, particularly the processing enzymes themselves. The present review focusses on recent insights into the molecular nature of the processing machinery, and the granule Ca2+-dependent subtilisin-related endopeptidases which catalyse the initial rate-limiting step in the enzymic conversion of proinsulin. Halban, P.A. 1994 ?Endocri Artic/En L94/41 Proinsulin processing in the regulated and the constitutive secretory pathway Diabetologia 037:S65-S72 ( Suppl. 2) SEP proinsulin; conversion; conversion intermediates; insulin; beta cell; secretory pathways; PANCREATIC BETA-CELL; SUBTILISIN FAMILY; ATT20 CELLS; C-PEPTIDE; SLOW CLEAVAGE; INSULIN; CONVERSION; IDENTIFICATION; ENDOPEPTIDASE; GRANULE PA Halban/Univ Geneva/Med Ctr/Rech Louis Jeantet Labs/1 Rue Michel Servet/CH-1211 Geneva 4, Switzerland| --- Proinsulin is converted to insulin in beta-cell granules. Conversion involves endoproteolytic cleavage at the two pairs of basic residues linking the insulin A- and B-chains to C-peptide. The sequence of events leading to complete conversion differs from one proinsulin species to the next. In man, the structure of the proinsulin molecule is such as to favour cleavage al the B-chain/C-peptide junction leading to the generation of des-31,32 split proinsulin as the predominant, naturally occurring conversion intermediate. Under normal circumstances, proinsulin conversion is largely completed before secretion, and neither the intact prohormone nor conversion intermediates are thus encountered in large quantities in the circulation. In some pathological situations, including non-insulin-dependent diabetes, insulinoma and familial hyperproinsulinaemia, unusually high ratios of des-31,32 split proinsulin and/or proinsulin to insulin have been reported. As we understand the biochemistry of proinsulin conversion in increasingly fine molecular detail, it should become possible to make use of such unusual ratios to provide insight into lesions underlying altered beta-cell function in disease states. Beck, S. 1993 MolBiGen Lette/En L94/42 Accuracy of DNA sequencing: Should the sequence quality be monitored? DNA Sequence 004: 215-217 (3) DNA databases; error analysis; genome analysis; major histocompatibility complex (MHC); ERROR ANALYSIS S Beck/Imperial Canc Res Fund/44 Lincolns Inn Fields/London WC2A 3PX, England| Chanat, E.; Weiss, U.; Huttner, W.B. 1994 Biochemi Artic/En L94/40 The disulfide bond in chromogranin B, which is essential for its sorting to secretory granules, is not required for its aggregation in the trans-Golgi network FEBS Lett 351: 225-230 (2) SEP 5 aggregation; dithiothreitol; granin; proteolysis; sorting; trans-Golgi network; SECRETOGRANIN-I; PROTEINS WB Huttner/Univ Heidelberg/Inst Neurobiol/Neuenheimer Feld 364/D-69120 Heidelberg, Germany| --- Chromogranin B (secretogranin I), a protein sorted to secretory granules in many endocrine cells and neurons, undergoes selective aggregation during the sorting process in the trans-Golgi network. Reduction of the single, highly conserved intramolecular disulfide bond of chromogranin B by exposure of intact PC12 cells to the thiol reducing agent dithiothreitol has previously been shown to cause its missorting to the constitutive pathway of secretion. Using saponin perforation of membrane vesicles in aggregative buffer mimicking the milieu in the lumen of the trans-Golgi network (pH 6.4, 10 mM calcium), we show here that treatment with dithiothreitol does not prevent the aggregation of chromogranin B in this compartment. This implies that the loop in the chromogranin B polypeptide that is formed by the disulfide bond has a critical role in the membrane recognition of aggregated chromogranin B during secretory granule formation. Arntzen, F.K.; Mulder, J.G.; Visser, J.H.M. 1994 AnimaSci Artic/En A94/35 Rapid and Non-Destructive Assessment of the Number of Eggs in Cysts of Potato Cyst Nematodes by Weighing Fund Appl Nematol 017: 299-301 (4) Potato Cyst Nematodes; Globodera-Rostochiensis; G-Pallida; Number of Eggs; Weighting FK Arntzen/Ctr Plant Breeding & Reprod Res/Dlo/POB 16/6700 AA Wageningen, Netherlands| --- Dry cysts of potato cyst nematodes, derived from greenhouse rearing, were weighed and afterwards the number of eggs was determined by crushing the cysts and counting the eggs. A high correlation (r = 0.96) was found between the number of eggs per dry cyst of potato cyst nematodes and cyst weight, measured with a supermicrobalance. The number of eggs per cyst can be assessed rapidly and in a non-destructive way by weighing. Carter, G.T.; Kikuchi, N.; Horasek, S.J.; Walsh, S.A. 1994 MicrCell Artic/En L94/35 The Use of Fluorescent Dextrans as a Marker of Sarcolemmal Injury Histol Histopathol 009: 443-447 (3) JUL Muscle Injury; Histology; Fluorescein Isothiocyanate-Dextran; Eccentric; Exercise; MUSCULAR-DYSTROPHY; MUSCLE; SERUM; MOUSE GT Carter/Univ Calif Davis/Sch Med/Dept Phys Med & Rehabil/Tb 191/Davis, CA 95616 USA| --- We investigated the use of intravenously injected fluorescent dextran molecules (FDx) as a histological marker of sarcolemmal injury. Using fluorescent microscopy, uptake of FDx (average MW 10 kD) was assessed in sections of quadriceps muscles from three models: 1) normal (C57BL/10SnJ) mice, 2) normal mice run downhill (0, 3, and 7 days post exercise), and 3) non-exercised mdx (dystrophin-deficient) mice. These were compared to serial sections stained with hematoxylin and eosin (H&E). In control muscles, strong fluorescence was seen between fibers (intercellular). Intracellular FDx was observed within cells of the quadriceps from normal mice run downhill at days 0 and 3 post exercise, but not at day 7. On H&E staining, muscle pathology was not observed until day 3, with regeneration by day 7. Intracellular FDx was also observed within mdx muscles, particularly in fibers that appeared pre-necrotic on H&E stained sections. FDx appears to be useful as a histological marker of changes in sarcolemmal integrity associated with muscle injury from eccentric exercise or muscle disease. Hartz, D.; Langhorne, J. 1994 Immunolo Artic/En L94/40 Immunization of mice with Escherichia coli containing an antigen of the malaria parasite Plasmodium chabaudi chabaudi expressed in lambda gt11 induces high antibody titres Immunol Lett 041: 217-223 (2-3) JUL lambda gt11 expression library; Plasmodium chabaudi; vaccination; NITROCELLULOSE SHEETS; PROTEINS; GENES J Langhorne/Max Planck Inst Immunbiol/Stubeweg 51/D-79108 Freiburg, Germany| --- Escherichia coli containing a recombinant malarial protein expressed in lambda gt11 have been evaluated as an antigen delivery system in vivo. They were generated by infecting non-suppressing E. coil cells with a clone from a cDNA library of Plasmodium chabaudi chabaudi in lambda gt11. This clone (termed clone 6) expresses part of a 93 kDa blood-stage antigen of P. c. chabaudi as beta-galactosidase fusion protein. Immunization of C57Bl/6 mice with these infected E. coli cells resulted in an antibody response to the malarial part of the fusion protein comparable to that obtained with purified fusion protein preparations. This method, therefore represents a rapid secondary screening of clones from lambda gt11 expression libraries for immunogenic and potentially protective components. In addition, the administration of whole infected E. coli obviates the need for an adjuvant. Ichimura, S.; Mita, K.; Numata, M. 1994 Biochemi Artic/En L94/35 Protein ubiquitination in the posterior silk glands of Bombyx mori Insect Biochem Molec Biol 024: 717-722 (7) JUL ubiquitin; fibroin; degeneration; posterior silk gland; Bombyx mori; PROGRAMMED CELL-DEATH; POLYUBIQUITIN GENE; MESSENGER-RNA; CONJUGATING ENZYME; ACTIVATING ENZYME; FIBROIN; EXPRESSION; PATHWAY; RAD6; ICP4 S Ichimura/Natl Inst Radiol Sci/Div Biol/Inage Ku/Chiba 263, Japan| --- Ubiquitin gene expression and the ubiquitination of proteins in the posterior silk glands (PSG) of B. mori were analyzed developmentally with respect to fibroin synthesis and degeneration. Two ubiquitin transcripts are expressed throughout larval stages, and the level of each transcript is regulated differently. The larger transcript, a polyubiquitin mRNA, was abundant during the molt stage, while levels of the smaller ubiquitin transcript increased immediately after molting. Only a single 65 kDa ubiquitinated protein was detected late in the 5th instar, and the amount increased up to spinning stage. This ubiquitinated protein may participate in the PSG degeneration. Figueira, A.; Janick, J.; Levy, M.; Goldsbrough, P. 1994 PlantSci Artic/En A94/40 Reexamining the Classification of Theobroma cacao L Using Molecular Markers J Amer Soc Hort Sci 119:1073-1082 (5) SEP RFLP; Rapd; Herrania; Cocoa; Taxonomy; RIBOSOMAL DNA; EVOLUTIONARY; GENES J Janick/Dept Hort/W Lafayette, IN 47907 USA| --- Genetic similarities among eight Theobroma and two Herrania species, including 29 genotypes of T. cacao, were estimated by rDNA polymorphism. A phenogram based on these genetic similarities significantly separated two clusters: one cluster included all Herrania and Theobroma species, except T. cacao, while the second contained 28 of 29 T. cacao genotypes. There was no clear distinction between Herrania and Theobroma species. Separation of 29 T. cacao genotypes, representing all races and various origins, had no congruency with the conventional classification into three horticultural races: Criollo, Forastero, and Trinitario. Genetic similarities in T. cacao, estimated with RAPD markers, indicated continuous variation among the generally similar but heterogeneous genotypes. The wild genotypes formed an outgroup distinct from the cultivated genotypes, a distinction supported by the rDNA data. The phenograms constructed from RAPD and rDNA data were not similar within the wild and cultivated cacao subsets. Anthonsen, H.W.; Baptista, A.; Drablos, F.; Martel, P.; Petersen, S.B. 1994 MicrCell Revie/En L94/41 The blind watchmaker and rational protein engineering J Biotechnol 036: 185-220 (3) AUG 31 protein engineering; protein sequence; homology; NMR; molecular dynamics; protein electrostatics; NUCLEAR-MAGNETIC-RESONANCE; SCANNING TUNNELING MICROSCOPY; AMINO-ACID-COMPOSITION; SOLID-STATE NMR; SECONDARY STRUCTURE PREDICTION; MULTIPLE-SITE TITRATION; TWO-DIMENSIONAL H-1-NMR; EGG-WHITE LYSOZYME; CRYSTAL-STRUCTURE; ELECTROSTATIC INTERACTIONS SB Petersen/Sintef/Unimed/Ctr MR/N-7034 Trondheim, Norway| --- In the present review some scientific areas of key importance for protein engineering are discussed, such as problems involved in deducting protein sequence from DNA sequence (due to posttranscriptional editing, splicing and posttranslational modifications), modelling of protein structures by homology, NMR of large proteins (including probing the molecular surface with relaxation agents), simulation of protein structures by molecular dynamics and simulation of electrostatic effects in proteins (including pH-dependent effects). It is argued that all of these areas could be of key importance in most protein engineering projects, because they give access to increased and often unique information. In the last part of the review some potential areas for future applications of protein engineering approaches are discussed, such as non-conventional media, de novo design and nanotechnology. Beckstead, J.H. 1994 MicrCell Artic/En L94/35 A simple technique for preservation of fixation-sensitive antigens in paraffin-embedded tissues J Histochem Cytochem 042:1127-1134 (8) AUG immunohistochemistry; fixation; cell surface markers; zinc; paraffin; SECTIONS; ANTIBODY; LIGHT JH Beckstead/Oregon Hlth Sci Univ/Dept Pathol/L113/Portland, OR 97201 USA| --- Immunohistochemistry is a powerful tool for tissue diagnosis and research. Although the frozen section has remained the gold standard for this important approach to evaluation of antigens in tissues, there is widespread acknowledgment of many limitations. Routine paraffin-embedded sections are widely used for morphological examination of tissues but are not optimal for antigen preservation. In this study, paraffin-embedded tissues fixed with a simple buffer containing zinc as the primary fixative were compared with tissues fixed with routine formalin, zinc-formalin, paraformaldehyde, ethanol, a variety of commercial (non-formalin-containing) fixatives that have been recommended for reduced toxicity and improved antigen survival, and frozen sections. Human lymphoid tissues and a group of antibodies to antigens (CD1, CD4, CD7, CD8, CD19) usually preserved only in frozen tissue were used as a model system. Fixation in a simple solution of zinc acetate and zinc chloride in a Tris-Ca acetate buffer resulted in antigen preservation comparable to that in frozen sections with antibodies to these cell surface markers, Morphological preservation was comparable to formalin-fixed sections. The work presents a new method that represents the closest approach yet to a technique that combines optimal antigenic survival with the convenience and morphological preservation of traditional formalin-fixed tissue embedded in paraffin. Dye, M. 1994 MicrCell Artic/En L94/40 The Enrichment of Rhizobium from a Model System Using Immunomagnetic Separation J Microbiol Meth 019: 235-245 (3) MAR Rhizobium; Immunomagnetic Separation; Enrichment; ESCHERICHIA-COLI; STAPHYLOCOCCUS-AUREUS; IMMOBILIZED LECTINS; RAPID ISOLATION; WHITE CLOVER; LEGUMINOSARUM; TRIFOLII; BACTERIA; FOODS; SALMONELLA M Dye/Afrc/Inst Grassland & Environm Res/Welsh Plant Breeding Stn/PLAs Gogerddan/Aberystwyth SY23 3EB, Wales| --- Using immunomagnetic separation up to 200-fold enrichment of Rhizobium strains from mixtures has been achieved. This is the first report successfully using indirect separation, in which antiserum was attached to cells rather than immunomagnetic beads, thus allowing unfractionated serum to be employed. Optimal reaction conditions have been defined and the critical stages identified. Incubation of cells with immunomagnetic beads for an hour is needed to maximise cell recovery from suspension and at least six washing steps are needed to remove loosely bound cells from the beads so that non-specific binding is minimised. It is also evident that some anti-Rhizobium sera are better than others at promoting cell recovery, although the reason for this has not been found. Belichenko, P.V.; Dahlstrom, A. 1994 Neurosci Artic/En L94/35 Dual channel confocal laser scanning microscopy of lucifer yellow-microinjected human brain cells combined with Texas red immunofluorescence J Neurosci Methods 052: 111-118 (2) JUN Lucifer Yellow; intracellular staining; immunofluorescence; double labelling; confocal laser scanning microscopy; human brain mapping; MONOAMINE OXIDASE-A; NEURONS; IDENTIFICATION; INJECTION; ANTIBODIES; RECEPTOR; CLONING; CDNA A Dahlstrom/Gothenburg Univ/Inst Neurobiol Nrcg/Dept Anat & Cell Biol/Medicinaregatan 5/S-41390 Gothenburg, Sweden| --- A method for visualization of individual human brain cells and their dendritic extensions in combination with immunofluorescence is described. Microinjection of Lucifer Yellow was used to reveal the dendritic morphology of cortical brain cells. Indirect immunofluorescence with Texas Red as label was used to investigate the distribution of 3 different groups of immunogens: enzymes (monoamine oxidase A and B), receptors (beta-adrenoceptor protein), and synaptic vesicle proteins (synapsin I and synaptophysin) in each cortical slice. A dual-channel confocal laser scanning microscope with an argon/krypton laser was used for imaging these double-stained fluorescent specimens. Lucifer Yellow and Texas Red were recorded simultaneously or separately, taking advantage of the different activating lines (488 lambda and 568 lambda) of the laser and using the two filter blocks (K1 and K2) supplied with the instrument (BioRad MRC-600) for recording the emission of either fluorophore. Using this technique we have demonstrated the localization of immunoreactive material in relatation to the dendritic morphology of cortical cells. Abbott, L.C.; Conforti, M.L.; Isaacs, K.R.; Crawley, J.N.; Sterchi, D. 1994 Neurosci Artic/En L94/42 A simplified technique for histologic analysis of central nervous system tissues using glycol-methacrylate plastic coupled with pre-embedding immunocytochemistry J Neurosci Methods 054: 23-29 (1) SEP tyrosine hydroxylase; catecholamine neuron; peroxidase-antiperoxidase; methacrylate; glycol methacrylate; brain; cerebellum; TYROSINE-HYDROXYLASE; LOCALIZATION; SECTIONS; RAT; IMMUNOHISTOCHEMISTRY; EXPRESSION; CELLS LC Abbott/Univ Illinois/Coll Vet Med/Dept Vet Biosci/2001 S Lincoln Ave/Urbana, IL 61801 USA| --- Paraffin and some plastic embedding techniques will destroy many antigens routinely detected by immunocytochemistry performed on frozen tissue sections. However, morphologic quality is compromised to varying extents in frozen tissue, even with the use of cryoprotection. We report a simple glycol-methacrylate (GMA) embedding technique using vibratome-sectioned mouse brain reacted for tyrosine hydroxylase (TH) immunoreactivity before plastic embedding. In this study we used a short (4 h) simple, GMA embedding procedure which subsequently provided 1.5-5.0 mu m sections yielding morphologic details superior to frozen or paraffin sections. Prior to embedding we used a peroxidase-antiperoxidase (PAP) reaction with the 3,3'diaminobenzidine tetrahydrochloride (DAB) chromogen visualizing TH. Several different counterstains were used, demonstrating the versatility of this embedding procedure. Black, M.B.; Lutz, R.A.; Vrijenhoek, R.C. 1994 AquatSci Artic/En A94/40 Gene flow among vestimentiferan tube worm (Riftia pachyptila) populations from hydrothermal vents of the eastern Pacific Mar Biol 120: 33-39 (1) AUG STARCH-GEL ELECTROPHORESIS; VARIABILITY; DISTANCE; DIFFERENTIATION; RECOLONIZATION; EQUILIBRIUM; EXTINCTION; FREQUENT; ECOLOGY; RIDGE MB Black/Rutgers State Univ/Cook Coll/Ctr Theoret & Appl Genet/Marine & Coastal Sci Bldg/New Brunswick, NJ 08903 USA| --- Allozyme data are presented for six discrete populations of the giant hydrothermal vent tube worm Riftia pachyptila Jones, 1981 collected throughout the species' known range along mid-ocean spreading ridges of the eastern Pacific Ocean, Contrary to an earlier report, levels of genetic variation are relatively high in this species. Estimates of gene flow based on F-statistics revealed that dispersal throughout the surveyed region is sufficiently high to counter random processes that would lead to losses of genetic diversity and significant population differentiation. R. pachyptila, like other species of tube worms, displays considerable morphologic variation among populations, but this diversity is not reflected in allozyme variation. Vestimentifera, in general, appear to show extensive phenotypic plasticity. In the light of the available genetic data, caution is warranted when making inferences about the taxonomic status of collections based on morphological variation alone. A general decrease in estimated rates of gene flow between geographically more distant populations supports the hypothesis that dispersal in this species follows a stepping-stone model, with exchange between neighboring populations in great excess of long-distance dispersal. High levels of gene flow have been recorded in a variety of vent fauna and may be a prerequisite for success of species found in the ephemeral habitats associated with regions of sea-floor hydrothermal activity. Hylland, K.; Kaland, T.; Andersen, T. 1994 AquatSci Artic/En A94/35 Subcellular Cd Accumulation and Cd-Binding Proteins in the Netted Dog Whelk, Nassarius-Reticulatus L Mar Environ Res 038: 169-193 (3) GASTROPOD LITTORINA-LITTOREA; HEAVY-METAL DETOXICATION; MYTILUS-EDULIS; METALLOTHIONEIN INDUCTION; CADMIUM BIOACCUMULATION; TERTIARY LYSOSOMES; MACOMA-BALTHICA; HELIX-ASPERSA; ZINC UPTAKE; ZN-BINDING K Hylland/Norwegian Inst Water Res/POB 173/N-0411 Oslo, Norway| --- The subcellular accumulation of Cd in different tissues of the marine gastropod Nassarius reticulatus was determined following exposure to 0.1, 0.3 and 0.9 mg Cd/litre seawater (nominal concentrations) and the importance of cytosolic Cd-binding components for the sequestration and immobilisation of the metal evaluated Different tissues from exposed whelks were removed, pooled, homogenised, the homogenates subjected to subcellular fractionation and fractions measured for Cu, Zn and Cd by atomic absorption spectrophotometry. Cytosols were further separated and heat-stable Cd-binding capacity determined. All subcellular fractions in different tissues accumulated Cd at all exposures. The total cytosolic protein concentration in some tissues was strongly affected, but there was no concentration-dependent increase in Cd-binding capacity of the heat-stable protein pool. The major cytosolic Cu- and Cd-binding components in all four tissues were low molecular weight (M(r) 5-10 kDa), whereas most cytosolic Zn coeluted with components of very low molecular weight. Erickson, P.A.; Lewis, G.P.; Fisher, S.K. 1993 *CurBook Revie/En L94/41 Postembedding immunocytochemical techniques for light and electron microscopy --- In: Methods in Cell Biology, Vol 37, pp. 283-310. Editor(s): DJ Asai. Academic Press Inc/525 B Street/Suite 1900/San Diego/CA 92101-4495. ISBN/ISSN 0-12-564137-0 Methods in Cell Biology, Vol 037: 283-310 () IMMUNO-CYTOCHEMICAL DETECTION; RETINAL-DETACHMENT; TISSUE; RECOVERY; CAT PA Erickson/Univ Calif Santa Barbara/Neurosci Res Inst/Santa Barbara, CA 93106 USA| Hale, I.L.; Matsumoto, B. 1993 *CurBook Revie/En L94/41 Resolution of subcellular detail in thick tissue sections: Immunohistochemical preparation and fluorescence confocal microscopy --- In: Methods in Cell Biology, Vol 38, pp. 289-324. Editor(s): B Matsumoto. Academic Press Inc/525 B Street/Suite 1900/San Diego/CA 92101-4495. ISBN/ISSN 0-12-564138-9 Methods in Cell Biology, Vol 038: 289-324 () ACETYLATED ALPHA-TUBULIN; ROD OUTER SEGMENT; IMMUNOCYTOCHEMICAL LOCALIZATION; MONOCLONAL-ANTIBODIES; ELECTRON-MICROSCOPY; PIGMENT EPITHELIUM; MEMBRANE-PROTEINS; GOLGI-APPARATUS; FROG ROD; CELLS IL Hale/Univ Calif Santa Barbara/Dept Biol Sci/Santa Barbara, CA 93106 USA| Himmelhoch, S. 1994 MicrCell Artic/En L94/41 A negative contrast stain for ultra-thin frozen sections Microsc Res Technique 029: 23-28 (1) SEP 1 morphology; immunolabeling; negative contrast; VIRAL MEMBRANE-PROTEINS; TRANS GOLGI CISTERNAE; SEMLIKI FOREST VIRUS; INTRACELLULAR-TRANSPORT S Himmelhoch/Weizmann Inst Sci/Ctr Electron Microscopy/Dept Sci Biol/IL-76100 Rehovot, Israel| --- Ultra-thin frozen sections are ideal substrates for immunolabeling in high resolution electron microscopy. However, visualization of subcellular structures is inferior to that obtained with corresponding plastic sections. Although negative staining is generally effective and even superior to positive staining, the accumulated stain is often too heavy, obscuring morphology and markers used for immunocytochemical localization of antigens. This paper describes the development of a modified negative contrast staining technique in which a high concentration of uranyl acetate is mixed with methyl cellulose at a low pH. Application of this stain to cryosections of cells and tissue resulted in improved visualization of morphological structures characterized by negative images of membranes and cell organelles. Use of this stain is advantageous for morphological and immunocytochemical studies involving ultra-thin frozen sections. (C) 1994 Wiley-Liss, Inc. Goldman, N.; Yang, Z.H. 1994 MolBiGen Artic/En L94/41 Codon-based model of nucleotide substitution for protein-coding DNA sequences Mol Biol Evol 011: 725-736 (5) SEP models; nonsynonymous substitutions; nucleotide substitution; phylogenetic estimation; protein-coding sequences; synonymous substitutions; ESTIMATING EVOLUTIONARY RATES; MAXIMUM-LIKELIHOOD; MITOCHONDRIAL-DNA; MOLECULAR EVOLUTION; STATISTICAL TESTS; PHYLOGENY; INFERENCE; GENES; SITES N Goldman/Natl Inst Med Res/Math Biol Lab/the Ridgeway/Mill Hill/London NW7 1AA, England| --- A codon-based model for the evolution of protein-coding DNA sequences is presented for use in phylogenetic estimation. A Markov process is used to describe substitutions between codons. Transition/transversion rate bias and codon usage bias are allowed in the model, and selective restraints at the protein level are accommodated using physicochemical distances between the amino acids coded for by the codons. Analyses of two data sets suggest that the new codon-based model can provide a better fit to data than can nucleotide-based models and can produce more reliable estimates of certain biologically important measures such as the transition/transversion rate ratio and the synonymous/nonsynonymous substitution rate ratio. Bustamante, J.O.; Liepins, A.; Hanover, J.A. 1994 Biochemi Revie/En L94/42 Nuclear pore complex ion channels (Review) Mol Membrane Biol 011: 141-150 (3) JUL-SEP nuclear envelope; nuclear pore complex; nucleocytoplasmic transport; ion channels; signal transduction; control of gene activity; SMOOTH-MUSCLE CELLS; RAT-LIVER NUCLEI; PERMEABILIZED MAMMALIAN-CELLS; SENSITIVE FLUORESCENT DYE; FIBROBLAST GROWTH-FACTOR; SALIVARY-GLAND CELLS; INTRACELLULAR CALCIUM; PROTEIN IMPORT; ENDOPLASMIC-RETICULUM; TEMPORAL RESOLUTION JO Bustamante/Univ Maryland/Sch Med/Ctr Heart/Dept Med/Div Cardiol/Baltimore, MD 21021 USA| --- It is currently thought that nuclear pore complexes (NPCs) primarily govern nucleocytoplasmic interactions via selective recognition and active transport of macromolecules. However, in various nuclear preparations, patch-clamp and fluorescence luminiscence and ion microscopy support classical microelectrode measurements indicating that monoatomic ion flow across the nuclear envelope (NE) is strictly regulated. Gating of large conductance nuclear envelope ion channels (NICs) somewhat resembles that of gap junctional channels. In other respects, NICs are distinct in that they require cytosolic factors, are blocked by wheat germ agglutinin and are blocked and/or modified by antibodies to epitopes of NPC glycoproteins. Therefore, NIC activity, recorded as electrical current/conductance is likely to be intrinsic to NPCs. This observation suggests a potential use for the patch-clamp technique in establishing the mechanisms underlying nuclear pore gating in response to cytosolic and nucleosolic factors such as transcription and growth factors, oncogene and proto-oncogene products and receptors far retinoids, steroids and thyroid hormone. NIC activity may also be useful in evaluating the mechanisms of nuclear import of foreign nucleic acid material such as that contained in virons and viroids. Finally, in consideration to the electrophysiological data accumulated so far, the study of nuclear pore ion channel activity may help our understanding of other important issues such as cell suicide, programmed cell death or apoptosis. Hay, F.S. 1994 AnimaSci Note/En A94/35 Surface Sterilisation of Heterodera trifolii Goffart (Nematoda, Tylenchida) and Its Monoxenic Culture on Root Cultures of White Clover (Trifolium repens L) N Z J Zool 021: 209-212 (2) Clover Cyst Nematode; Gnotobiotic Culture; Sterilisation; Heterodera-Trifolii FS Hay/Agres Grasslands Res Ctr/Private Bag 11008/Palmerston North, New Zealand| --- Various disinfectants and antibiotics were tested for their ability to eliminate contaminant organisms from second stage juveniles (J2) of clover cyst nematode (Heterodera trifolii Goffart). Sterile J2 were produced by alternating treatments of dilute Hibitane (chlorhexidine gluconate 1% w/v, isopropyl alcohol 0.8%) or Dettol (1% w/v chlorxylenol) with antibiotic (0.1% w/v Penicillin-G/Streptomycin sulphate BP). A convenient method involved alternate treatments with Hibitane (15 min), antibiotic (16 h), and Hibitane (15 min) with sterile water rinses after each treatment. Following sterilisation, H. trifolii was successfully reared on root cultures of white clover (Trifolium repens L.) grown on White's medium. Some 21-24% of sterilised juveniles formed egg-containing adult females on root cultures. Charlesworth, B.; Sniegowski, P.; Stephan, W. 1994 Multidis Revie/En L94/40 The evolutionary dynamics of repetitive DNA in eukaryotes Nature 371: 215-220 (6494) SEP 15 ELEMENT COPY NUMBER; GROUP-II INTRON; DROSOPHILA-MELANOGASTER; TRANSPOSABLE ELEMENTS; POPULATION-GENETICS; SATELLITE DNA; Y-CHROMOSOME; CENTROMERIC HETEROCHROMATIN; HIGH-FREQUENCY; TANDEM ARRAYS B Charlesworth/Univ Chicago/Dept Ecol & Evolut/1101 E 57TH St/Chicago, IL 60637 USA| --- Repetitive DNA sequences form a large portion of the genomes of eukaryotes. The 'selfish DNA' hypothesis proposes that they are maintained by their ability to replicate within the genome. The behaviour of repetitive sequences can result in mutations that cause genetic diseases, and confer significant fitness losses on the organism. Features of the organization of repetitive sequences in eukaryotic genomes, and their distribution in natural populations, reflect the evolutionary forces acting on selfish DNA. Chen, S.; Roseman, A.M.; Hunter, A.S.; Wood, S.P.; Burston, S.G.; Ranson, N.A.; Clarke, A.R.; Saibil, H.R. 1994 Multidis Artic/En L94/40 Location of a folding protein and shape changes in GroEL-GroES complexes imaged by cryo-electron microscopy Nature 371: 261-264 (6494) SEP 15 CHAPERONIN GROEL; CENTRAL CAVITY; BINDING; SURFACE; CYCLE; ATP S Chen/Univ London Birkbeck Coll/Dept Crystallog/Malet St/London WC1E 7HX, England| --- PROTEIN folding mediated by the molecular chaperone GroEL occurs by its binding to non-native polypeptide substrates and is driven by ATP hydrolysis(1). Both of these processes are influenced by the reversible association of the co-protein, GroES (refs 2-4). GroEL and other chaperonin 60 molecules(5) are large, cylindrical oligomers consisting of two stacked heptameric rings of subunits(6,7); each ring forms a cage-like structure(8) thought to bind polypeptides in a central cavity(8-10). Chaperonins play a passive role in folding by binding or sequestering folding proteins to prevent their aggregation(11-13), but they may also actively unfold substrate proteins trapped in misfolded forms, enabling them to assume productive folding conformations(14-16). Biochemical studies show that GroES improves the efficiency of GroEL function(2,3,17), but the structural basis for this is unknown. Here we report the first direct visualization, by cryo-electron microscopy, of a non-native protein substrate (malate dehydrogenase) bound to the mobile, outer domains at one end of GroEL. Addition of GroES to GroEL in the presence of ATP causes a dramatic hinge opening of about 60 degrees. GroES binds to the equivalent surface of the GroEL outer domains, but on the opposite end of the GroEL oligomer to the protein substrate. Adamkewicz, S.L.; Harasewych, M.G. 1994 AquatSci Artic/En A94/41 Use of Random Amplified Polymorphic DNA (RAPD) Markers to Assess Relationships Among Beach Clams of the Genus Donax Nautilus 108: 51-60 ( Suppl. 2) AUG 11 Rapd; PCR; Phylogeny; Biogeography; Donax SL Adamkewicz/George Mason Univ/Dept Biol/Fairfax, VA 22030 USA| --- The polymerase chain reaction was used to amplify genomic DNA from nine populations of donacid clams representing six taxa occurring in three sympatric pairs. The randomly amplified polymorphic DNA (RAPD) markers produced by this technique successfully distinguished among all taxa. Each taxon possessed a unique subset of markers and one member of each sympatric pair differed from the other by several markers. The taxa also separated clearly into two groups, one North American and the other Caribbean. Use of RAPD markers as characters in a cladistic analysis produced well resolved phylogenetic trees of high consistency. Backeljau, T.; Breugelmans, K.; Leirs, H.; Rodriguez, T.; Sherbakov, D.; Sitnikova, T.; Timmermans, J.M.; Vangoethem, J.L.; Verheyen, E. 1994 AquatSci Artic/En A94/41 Application of Isoelectric Focusing in Molluscan Systematics Nautilus 108: 156-167 ( Suppl. 2) AUG 11 Mollusca; Systematics; Phylogeny; Population Genetics; Protein Electrophoresis; Isoelectric Focusing T Backeljau/Royal Belgian Inst Nat Sci/Vautierstr 29/B-1040 Brussels, Belgium| --- The application of isoelectric focusing (IEF) in molluscan systematics is reviewed and illustrated using literature data and unpublished analyses. IEF can be used as any other electrophoretic method, but is most appropriate for: (1) generating complex species-specific banding profiles, (2) assessing overall genetic similarities, (3) supplementing conventional electrophoretic techniques by resolving hidden protein variation and (4) investigating minute organisms. Bennett, R.N.; Wallsgrove, R.M. 1994 PlantSci Revie/En A94/42 Secondary metabolites in plant defence mechanisms New Phytol 127: 617-633 (4) AUG cyanogenic glucosides; alkaloids; phenolics; phytoalexins; salicylic acid; methyl jasmonate; glucosinolates; RAPE BRASSICA-NAPUS; PHENYLALANINE AMMONIA-LYASE; BICOLOR L MOENCH; PATHOGENESIS-RELATED PROTEINS; CYANOGENIC GLUCOSIDE DHURRIN; SYSTEMIC ACQUIRED-RESISTANCE; VIRUS-INOCULATED TOBACCO; 2-SPOTTED SPIDER-MITE; OILSEED RAPE; SALICYLIC-ACID RN Bennett/Rothamsted Exptl Stn/Afrc/Inst Arable Crops Res/Dept Biochem & Physiol/Harpenden AL5 2JQ/Herts, England| --- Many secondary metabolites found in plants have a role in defence against herbivores, pests and pathogens. In this review, a few examples are described and discussed, and some of the problems in determining the precise role(s) df such metabolites highlighted. The role of secondary metabolites in defence may involve deterrence/anti-feedant activity, toxicity or acting as precursors to physical defence systems. Many specialist herbivores and pathogens do not merely circumvent the deterrent or toxic effects of secondary metabolites but actually utilize these compounds as either host recognition cues or nutrients (or both). This is true of both cyanogenic glucosides and glucosinolates, which are discussed in detail as examples of defensive compounds. Their biochemistry is compared and contrasted. An enormous variety of secondary metabolites are derived from shikimic acid or aromatic amino acids, many of which have important roles in defence mechanisms. Several classes of secondary products are 'induced' by infection, wounding or herbivory, and examples of these are given. Genetic variation in the speed and extent of such induction may account, at least in part, for the difference between resistant and susceptible varieties. Both salicylates and jasmonates have been implicated as signals in such responses and in many other physiological processes, though their prescise roles and interactions in signalling and development are not fully understood. Hojnacki, J.L. 1994 Biochemi Revie/En L94/35 Alcohol's influence on plasma lipoproteins: A nonhuman primate model Nutr Res 014:1241-1295 (8) AUG alcohol; lipoproteins; coronary heart disease; HIGH-DENSITY-LIPOPROTEIN; ESTER TRANSFER PROTEIN; APOLIPOPROTEIN-A-I; CORONARY HEART-DISEASE; LECITHIN-CHOLESTEROL ACYLTRANSFERASE; MONKEYS SAIMIRI-SCIUREUS; SQUIRREL-MONKEYS; SERUM-LIPOPROTEINS; ARTERY DISEASE; FAMILIAL HYPERCHOLESTEROLEMIA JL Hojnacki/Univ Massachusetts/Dept Biol Sci/Grad Biochem Program/Lowell, MA USA| --- Ethanol (EtOH) is a common component of the American diet which can contribute 5-18% of the total calories consumed by nonalcoholics and 35-50% of the total energy intake of alcoholics. Moderate alcohol consumption may protect against coronary heart disease (CHD) while excessive drinking has adverse cardiovascular effects. The underlying basis of the alcohol-heart disease relationship may involve the ability of this drug to modify the level of circulating lipoproteins, particularly atherogenic low density lipoproteins (LDL) and antiatherogenic high density lipoproteins (HDL). In an effort to overcome a number of dietary-lifestyle variables and intake reporting errors associated with human studies, an animal model (atherosclerosis-susceptible male squirrel monkeys) was developed which enabled investigators to deliver quantitative doses of EtOH (vodka) (substituted isocalorically for carbohydrate) to monkeys as part of a chemically defined liquid diet. The first part of this review describes experiments which evaluate the effect of alcohol dose (low, moderate, high), drinking period (acute vs. chronic), and drinking pattern (regular vs. binge) on lipoprotein composition, while the second part discusses the enzymatic/metabolic basis for the observed lipoprotein alterations. The concluding section proposes that high dose (24% calories) alcohol may induce alterations in liver membrane and/or lipoprotein receptors/binding sites which may slow the clearance of lipoproteins from the circulation and thus initiate a sequence of metabolic changes leading to elevations in LDL and HDL lipid and protein components. Enhanced de novo synthesis in response to high EtOH intake may further increase the plasma HDL concentration. An extended residence time in circulation of HDL particles may be beneficial in sequestering peripheral cholesterol for eventual excretion via the reverse cholesterol transport pathway given that HDL hepatic lipid degradation and sterol/bile acid excretion remain active in animals fed the high alcohol regimen. On the other hand, a sustained elevation in plasma LDL would promote the progression of atherosclerosis. The close similarity between humans and squirrels monkeys in their lipoprotein response to alcohol emphasizes the pathophysiological relevance of this animal model, and the valuable role they may play in providing a greater understanding of the relationship between ethanol, lipoproteins, and CHD. Artursson, P.; Lindmark, T.; Davis, S.S.; Illum, L. 1994 Pharmaco Note/En L94/40 Effect of chitosan on the permeability of monolayers of intestinal epithelial cells (Caco-2) Pharmaceut Res 011:1358-1361 (9) SEP chitosan; Caco-2; permeability; nasal epithelium; drug absorption; TIGHT JUNCTIONS; DRUG ABSORPTION; TRANSPORT; INVITRO; CULTURE; CYTOSKELETON; MDCK P Artursson/Univ Uppsala/Ctr Biomed/Dept Pharmaceut/Box 580/S-75123 Uppsala, Sweden| Araya, A.; Begu, D.; Litvak, S. 1994 AniPlaSc Revie/En L94/35 RNA editing in plants Physiol Plant 091: 543-550 (3) JUL chloroplasts; codon; organelle; higher plants; mitochondria; RNA editing; B MESSENGER-RNA; MITOCHONDRIAL ATP-SYNTHASE; MALE-STERILE CYTOPLASM; OENOTHERA MITOCHONDRIA; TRYPANOSOME MITOCHONDRIA; PHYSARUM-POLYCEPHALUM; SEQUENCE SIMILARITIES; MAIZE CHLOROPLASTS; INTRON SEQUENCES; GENE TRANSCRIPT A Araya/CNRS/Inst Biochim Cellulaire/1 Rue Camille St Saens/F-33077 Bordeaux, France| --- Higher plant mitochondrial RNAs undergo predetermined modifications which involve differences of splicing and trimming of the primary transcripts. These post-transcriptional modifications are specific C-to-U changes occurring mostly in the coding regions of mRNAs without changing the reading frame. Editing of mRNAs can lead to the formation or initiation of stop codons. Plant mitochondrial proteins issued from edited mRNAs are more similar to non-plant homologous proteins suggesting that this process is involved in the production of functional polypeptides. RNA editing in non-coding regions are also observed and may represent a new mechanism for modulating gene expression. Three possible biochemical mechanisms can account for RNA editing in plant mitochondria: nucleotide replacement, base exchange and deamination. Although some evidence shows that RNA editing proceeds by a deamination mechanism, several questions remain to be solved: What are the signals recognised by the biochemical machinery for such a specific process? What are the reasons that make an additional process acquired by land plant mitochondria for faithful gene expression? Hirai, M.Y.; Fujiwara, T.; Goto, K.; Komeda, Y.; Chino, M.; Naito, S. 1994 AniPlaSc Artic/En L94/42 Differential regulation of soybean seed storage protein gene promoter-GUS fusions by exogenously applied methionine in transgenic Arabidopsis thaliana Plant Cell Physiol 035: 927-934 (6) SEP Arabidopsis thaliana; beta-conglycinin; immature seed culture; L-methionine; seed storage protein genes; transgenic plants; AGROBACTERIUM-TUMEFACIENS; BETA-CONGLYCININ; MESSENGER-RNA; ENCODES; TRANSFORMATION; CLONING; EXPRESSION; BINDING; SUBUNIT; LOCUS MY Hirai/Univ Tokyo/Fac Agr/Dept Agr Chem/Bunkyo Ku/Tokyo 113, Japan| --- Expression of the gene encoding the beta subunit of beta-conglycinin, the 7S seed storage protein of soybean (Glycine max [L.] Merr.), has been shown to be down-regulated by exogenously applied L-methionine in in vitro soybean cotyledon cultures, whereas expression of the gene encoding the alpha' subunit is not affected. We constructed transgenic Arabidopsis thaliana (L.) Heynh. carrying the beta-glucuronidase (GUS) reporter gene under the control of the promoter regions from either the alpha' or beta subunit gene. An in vitro culture system of immature siliques of A. thaliana was developed for exogenous application of L-methionine to immature seeds. Expression of the beta subunit gene promoter-GUS fusion was down-regulated by the application of L-methionine, and this response was reversible. As an alternative way to apply L-methionine, A. thaliana plants were grown on rockwool and irrigated with L-methionine-supplemented medium. GUS activity driven by the beta subunit gene promoter was repressed by L-methionine, and the degree of repression depended on the concentration of L-methionine in the medium. On the other hand, the alpha' subunit gene promoter-GUS fusion did not show such a response. These results indicate that A. thaliana has a system to differentially regulate the expression of the beta-conglycinin genes by L-methionine at the level of transcription. This work establishes a system to genetically analyze plants' responses to nutritional stimuli. Compton, M.E. 1994 PlantSci Revie/En A94/42 Statistical methods suitable for the analysis of plant tissue culture data Plant Cell Tissue Organ Cult 037: 217-242 (3) JUN analysis of variance; data transformation; mean separation; statistical analysis; FLOWER MORPHOGENESIS; SHOOT; EXPLANTS; ROOT ME Compton/Univ Florida/Ifas/Cent Florida Res & Educ Ctr/5336 Univ Ave/Leesburg, FL 34748 USA| --- Statistical analyses are an essential part of biological research. Statistical methods are available to biological researchers that range from very simple to extremely complex. Therefore, caution should be used when selecting a statistical method. When possible it is best to avoid complicated statistical procedures that are difficult to interpret and may hinder the researcher's ability to make treatment comparisons. Instead a method should be chosen that compliments a logical and practical treatment design. Statistics should be used as a tool to compare treatments of interest and should not dictate the treatments. Experimental designs should take into account the eventual analysis, otherwise one could conceive of a design that could not be analyzed or, when analyzed, would not answer the desired questions. Therefore, time should be spent before conducting an experiment to plan an experimental design and analysis that best compliments the treatment scheme and questions to be answered. The purpose of this paper is to present examples of experimental designs, means separation procedures, data transformations and presentation methods suitable for plant cell and tissue culture data. Bauwens, S.; Katsanis, K.; Vanmontagu, M.; Vanoostveldt, P.; Engler, G. 1994 AniPlaSc Artic/En L94/35 Procedure for whole mount fluorescence in situ hybridization of interphase nuclei on Arabidopsis thaliana Plant J 006: 123-131 (1) JUL INSITU HYBRIDIZATION; CHROMATIN; LOCALIZATION; MICROSCOPY; SEQUENCES; RDNA; DNA S Bauwens/State Univ Ghent/Genet Lab/Kl Ledeganckstr 35/B-9000 Ghent, Belgium| --- A procedure for whole mount fluorescence in situ hybridization (FISH) on plant tissue is reported. The technique was demonstrated on seedlings and flowers of Arabidopsis thaliana L. with rDNA as a probe, labelled, both for direct and indirect detection. It was found that fixation in 1% formaldehyde yielded the best results with respect to morphology and hybridization efficiency. The combination of whole mount FISH and confocal scanning laser microscopy allowed the nuclear localization of the rDNA loci in all tissues of both seedlings and flowers. Direct labelling yielded the best signal-to-noise ratio, especially in the apical zones of the seedlings. The technique was further illustrated on seedlings of A, thaliana in double labelling experiments with rDNA and a tandemly repeated, 500 bp sequence of A. thaliana. Although nuclei in all tissues in the seedling exhibited both signals, hybridization efficiency for both signals was reduced in the dense, apical zones as compared with single labelling experiments with rDNA. Elmayan, T.; Tepfer, M. 1994 AniPlaSc Artic/En L94/40 Synthesis of a bifunctional metallothionein beta-glucuronidase fusion protein in transgenic tobacco plants as a means of reducing leaf cadmium levels Plant J 006: 433-440 (3) SEP TISSUE-SPECIFIC EXPRESSION; NICOTIANA-TABACUM-L; MAMMALIAN METALLOTHIONEIN; RIBONUCLEIC-ACID; GENE; SEEDLINGS; SEQUENCE; PROMOTER; RNA M Tepfer/Inra/Biol Cellulaire Lab/F-78026 Versailles, France| --- Chimeric genes under the control of a CaMV 35S promoter with a doubled enhancer (35S(2)) that encode a mammalian metallothionein (hMTII), or an Escherichia coil beta-glucuronidase (GUS), or a hMTII/GUS fusion protein were introduced into the genome of tobacco (Nicotiana tabacum cv. PBD6). Transcripts and Cd-binding proteins of expected size were observed in plants expressing either the 35S(2)-hMTII or the 35S(2)-hMTII/GUS gene, and in the latter plants a protein with GUS activity that was larger than the native GUS enzyme was observed. Thus, plants expressing the hMTII-GUS gene synthesize a bifunctional protein, with both GUS and Cd-binding activity. In an in vitro assay, seedlings expressing either one of these genes had 60-70% lower Cd concentration in their shoots than controls, and Cd translocation to the shoot system was reduced (similar to 20% of Cd absorbed was translocated), compared with that in controls expressing a 35S(2)-GUS gene, where similar to 50% of the Cd absorbed was translocated. Chia, T.F.; Chan, Y.S.; Chua, N.H. 1994 AniPlaSc Artic/En L94/40 The firefly luciferase gene as a non-invasive reporter for Dendrobium transformation Plant J 006: 441-446 (3) SEP TRANSGENIC PLANTS; CELLS; EXPRESSION NH Chua/Rockefeller Univ/Plant Molec Biol Lab/1230 York Ave/New York, NY 10021 USA| --- Here a screening method is described for transformed tissues and transgenic plants of Dendrobium (Orchidaceae) using the firefly luciferase gene (luc) as a combined marker/reporter gene. Protocorm-like-bodies (PLB) were bombarded with tungsten particles (1.3 mu m) coated with plasmids carrying a 35S-luc chimeric gene. Three weeks after bombardment 1 mM luciferin was added to the tissues and transformed cells were identified by virtue of their bioluminescence as monitored by low-light video microscopy in combination with a real-time photon imaging technique. Transformed tissues were excised, allowed to proliferate, and then subjected to a second round of screening. After three rounds of growth and screening, transformed Dendrobium tissues expressing luciferase were used to generate transgenic plants. Southern blot analysis of several transgenic lines confirmed the integration of the luciferase gene into the orchid genome. It is thought that this procedure can be used for transformation of not only orchids but other species as well. Albrecht, C.; Laurent, P.; Lapeyrie, F. 1994 AniPlaSc Artic/En L94/40 Eucalyptus root and shoot chitinases, induced following root colonization by pathogenic versus ectomycorrhizal fungi, compared on one- and two-dimensional activity gels Plant Sci 100: 157-164 (2) Alternaria; Botrytis; chitinase; ectomycorrhiza; Eucalyptus; Fusarium; Phytophthora; Pisolithus; symbiosis; SOMATIC EMBRYO MUTANT; SYSTEMIC INDUCTION; PLANTS; RHIZOBIUM; BETA-1,3-GLUCANASE; ELECTROPHORESIS; EXPRESSION; RESISTANCE; INFECTION; PARASITE F Lapeyrie/Inra/Ctr Nancy/Equipe Microbiol Forestiere/F-54280 Champenoux, France| --- The present work deals with the effect of root fungal colonization on chitinases activities in Eucalyptus seedlings. Plant chitinases induced during pathogenic infection are thought to be directed against the fungus, but chitinases induced by ectomycorrhizal fungi may contribute to ectomycorrhizal ontogenesis. Plant responses were compared to determine whether plants induce different chitinases activities in contact with symbionts and pathogens, and whether chitinases are induced systemically in both cases. Despite 2-D analysis of Eucalyplus root chitinolytic activities, induced following root colonization by pathogenic or ectomycorrhizal fungi, it was not possible to differentiate between both infections. Moreover, ectomycorrhizal colonization, as pathogenic infections, led to systemic induction of chitinase activities far from the site of inoculation. Contrasting with roots, the chitinase activities induced in shoots were not positively correlated with ectomycorrhizal strain aggressiveness. The differential stimulation of root chitinase activity by aggressive or non-aggressive ectomycorrhizal strains was related to induction of five additional isoforms in response to contact with the most aggressive strains. Golding, G.B.; Tsao, N.; Pearlman, R.E. 1994 Multidis Artic/En L94/35 Evidence for intron capture: An unusual path for the evolution of proteins Proc Natl Acad Sci USA 091: 7506-7509 (16) AUG 2 PHOSPHOGLYCERATE KINASE; TOPOGENIC SIGNAL; GENES; EXONS; SEQUENCES; PIECES; FAMILY GB Golding/Mcmaster Univ/Dept Biol/Hamilton L8S 4K1/on, Canada| --- Most new genes are thought to evolve from preexisting genes but duplications of entire genes or shuffling of preexisting exons provides only a limited repertoire of new sequences that can be presented to a tell. Only pieces that previously existed can be used in the construction and any further divergence depends on the slow accumulation of mutations. We show here the presence of a small, in-frame intron in a ciliate phosphoglycerate kinase gene and the insertion of an unusually random amino acid sequence at the same position in trypanosome phosphoglycerate kinase. The unusual sequences in trypanosomes were likely to have originally been introns that have been subsequently captured by the protein and have now been incorporated as part of the coding sequence. Via this path a truly unique sequence can be incorporated into an existing protein, leading in time to the evolution of a new, functionally distinct protein. Hecht, M.H. 1994 Multidis Note/En L94/41 De novo design of beta-sheet proteins Proc Natl Acad Sci USA 091: 8729-8730 (19) SEP 13 RIBONUCLEASE; TRANSITION; TEMPLATE; ACIDS MH Hecht/Princeton Univ/Dept Chem/Princeton, NJ 08544 USA| Dohlsten, M.; Abrahmsen, L.; Bjork, P.; Lando, P.A.; Hedlund, G.; Forsberg, G.; Brodin, T.; Gascoigne, N.R.J.; Forberg, C.; Lind, P.; Kalland, T. 1994 Multidis Artic/En L94/41 Monoclonal antibody-superantigen fusion proteins: Tumor-specific agents for T-cell-based tumor therapy Proc Natl Acad Sci USA 091: 8945-8949 (19) SEP 13 COLON-CARCINOMA CELLS; RECEPTOR; IMMUNOTHERAPY; MOLECULES; SEQUENCE; BINDING; CHAIN; GENE T Kalland/Pharm Oncol Immunol/Scheelevagen 22/S-22363 Lund, Sweden| --- The bacterial superantigen staphylococcal enterotoxin A (SEA) is an extremely potent activator of T lymphocytes when presented on major histocompatibility complex (MHC) class II molecules. To develop a tumor-specific superantigen for cancer therapy, we have made a recombinant fusion protein of SEA and the Fab region of the C215 monoclonal antibody specific for human colon carcinoma cells. SEA as part of a fusion protein showed a >10-fold reduction in MHC class II binding compared to native SEA, and accordingly, the affinity of the FabC215-SEA fusion protein for the C215 tumor antigen was approximate to 100 fold stronger than to MHC class II molecules. The FabC215-SEA fusion protein efficiently targeted T cells to lyse C215(+) MHC class II- human colon carcinoma cells, which demonstrates functional substitution of the MHC class II-dependent presentation of SEA with tumor specificity. Treatment of mice carrying B16 melanoma cells expressing a transfected C215 antigen resulted in 85-99% inhibition of tumor growth and allowed long-term survival of animal. The therapeutic effect was dependent on antigen-specific targeting of the FabC215-SEA fusion protein, since native SEA and an antigen-irrelevant FabC242-SEA fusion protein did not influence tumor growth. The results suggest that Fab-SEA fusion proteins convey superantigenicity on tumor cells, which evokes T cells to suppress tumor growth. Hwang, D.J.; Roberts, I.M.; Wilson, T.M.A. 1994 Multidis Artic/En L94/41 Expression of tobacco mosaic virus coat protein and assembly of pseudovirus particles in Escherichia coli Proc Natl Acad Sci USA 091: 9067-9071 (19) SEP 13 plant virus; origin-of-assembly sequence; protein acetylation; RNA packaging; T7 RNA polymerase; NUCLEOTIDE-SEQUENCE; DIRECTED MUTAGENESIS; RNA; ORIGIN; INVITRO; VISUALIZATION; TRANSCRIPTS; LOCATION; RECOVERY; COPIES TMA Wilson/Scottish Crop Res Inst/Dept Virol/Dundee DD2 5DA, Scotland| --- The bidirectional self-assembly of tobacco mosaic virus (TMV, common or U1 strain) has been studied extensively in vitro. Foreign single-stranded RNA molecules containing the TMV origin-of-assembly sequence (GAS, 75-432 nt in length) are also packaged by TMV coat protein (CP) in vitro to form helical pseudovirus particles. To study virus assembly in vivo requires an easily manipulated model system, independent of replication in plants. The TMV assembly machinery also provides a convenient means to protect and recover chimeric gene transcripts of almost any length or sequence for a variety of applications. Native TMV CP expressed in and purified from Escherichia coil formed nonhelical, stacked aggregates after dialysis into pH 5 buffer and was inactive for in vitro assembly with TMV RNA. U1 CP derivatives in which the second amino acid was changed from Ser to Ala or Pro, nonacetylated N termini found in two natural strains of the virus, failed to remediate these anomalous properties. However, in vivo coexpression of CP and single-stranded RNAs (up to approximate to 2 kb) containing the TMV GAS gave high yields of helical pseudovirus particles of the predicted length (up to 7.4 +/- 1.4 mu g/mg of total bacterial protein). If the GAS-containing RNA was first recruited into bacterial polyribosomes, elongation of pseudovirus assembly was blocked. In vivo, E. coil expression of a full-length cDNA clone of the TMV genome (6.4 kb) resulted in high, immunodetectable levels of CP and assembly of sufficient intact genomic RNA to initiate systemic infection of susceptible tobacco plants. Connan, R.M.; Wise, D.R. 1994 AniPlaSc Artic/En L94/41 Further studies on the development and survival at low temperatures of the free living stages of Trichostrongylus tenuis Res Vet Sci 057: 215-219 (2) SEP RED GROUSE; NEMATODE RM Connan/Univ Cambridge/Dept Clin Vet Med/Madingley Rd/Cambridge CB3 0ES, England| --- To assess the ability of the free living stages of Trichostrongylus tenuis, a pathogen of red grouse, to survive the winter in significant numbers, the temperatures prevailing during the autumn, winter and spring of 1991-92 on the North Yorkshire moors were simulated in an incubator into which replicate cultures of T tenuis eggs were placed at intervals. September and early October eggs developed into larvae which survived over winter and were infective the following spring. few November to February eggs survived to become larvae but early March eggs were reasonably successful. Continuous temperatures of -15 degrees C were lethal to infective larvae within 12 days, but significant numbers of larvae survived temperatures of -10 degrees C or higher for up to three weeks and remained infective. Hernandez, F.; Rodriguez, E.; Gamboa, M.D.; Coto, E.; Delosacuna, M. 1994 Biology Note/En A94/41 Ultrastructural View of the Bacterium Mobilucus mulieris - An Approach to Understand Some Problems for Their Isolation Rev Biol Trop 042: 101-104 ( Suppl. 2) AUG Mobiluncus; Bacterial Vaginosis; Anaerobic Curved-Shaped Rod F Hernandez/Univ Costa Rica/Fac Microbiol/San Jose, Costa Rica| Chaves, R.L. 1994 Biology Artic/En A94/41 Differentiation with SEM of 6 Species of Meloidogyne (Nemata, Heteroderidae) Found in Costa-Rica Rev Biol Trop 042: 113-120 ( Suppl. 2) AUG Root-Knot Nematodes; Meloidogyne; SEM; Systematics; Costa-Rica; Morphology RL Chaves/Univ Costa Rica/Escuela Fitotecn/Ctr Invest Protecc Cultivos/San Jose, Costa Rica| --- The morphology of one isolate each of Meloidogyne incognita, M. javanica, M. hapla, M. exigua, M. salasi, and M. arabicida, from Costa Rica was studied with the scanning electron microscope. Good characteristics for the differentiation of the six species were found in the labial and cephalic regions of females, males, and second-stage juveniles, but the single most reliable morphological character was the female perineal pattern. Hernandez, F.; Rivera, P.; Hosaka, Y. 1994 Biology Artic/En A94/41 Immuno-Gold Replica Technique for Ultrastructural Localization of Antigens Rev Biol Trop 042: 179-182 ( Suppl. 2) AUG Sendai Virus; Immunolabelling; Immunoelectronmicroscopy; Replica; Ultrastructure F Hernandez/Univ Costa Rica/Fac Microbiol/San Jose, Costa Rica| --- We developed a simple method for immunolabelling viral glycoproteins on surface of infected cell monolayers. Cells 9 hours post-infected with Sendai virus were fixed and treated with polyclonal antibody anti HN glycoprotein (Rabbit IgG), labelled with goat immunoglobulin anti rabbit IgG conjugated with colloidal gold particles. Then, the cells were shadowed with platinum-carbon, covered with nitrocellulose glue, and digested with domestic bleach, washed, and replica fragments were caught with uncovered grid. Durettedesset, M.C.; Cabaret, J. 1994 Biology Artic/En A94/42 The distances between cuticular ridges follow a Gaussian function in ostertagiine nematodes: The potential use of this phenomenon as a taxonomic criterion Syst Parasitol 029: 13-22 (1) SEP TRICHOSTRONGYLIDAE; RUMINANTS; PATTERNS MC Durettedesset/Museum Natl Hist Nat/Biol Parasitaire Protistol/& Helminthol Lab/61 Rue Buffon/F-75235 Paris 05, France| --- The distribution of distances between cuticular ridges was studied in six genera of ostertagiines. It was well fitted by a Gaussian function of the position of the inter-ridges on both the dorsal and ventral regions of the synlophe. The three parameters of the fitted function were very similar in individuals of the same species but of different origin or morphs, similar in different species of the same genus, but often differed between genera. Further comparative evaluation of the inter-ridge distance is required in order to assess its value as a taxonomic criterion. Bundy, D.A.P. 1994 ExpBioMe Artic/En L94/35 Immunoepidemiology of intestinal helminthic infections .1. The global burden of intestinal nematode disease Trans R Soc Trop Med Hyg 088: 259-261 (3) MAY-JUN TRICHURIS-TRICHIURA; MORBIDITY; CHILDREN; PREVALENCE; ASCARIASIS; HOOKWORM; HUMANS DAP Bundy/Univ London Imperial/Coll Sci Technol & Med/Dept Biol/WHO/London SW7 2BB, England| --- Estimates of the world-wide prevalence of intestinal nematode infections indicate that there are more than 1000 million people infected, and several million cases of clinical helminthiases. Recent studies suggest that the morbidity has been underestimated and that moderate intensities of infection may have important developmental consequences, particularly for children of school age. Firek, S.; Whitelam, G.C.; Draper, J. 1994 MolBiGen Artic/En L94/41 Endoplasmic reticulum targeting of active modified beta-glucuronidase (GUS) in transgenic tobacco plants Transgenic Res 003: 326-331 (5) SEP GUS; endoplasmic reticulum; protein targeting; signal peptide; PROTEIN; CELLS; TRANSFORMATION; EXPRESSION; SECRETION; TRANSPORT; VECTORS; FUSIONS; MARKER; YEAST S Firek/Univ Leicester/Dept Bot/Univ Rd/Leicester LE1 7RH, England| --- We have investigated targeting to the endoplasmic reticulum (ER) of wild-type GUS and a modified form (GUS S358) by making an N-terminal fusion of the beta-glucuronidase (GUS) enzyme with the wheat alpha-amylase signal peptide. In vitro studies demonstrated that the modified GUS (S358) lacked the glycosylation site present within the wild-type enzyme. Analysis of transgenic tobacco plants revealed that the modified GUS enzyme retained activity upon passage to the ER. When further experiments were carried out to determine the cellular location of the modified GUS enzyme, it was found that (contrary to expectation) the majority of GUS activity was retained within the cell and was not secreted to the cell surface via the default pathway. The data indicated that the modified GUS enzyme is an unsuitable reporter enzyme for studying protein secretion. Hengen, P.N. 1994 Biochemi Note/En L94/41 Methods and reagents - Recovering DNA from agarose gels Trends Biochem Sci 019: 388-389 (9) SEP INEXPENSIVE MICRO-ELECTROELUTION; MOLECULAR-WEIGHT DNA; NUCLEIC-ACID; ELECTROPHORESIS; PURIFICATION; ACRYLAMIDE; ELUTION; EFFICIENT; FRAGMENTS PN Hengen/NCI/Frederick Canc Res & Dev Ctr/Frederick, MD 21702 USA| --- Methods and reagents is a unique monthly column that highlights current discussions in the newsgroup bionet.molbio.methds-reagnts, available on the Internet. A commonly occurring theme on the net is the recovery of DNA, and this month's column discusses the pros and cons of various methods used to extract DNA fragments directly from agarose gels. For details on how to partake in the newsgroup, see the accompanying box. Cortese, R.; Felici, F.; Galfre, G.; Luzzago, A.; Monaci, P.; Nicosia, A. 1994 Biotechn Revie/En A94/35 Epitope discovery using peptide libraries displayed on phage Trends Biotech 012: 262-267 (7) JUL HUMAN H-FERRITIN; FILAMENTOUS BACTERIOPHAGE; DISCONTINUOUS EPITOPES; MONOCLONAL-ANTIBODY; BINDING PEPTIDES; MULTIPLE DISPLAY; FOREIGN PEPTIDES; PROTEIN; LIGANDS; IDENTIFICATION R Cortese/Ist Ric Biol Molec P Angeletti/Via Pontina km 30600/I-00040 Pomezia, Italy| --- Peptides displayed on phage, which mimic continuous and discontinuous epitopes, can be selected using purified antibodies or preparations of polyclonal serum. This review describes recent advances in this field, discusses the application of phage-display technology to the diagnosis of human diseases, and presents new ideas for the preparation of vaccines directed against specific epitopes on a pathogen. Breaker, R.R.; Joyce, G.F. 1994 Biotechn Revie/En A94/35 Inventing and improving ribozyme function: Rational design versus iterative selection methods Trends Biotech 012: 268-275 (7) JUL TETRAHYMENA RIBOZYME; INVITRO SELECTION; RNA ENZYME; DIRECTED EVOLUTION; NUCLEIC-ACIDS; CLEAVAGE; AMPLIFICATION; SEQUENCES; REPLICATION; DEPENDENCE RR Breaker/Scripps Clin & Res Inst/Dept Chem/10666 N Torrey Pines Rd/La Jolla, CA 92037 USA| --- Two major strategies for generating novel biological catalysts exist. One relies on our knowledge of biopolymer structure and function to aid in the 'irrational design' of new enzymes. The other, often called 'irrational design', aims to generate new catalysts, in the absence of detailed physicochemical knowledge, by using selection methods to search a library of molecules for functional variants. Both strategies have been applied, with considerable success, to the remodeling of existing ribozymes and the development of ribozymes with novel catalytic function. The two strategies are by no means mutually exclusive, and are best applied in a complementary fashion to obtain ribozymes with the desired catalytic properties. Fink, L.M.; Hsu, P.L. 1994 ExpBioMe Edito/En L94/35 Bacteriophage epitope libraries - The generation of specific binding proteins and peptides in vitro Virchows Archiv 424: 1-6 (1) bacteriophages; filamentous phage; epitope libraries; recombinant antibodies; panning; COMBINATORIAL ANTIBODY LIBRARIES; NEUTROPHIL ELASTASE INHIBITORS; BY-PASSING IMMUNIZATION; FILAMENTOUS BACTERIOPHAGE; MONOCLONAL-ANTIBODIES; AFFINITY MATURATION; MOLECULAR EVOLUTION; DISPLAY LIBRARIES; PHAGE ANTIBODIES; GENE LIBRARIES LM Fink/John L Mcclellan Mem Vet ADM Med Ctr/Pathol & Lab Med Serv 113LR/4300 W 7TH St/Little Rock, AR 72205 USA| --- New concepts and methodologies that can be used to generate proteins, such as specific variable regions of immunoglobulins and other binding peptides in an in vitro selection system are reviewed. These technologies can also be used to alter the kinetics, affinity and avidity of various binding interactions. The nature of epitopes recognized by specific antibodies or receptors can be delineated using selected epitopes displayed on bacteriophages. The basic principle of the technology is predicated upon the belief that if one has a large enough variety of keys, one can open any given lock. The range of utility of these systems to generate new reagents will impact upon the development of new diagnostic and therapeutic reagents. This technology should allow for a much wider range of probes which may have increased binding capacity and allow the development of more sensitive assays with higher signal to noise ratios. These reagents can be produced more efficiently without the use of animals and will be used in diagnostic and experimental pathology. This brief review presents a concise description of the concepts and uses of this new technology. Selected references and reviews are given as sources for further details. Daniel, C.; Lacroix, M.; Talbot, P.J. 1994 MicrCell Artic/En L94/35 Mapping of linear antigenic sites on the S glycoprotein of a neurotropic murine coronavirus with synthetic peptides: A combination of nine prediction algorithms fails to identify relevant epitopes and peptide immunogenicity is drastically influenced by the nature of the protein carrier Virology 202: 540-549 (2) AUG 1 MOUSE HEPATITIS-VIRUS; MULTIPLE-SCLEROSIS PATIENTS; CENTRAL-NERVOUS-SYSTEM; SPIKE GLYCOPROTEIN; T-CELL; MONOCLONAL-ANTIBODIES; SEQUENCE-ANALYSIS; STRAIN-JHM; INFECTION; GENE PJ Talbot/Univ Quebec/Inst Armand Frappier/Virol Res Ctr/531 Blvd Prairies/Laval H7N 4Z3/Pq, Canada| --- The elucidation of the antigenic structure of the S glycoprotein of murine coronaviruses will provide further understanding of the complex pathogenicity of these viruses. In order to identify linear antigenic determinants, the primary structure of the S glycoprotein of murine hepatitis virus strain A59 was analyzed with a combination of nine epitope prediction algorithms. Fifteen potential epitopes were synthesized chemically and injected into BALB/c mice to study their biological relevance. This approach failed to identify novel important epitopes. Furthermore, the algorithms were unable to identify as antigenic the previously mapped immunodominant epitope A [C. Daniel, R. Anderson, M. J. Buchmeier, J. O. Fleming, W. J. M. Spaan, H. Wege, and Talbot, P. J. (1993). J. Virol. 67, 1185-1194]. Interestingly, peptide A coupled to KLH induced an immune response that simulated the immune response induced by the corresponding region of the protein much more accurately than when the same peptide was coupled to BSA. This included drastically enhanced competition with monoclonal antibodies and protection from virus challenge. These findings emphasize the shortcomings of amino acid sequence-based epitope prediction algorithms and demonstrate the critical importance of the carrier when synthetic peptides are considered as potential vaccines. (C) 1994 Academic Press, Inc. Deswarte, C.; Peyrebrune, S.; Canut, H.; Roustan, J.P.; Fallot, J. 1994 AgriAgro Note/En A94/35 Purification of Plasma Membrane Vesicles from Vitis vinifera CV Gamay Suspension Cells by Free-Flow Electrophoresis Vitis 033: 99-100 (2) JUN EUTYPA-LATA; TONOPLAST; FRACTIONS; LEAVES C Deswarte/Ensat/InP/145 AV Muret/F-31076 Toulouse, France| are known, > 40 of which with their complete amino acid sequences. We have compared these sequences and the available three-dimensional structures (subtilisin BPN', subtilisin Carlsberg, thermitase and proteinase K). The mature enzymes contain up to 1775 residues, with N-terminal catalytic domains ranging from 268 t FLOW DIAGRAM OF REFBASE 2.1 Use this diagram to find your way through the program. Note that a number of menus and program-options (e.g. FILE, DISPLAY, KEYWORDS) can be accessed via more than one route. For simplicity, the possibilities of DISPLAY RECORDS and its link with sub-menus are shown only once. When DISPLAY RECORDS is entered via PROFILE SEARCH, it is not possible to enter the submenus KEYWORDS, EDIT BLOCK, or AMEND. _______ _______________ _______________ | | | | _________ _________ | | | CHAIN |<=>| FILE MENU | | | | | | PROGRAM START | | | |_______________| | PROFILE|<=>| DISPLAY | |_______________| | SEARCH| | | | | | RECORDS | || || | |<=>| SELECT MENU | | SEARCH | |_________| ____\/_____ || | MENU | |_______________| | | __________ | | || | | | | | MENU | | | | FILE MENU | || |_______|==>|DISPLAY RECORDS| |________| | KEYWORDS | |___________| || /\ |_______________| /\ | MENU | || || || || || |__________| ____\/________\/______\/_____________\/_____________\/____ /\ | | || | | ____\/___ | MAIN MENU | | | | |<=>| INPUT | |__________________________________________________________| | RECORDS | /\ /\ /\ /\ /\ /\ /\ /\ /\ /\ |_________| || || || || || || || || || || /\ || __\/__ __\/___ __\/___ ___\/___ _\/_ || || || || || || | | | | | | || || || || || || | FILE | EDIT | PRINT |KEYWORDS|HELP| || || || || __\/___ || | MENU | BLOCK | MENU | MENU | | || || || || | | || |______|_______|_______|________|____| || || || _\/___ | SHOW | \/________________________ || || || | | | BLOCK | | | _____________\/ || || |SELECT| |_______| | DISPLAY RECORDS | | | || || | MENU | | ______________________ | | FIELDS MENU | || || |______| _______ | | | | |_______________| || || || | | | | card view | | /\ || ||___\/___ | SHOW | | |______________________| | || || | | | BLOCK | | /\ | _______\/________|| | DISPLAY | |_______| | || [F8] | | | | RECORDS | /\ | _________\/___________ | | SEARCH & REPLACE | |_________| || | | | | |__________________| _________\/___ | | table view | | | | | | | |<============================>| AMEND RECORD | | | [F9] | | _______________ |______________| | | normal <==> expanded | | | | /\ | | /\ /\ | |<=>| EDIT BLOCK | || | | || [F10] || | | |_______________| ______\/_______ | | \/ \/ | | _______________ | | | | titles titles | | | | | KEYWORDS MENU | | |______________________| |<=>| KEYWORDS MENU | |_______________| |__________________________| |_______________| unt of space that GEMDOS reserves for storing the file names with their drive paths: their total length should not exceed 127 characters. You can only load .REF or .ISS files. FLOW DIAGRAM OF REFBASE 2.1 Use this diagram to find your way through the program. Note that a number of menus and program-options (e.g. FILE, DISPLAY, KEYWORDS) can be accessed via more than one route. For simplicity, the possibilities of DISPLAY RECORDS and its link with sub-menus are shown only once. When DISPLAY RECORDS is entered via PROFILE SEARCH, it is not possible to enter the submenus KEYWORDS, EDIT BLOCK, or AMEND. Ŀ Ŀ Ŀ Ŀ Ŀ PROGRAM START CHAIN <=> FILE MENU PROFILE <=> DISPLAY ͵ RECORDS || || SEARCH <=>SELECT MENU SEARCH \/ || ͵ Ŀ || MENU ==> DISPLAY MENU Ŀ FILE MENU || RECORDS KEYWORDS || /\ /\ MENU || || || || || \/ \/ \/ \/ \/ /\ Ŀ || \/ MAIN MENU Ŀ <=> INPUT RECORDS /\ /\ /\ /\ /\ /\ /\ /\ /\ /\ || || || || || || || || || || /\ || \/ \/ \/ \/ \/ || || || || || || Ŀ || || || || \/ || FILE EDIT PRINT KEYWORDSHELP || || || || Ŀ || MENU BLOCK MENU ******************************************************************** Deze diskette is samengesteld door de Stichting ST, Postbus 11129, 2301 EC Leiden. Onze bibliotheek van public domain programma's omvat op dit moment (zomer 1992) al meer dan achthonderd disks. Daarop vindt u programma's op elk gebied, van tekstverwerker en database tot de leukste spelletjes, de fraaiste tekenprogramma's en de handigste utilities. Ook bevat onze bibliotheek een speciale afdeling voor public domain disks met Macintosh software, die te gebruiken zijn onder de ALADIN emulator. Deze MAC-PD serie bevat tot nu toe ongeveer vijfendertig disks. ******************************************************************** U vindt in het twee maandelijks tijdschrift "ST" (Onafhankelijk tijd- schrift van en voor gebruikers van Atari ST computers) een overzicht en een bespreking van de inhoud van de nieuwe public-domain diskettes. Dit tijdschrift bevat tevens een bestelkaart zodat U vlot over de software kunt beschikken. De november/december uitgave bevat een compleet overzicht van de Public Domain bibliotheek op dat moment. De Stichting ST geeft ook een speciale PD catalogus disk uit. Deze public domain disk is geproduceerd en gedistribueerd door: ************** Stichting ST afd. Software Bakkersteeg 9A 2311 RH LEIDEN ************** Ondanks onze controle komt het af en toe voor dat een diskje niet goed is gecopieerd.Mocht U dit overkomen, aarzel dan niet en stuur de defecte disk aan ons terug. U krijgt dan direct een vervangende disk toegestuurd. ************************************************************************ Teneinde het voor ons mogelijk te maken om productiefouten op te sporen en vervolgens in de toekomst te vermijden, zijn alle disks, geproduceerd door de Stichting ST, voorzien van een groen productienummer. ************************************************************************ MENU || || || \/ SHOW \/ || || || Ŀ BLOCK Ŀ \/ || || SELECT DISPLAY RECORDS Ŀ || || MENU FIELDS MENU || || Ŀ || || || Ŀ card view /\ || || \/ SHOW || || Ŀ BLOCK /\ \/ || DISPLAY || [F8] Ŀ RECORDS /\ \/ SEARCH & REPLACE || Ŀ \/ table view Ŀ <============================> AMEND RECORD [F9] normal <==> expanded Ŀ /\ /\ /\ <=> EDIT BLOCK || || [F10] || \/ \/ \/ Ŀ titles titles Ŀ KEYWORDS MENU <=> KEYWORDS MENU ome | Cursor Up | Page Up | +-------------+-------------+-------------+ | (4) | | (6) | | Cursor Left | | Cursor Right| +-------------+-------------+-------------+ | (1) | (2) | (3) | | End | Cursor Down | Page Down | +-------------+-------------+-------------+ Pressing "F" or "f" during table view or keywords view switcheRRRRRRR EEEEEEEE FFFFFFFF BBBBBBB AAAAAA SSSSSS EEEEEEEE RR RR EE FF BB BB AA AA SS SS EE RR RR EE FF BB BB AA AA SS EE RRRRRRR EEEEEE FFFFFF BBBBBBB AAAAAAAA SSSSSS EEEEEE RR RR EE FF BB BB AA AA SS EE RR RR EE FF BB BB AA AA SS SS EE RR RR EEEEEEEE FF BBBBBBB AA AA SSSSSS EEEEEEEE Manual to REFBASE Version 2.1 - 9 november 1994 Author: Jan M. de Boer Department of Nematology Wageningen Agricultural University P.O. Box 8123 6700 ES Wageningen THE NETHERLANDS Telephone: 08370 82427 (NL) / +31 8370 82427 (Foreign) Fax: 08370 84254 (NL) / +31 8370 84254 (Foreign) E-mail: Jan.deBoer@MEDEW.NEMA.WAU.NL Version 2.1 of REFBASE succeeds earlier versions which were released on the following dates: 23 September 1991 - Preliminary version 12 January 1992 - Version 1.0 11 February 1992 - Version 1.1 13 April 1992 - Version 1.2 9 July 1992 - Version 1.3 14 August 1992 - Version 1.4 This manual succeeds the previous manuals. For convenience a separate file "UPDATE.TXT" is included as well to inform earlier users of the changes that since version 1.4. REFBASE 2.1 is Public Domain. You are allowed to pass on copies of the software provided that all original files and programs of the package are included. The author has used REFBASE intensively for three years now (both in ST- High and TT-High resolution), and version 2.1 appears to be free of major bugs. Nevertheless, the author takes no responsibility for any damage to data or hardware caused by remaining defects in the program. REFBASE was written in GFA-Basic 3.60. A few pieces of assembly code have been included as well. These were compiled with the GFA-Assembler. This manual contains the following sections: 1. INTRODUCTION 2. COMPATIBILITY 3. START/QUIT 4. MAIN MENU 5. INPUT 6. DISPLAY 7. FONTS 8. AMEND RECORDS 9. BLOCK FUNCTIONS 10. SCREEN COLOUR 11. SORTING 12. GOTO 13. SEARCHING/SELECTION 14. TEXT MODE 15. TAGGING 16. LOADING FILES 17. MEMORY MANAGEMENT 18 .SAVING FILES 19. DELETING RECORDS 20. FIND DUPLICATES 21. CASE CONVERSION 22. RECORDS MENU 23. FIELDS MENU 24. MODE MENU 25. THE MOUSE 26. KEYWORDS 27. VIDEO-RECORDER BUTTONS 28. PRINTING 29. CHAIN SEARCH 30. PROFILE SEARCH 31. FILE FORMAT / DATA EXCHANGE 32. SUPPORTING PROGRAMS 33. LIMITS OF REFBASE ______________________________________________________________________ 1. INTRODUCTION REFBASE is a database program for storing scientific references. REFBASE has been designed primarily for handling titles from publications which have appeared in journals; for storing book-titles the (fixed) record layout may be less convenient. Like a word processor, REFBASE loads its data files completely into the memory of the computer. The maximum size of files to be displayed or sorted is therefore limited by the amount of RAM that you have installed. If you have more records than will fit in the computer's memory, you can store them in several smaller files, which can then still be "chain searched" in a single run. The basic design of REFBASE was taken from Data Manager Professional and many key functions and other interface-features are therefore still identical in both programs. The aim was to develop a powerful database program that would overcome the severe limitations of DM-Professional. Even compared with modern relational databases such as Phoenix 2.0, REFBASE in unsurpassed in handling literature references, due to its speed, its flexible exchange records between different files, its special features, and its capacity to search an almost unlimited amount of records in a single run. ______________________________________________________________________ 2. COMPATIBILITY REFBASE 1.4 was developed on a Mega ST4 with TOS 1.4. Further development to version 2.1 was accomplished on an Atari TT with TOS 3.06. The following screen resolutions are supported: [1] ST-high 640x400, monochrome (thoroughly tested) [2] TT-high 1280x960, monochrome (thoroughly tested) [3] TT-medium 640x480, 16 colours (sufficiently tested) [4] GEMULATOR 640x400, monochrome (sufficiently tested) [5] GEMULATOR 640x480, monochrome (sufficiently tested) Although REFBASE can operate perfectly well from floppy disk, the user is advised to use a harddisk if more than a few hundred records are to be stored. The following minimal amounts of RAM are necessary for sensible use of REFBASE 2.1: Resolutions [1], [4] and [5]: 1.5 Mb Resolutions [2] and [3]: 2.5 Mb REFBASE 2.1 can be configured for use in TT-RAM on the Atari TT. There is however one limitation: modifying file attributes via the FILE menu will give a GEMDOS error message if data are stored in TT-RAM. This error does not occur if the data are stored in ST-RAM. I have no explanation for this bug. REFBASE 2.1 has NOT been tested on the Atari Falcon 030, but it is likely that the program will run on this machine too, provided that the right screen resolutions are selected. However, it has been reported that GFA- BASIC programs (and therefore also REFBASE) refuse to print when run on the Falcon 030 (see the Dutch magazine "ST", issues 49 and 50). To solve this problem, you must install an AUTO-folder program, which can be found on the PD-disk "ST 50" of Stiching ST, Bakkersteeg 9a, Leiden, The Netherlands. REFBASE 2.1 (and its supporting programs) are not proper GEM programs and therefore they DO NOT operate properly with MULTI-TOS. I have not tested REFBASE 2.1 with other multitasking operating systems. WARNING: do NOT use the text editor EVEREST 1.5 (july 1992) for creating or editing text files which are to be loaded by REFBASE (or its supporting programs). EVEREST saves text files without a terminal end-of- line sequence (CR+LF). Because of this, the last line of such text files is not recognized by REFBASE. ___________________________________________________________________ 3. START/QUIT After a double click on REFBASE.PRG, the FILE menu will be displayed. To load a file see Section 16 (LOADING FILES). Click on EXIT or press ESC to enter the main menu. With TOS 2.06 and higher, you can also start REFBASE by dragging a database file (*.REF) to REFBASE.PRG in the destop. The file will be loaded and REFBASE proceeds straight to the main menu. During a program start, the current drive will be scanned for info files (REFBASE.MOD and REFBASE.PRN), which will be loaded if found. On ATARI TT's with TT-high resolution, pressing the ALTERNATE, SHIFT or CONTROL key during program startup will cause REFBASE to enter its "high screen" mode, in which the full height of the screen is used. Otherwise REFBASE enters its normal "low screen" mode, in which only half of the screen area is used. (This latter mode allows faster scrolling). You can quit REFBASE from the main menu by clicking on EXIT, or pressing ESC, and answering the alert box. With CONTROL-X you can quit REFBASE immediately from most points in the program and return to the Desktop without having to answer an alert box. ____________________________________________________________________ 4. MAIN MENU Pressing HELP in the main menu gives a summary of the key functions. The two rows of menu options at the top of the screen are selectable both via the function keys and with the mouse. With F1 (Acc/Cpx) a drop down menu is created with which you can access accessories such as the CPX control panel. You return to the main menu by pressing ESCAPE or clicking on "Back to main menu". (During Display the function of F1 is changed to a Fix/Float cursor toggle) The other function key options are explained in the different sections of the manual. Other mouse selectable functions in the main menu are: Chain search - See 29. CHAIN SEARCH Display all records - See 6. DISPLAY Display selected records - See 6. DISPLAY Display tagged records - See 6. DISPLAY Show selection rule - See 13. SEARCHING/SELECTION Profile Search - See 30. PROFILE SEARCH Save mode preferences - See 24. MODE MENU Read drive - to show/enter the drive from which files will be loaded Write drive - to show/enter the drive to which files will be written EXIT - to return to the Desktop Disk space - To ask for the free space on a specified drive File size - To calculate the size of the file(s) loaded, and the average record size Not selectable items are: The date and clock - change them via the control panel Free memory - this value is automatically updated whenever operations affecting memory space are performed. The file name "window" - this shows the file(s) currently loaded ____________________________________________________________________ 5. INPUT Click/press on INPUT (F5) to enter new records. Each record consists of 10 fields for the following parts of a reference: FIELD LABEL SIZE in USE characters (ST-High) 1 authors 70 x 2 2 year 4 3 subject 8 For dividing records in main categories 4 read/ 8 To indicate whether or when an article document has been read; you can also use this field to store the document type (e.g. article, note, review) 5 file 6 For a short code to indicate the file from which record originates, or to which it must be added. 6 title 70 x 5 7 journal 50 x 2 including volume and page numbers 8 date 8 To store the date you entered the record 9 keywords 70 x 7 10 remarks 70 x 21 A multi-functional large text field, suitable for entering remarks, storing author's addresses, abstracts, or marking labels. The size and position of these fields is fixed. It is not possible to rearrange or modify the field sizes to your own demands. All fields are text fields. In TT-medium or TT-high resolution, the size of some of these fields is automatically increased, to make use of the larger screen size. You start entering data in the first field. With the TAB or CURSOR DOWN keys you can move to the next field, and with SHIFT TAB or the CURSOR UP key you can return to previous fields. You can also place the cursor at the start of any field by clicking on it with the mouse. The fields 1, 6, 7, 9, and 10 are "multi-line" fields. Usually text in a multi-line field is automatically formatted when entering or inserting text. If this does not occur, you can induce a reformat by deleting (and re-typing) a character in the preceding line. Text reformatting follows the style of 1ST Word Plus, i.e. formatted lines end with either a space or a hyphen (-). Internally a multi-line field is stored as a single (long) line. It is therefore not possible to create "new lines" by pressing the RETURN key. As soon as you enter the remarks field with the cursor it will be shown in full size. You leave the remarks field again with SHIFT TAB or the CURSOR UP key. The field sizes shown in the table above are the limits for manual data entry. If you wish you can overrule these limits with the "paste block" or "search and replace" functions. The remarks field actually can display 42 lines (two screens) of text (ST-High screen resolution), and is therefore suitable for displaying abstracts. The program CC31HELP.PRG can be used to convert records with abstracts from the Current Contents on Diskette into REFBASE format: the abstracts will then be placed in the remarks field. It is very well possible that you cannot gain access to the lower part of the abstract using the amend function (section 8), because the text-edit of facilities of REFBASE do not support scrolling within a field. Therefore any additional comments that you want to store with the abstract should be entered at the start of the remarks field. Other key functions are: BACKSPACE - erase character left of cursor DELETE - erase character at cursor position RETURN - moves cursor to next line. CLRHOME - erase the contents of a field CONTROL "B" - show block CONTROL "P" - paste block at cursor position CONTROL "K" - enter keywords menu CONTROL "=" - produces a box showing the special characters (ASCII>127). Click on the desired character to insert it at the cursor position. Press ESC to quit the box. (With the new TOS versions 2.06 and 3.06 you can also enter special characters by pressing ALTERNATE + ASCII code). SHIFT + CURSOR LEFT/RIGHT - moves cursor to start/end of line SHIFT + CURSOR UP/DOWN - moves cursor to first/last line of field SHIFT + DELETE - delete line CONTROL + CURSOR LEFT/RIGHT - moves cursor one word left/right CONTROL + DELETE - deletes word at cursor position UNDO - restores field contents The contents of field 5 is automatically converted to upper case after entry. In fields 4 and 8, pressing the '#' key enters the system date in the format YY/MM/DD (this format is easy to sort, but will require adaptations when the year 2000 is reached!). Use the journal field for storing ABBREVIATED journal names. If the length of the text is limited to the field width of 50 characters, the journals can be easily viewed "table view". Should you by any chance be confronted with longer journal names (e.g. from CD-ROM export files), the journal field will be large enough (2x 50 characters) to display them in full in "card view". To ensure correct sorting of records on the journal field, it is advised to be very consequent when typing in the journal names. The author uses the following format: J Examples 012: 12-18 (2) The volume numbers consist of three digits, if necessary one or two of them are typed as zero's. The starting page number always occupies four character positions, of which up to three of may be leading spaces. If desired, the issue number can be placed at the end of the line in brackets; in this way it will have no influence on sorting. (For "J BIOL CHEM" and "PROC NATL ACAD SCI USA" you should reserve 5 character positions for the first page number, since the annual volumes of these journals always have more than 10000 pages). By pressing INSERT the record is accepted and added to the file. Automatically a new blank record is displayed. You can stop data entry, or reject a record, by pressing ESCAPE. During data entry a beep will sound when CAPS LOCK is on. After entering new or amended records by pressing INSERT, (1) all fields (except the journal field) are automatically checked for double spaces, which can be removed by answering an alert box, (2) in multi-line fields, lines that did not yet end with a space or a hyphen "-" are automatically provided with a terminal space, and (3) any lingering spaces at the end of the fields are automatically removed. _____________________________________________________________________ 6. DISPLAY Press "A" or "F3", or click on "Display" or "Display all records" to show the records in the file(s) currently loaded. Alternatively, pressing "S" or "D" or clicking on "Display selected records" or "Display tagged records" will respectively show the selected or the tagged records. You can scroll through the file with the CURSOR UP and CURSOR DOWN keys. By simultaneously pressing CONTROL or SHIFT, you can scroll through the file in steps of 20 records or 1/10 file length. During display, the keyboard sound is switched off, so that you will not continuously hear the cursor keys while scrolling. With F8 ("View") or INSERT of "V" you can switch between "Card view" and "Table view". In "Table view" you can use F9 ("Expand") to switch between a compact one-screen table, and an expanded five screen wide table. In the expanded table mode you switch between screens with the CURSOR LEFT and CURSOR RIGHT keys. You can also switch to table view by double clicking on the displayed record with the LEFT mouse button. In "table view" pressing F1 switches between a fixed and a floating cursor. The LEFT mouse button can be used to place the cursor on any desired record. If you double-click on a record, REFBASE switches back to card view. In "table view" pressing CONTROL CURSOR UP/DOWN will jump one screen full of records backward/forward. You can also scroll one screen forward or backward by using the SPACEBAR or the BACKSPACE key. From the "Table view" you can press F10 to enter the "Title view" mode. You can use the CURSOR UP/DOWN keys in combination with the CONTROL or SHIFT key to scroll through the titles. Pressing CURSOR LEFT or CURSOR RIGHT will start an automatic soft scroll, which can be stopped by pressing any key. In "Title view" the "expand" function (F9) is inactive. You can switch between "Title view" and "Card view" by pressing F8 or INSERT. The normal table view is restored by pressing F10 again. In the mode menu the speed of the automatic "Title view" soft scroll can be varied by choosing between 0 and 9 "units of pause" between consecutive records (one unit of pause is 400 ms). You can also change the scroll pause time directly from within the "title view" by pressing "P". You can tag a record by pressing "T". Tagged records are shown with a spotted "pseudo-grey" background. To release a tag press "T" a second time. You can use the tagging facility to pick out manually a selection of records, for instance for printing, or for saving in a separate file. (see also 15. TAGGING). Tagging operations can also be performed with the RIGHT mouse button. Pressing the mouse a second time will release the tag again. In table view you can (un)tag a series of records by keeping the right mouse button depressed. With CONTROL-CLRHOME you can jump to the first record in the file; with CONTROL-Z you can jump to the last record in the file. The numeric key pad can also be used to scroll through the records: +-------------+-------------+-------------+ | (7) | (8) | (9) | | First record| Cursor Up | Page Up | +-------------+-------------+-------------+ | (4) | | (6) | | Cursor Left | | Cursor Right| +-------------+-------------+-------------+ | (1) | (2) | (3) | | Last record | Cursor Down | Page Down | +-------------+-------------+-------------+ In "Card view" a copy of the current record can be made by pressing CONTROL-D. The duplicate record will then be placed at the bottom of the file. In "Card View" pressing CONTROL-P prints the current record in full "card" format to the parallel printer port, with a maximum line length of 78 characters (Pica width). No printer control codes are given, except for a formfeed at the end of the record. In "Card view" pressing CONTROL-M activates a menu with which marking labels can be inserted at the start of the Remarks field. Use this to indicate what you want to do with the record. The marking labels are placed between {}-brackets. You add (or remove) the labels by pressing their first letter. Press "O" (= Order library) if you want to order a copy of the article via the library, or "R" if you intend to ask for a reprint. By pressing "D" (= Done + date) you can mark the date that the request for the article was sent away. Alternatively use "F" if you want to fetch the article from the nearest library, or "L" if you just want to look it up. If by any chance a journal issue was not present in the library (e.g. to the binder) you can come back later, and mark the record with "M" (= Missing + date). With "A" (= Add) you can enter a text yourself. Pressing "C" (= Clear) removes all marking labels in the current record. You can switch off the mark menu by pressing CONTROL-M a second time. Both in card view and table view pressing HELP displays the remarks field in full screen. In order to accommodate for large abstracts to be stored in this field, the remarks field actually consists of two full screens, and you can switch between them by pressing the CURSOR UP and CURSOR DOWN keys. This two-screen facility, however, will only work if there is enough text in the remarks field to fill more than one screen. Also it does not work during manual data entry: in that case you are allowed to type in only a single screen full of text. You can return to the normal display mode by pressing HELP, ESC, or UNDO. If the text in a multi-line field is too large to be displayed, the bottom line of the field will terminate with a ">>". If such a field occurs, editing its text in the normal way with "amend" (Section 8) may give problems because the limit for entering text in this field is already reached. With a small multi-line field (Authors, Title, or Keywords) it is possible to copy its contents to the block buffer (see below), which offers more space for editing. Then, after editing, you can copy the text back to the field. In "card view" pressing CONTROL and clicking with the LEFT mouse button on a field activates a popup menu, with which the field contents can be erased, copied to the block buffer, modified by paste operations (see 9. BLOCK FUNCTIONS), or converted to lower case. You leave the Display mode by pressing or clicking F3 again, or by pressing ESC or UNDO. During "table view", the current position in the file is indicated by a moving slider box ([]) at the top of the screen. This box only shows where you are in the file: it cannot be used for scrolling. ____________________________________________________________________ 7. FONTS During record display in "table view" and during display of keywords pressing "F" or "f" switches between the 8*16 and 8*8 font. In "card view" and "title view" only the 8*16 font is used. __________________________________________________________________ 8. AMEND RECORDS In "Display mode" you can modify the contents of the current record by pressing or clicking F6 ("Amend"). The cursor is placed in the first field, and you can add or delete text as described in Section 5 (INPUT). Press INSERT to accept the modifications, press ESCAPE to exit "Amend" and leave the original record unchanged. ____________________________________________________________________ 9. BLOCK FUNCTIONS You can cut and paste text between records using the block buffer. Although in theory the maximum size of this buffer is 32767 characters, the block editor will only allow you to type in a single screen full of text. You enter the block editor by pressing "B" in the main menu or during display. If you are entering or editing a record, access to the block editor is denied, and you can only "show" the block by pressing CONTROL- B. After having typed in a block text you must press INSERT to save it to the block buffer. Pressing ESC rejects the entered block text, and leaves the original block unchanged. When records are displayed in "card view", CONTROL + clicking with the mouse on any field activates a selection box with which you can copy the contents of this field to the block buffer, or paste the block contents to the start or the end of the field. "Fill with block" completely replaces the field contents by the block text. Block copies that are made like this ignore any limitations imposed on the field size. If you are entering or editing records, pressing CONTROL-P will paste the contents of the block buffer at the current cursor position. In this case the block copy will stop as soon as the field is full. In the Fields menu, choosing "Paste block" will allow you to insert a block text in a given field in a range of records. There is no check for sufficient memory space if text is added to the records by block paste operations, since in most cases this will not be necessary. ____________________________________________________________________ 10. SCREEN COLOUR (1) ST-High resolution In the main menu and during "Display" the screen colours can be inverted by pressing "I" or CONTROL-I. Inverting the screen influences the line length in "Table view": with white characters on a dark background, the full width of the screen is used, and two extra characters per line are displayed. The menu bar at the top of the screen will always be shown in black. (2) TT-medium resolution REFBASE uses the color-setup as installed by the control-panel. It is not possible to invert the screen by pressing "I". (3) TT-High resolution It is not possible to invert the screen by pressing "I". ____________________________________________________________________ 11. SORTING The records can be sorted by pressing or clicking on F4 ("Sort") and selecting the desired sort field in the selection box. The current sort is marked with an asterisk (*). Via the "Mode" menu (Section 24) you can indicate by activation (=>) of "Recall previous sorts" whether or not you want REFBASE to store the sort sequence. If this option is active, then "stored sorts" are marked in the sort selection box with a dot (.). If you sort on a field marked with a dot, REFBASE does not perform a sort, but instead uses the stored sort sequence to arrange the records. With large files this option allows instant switching between different sort sequences (e.g. authors and journals) without having to wait. The maximum number of stored sort sequences is three. If more new sort sequences are added, the oldest ones are discarded. Stored sorts are erased if extra files are loaded, or if records are added or deleted. For multi-level sorts you simply do multiple sorts after each other, starting with the innermost level. You may need to switch off "Recall previous sorts" via the Mode menu if you want to sort like this. During a sort only the first 60 characters of a field are considered. The sorting algorithm uses a recursive "quick sort" procedure. Generally this sort will be done very quickly. However, there is an exception: if two identical or nearly identical files are loaded that were already sorted on a given field, then a first sort on this same field may take much more time than usual. ____________________________________________________________________ 12. GOTO By pressing or clicking on F7 ("Goto") during record display you can instantly jump (by binary search) to a specified position in the file. "Goto" only works with the field that the records are sorted on. Depending on the display mode, you can jump through all records in the file, or only through a subset of selected or tagged records. To accomodate users of Phoenix 2.0, the GOTO function can also be activated by pressing ALTERNATE + "U". ____________________________________________________________________ 13. SEARCHING/SELECTION By pressing or clicking on F2 ("Select") you can search for records using one or more selection criteria. By answering selection boxes you can choose successively a field to be searched, a condition, and a search text. In addition to the normal fields, it is possible to search the "BASIC" pseudo field, which is a simultaneous search in both the title and the keywords field. (This idea of a "BASIC" field was taken from the search facilities of the Current Contents on Diskette software). A maximum of 6 selection criteria can be combined by clicking/pressing F3 ("AND") or F4 ("OR"). As soon as the selection rules have been entered, the search can be started by clicking/pressing F10 ("Accept"). After the search, an alert box shows the number of records found and asks whether you want to see them. After each search the record selection remains available. The selected records can be displayed at any time by clicking on "Display selected records" or pressing "S". Pressing "R" or clicking on "Display selection rule" shows the selection rule that belongs to the current record selection. When searching with "Includes" and "Does not include", the "?" and "*" may be used as wildcards. The "?" is a placeholder for one unknown character. Similarly "???" specifies three unknown characters. The "*" is placeholder for a variable number of unknown characters. It is not allowed to let the search text begin or end with a "*" or "?", nor is it allowed to use the combinations "?*", "*?" or "**". If desired, searching with wildcards can be switched off via the "Mode" menu (Section 24). "Includes" and "Does not include" searching uses a "quickfind" algorithm, which was described in the Dutch magazine "ST", issue 31 (may/june 1991). Although this search routine appears to function correctly, it still is possible to switch it off in the "Mode" menu. Searching will then proceed with the standard search command (= INSTR) of GFA-BASIC. The speed of the quickfind algorithm depends on the length of the search text: the more characters you type in, the faster the search will be. The quickfind algorithm works both in "ASCII" and "Alpha" text mode (see below). The alphabetical search, however, will only work correctly with the normal character set (ASCII code <128). If you want to search in "Alpha" mode for special characters such as , , and you must INACTIVATE the quickfind routine via the mode menu. If necessary, you can permanently keep the quickfind routine inactive by saving the mode preferences. Via the "Mode" menu you can choose for searching with what I have called "partial equation". This implies that in tests involving "<=", "=", ">", or ">=" only the first few characters of a field are examined. The effect is that searching is done in a more 'natural' way, instead of following strict computer logic. For instance: The search condition "Authors <= E" will normally NOT select records of which the authors field begins with "Ea.." to "Ez..". With partial equation these records are included as well, so that you end up with all authors of which the name begins with A, B, C, D, or E, just as you wanted. If you deselect 'partial equation', the search conditions "Begins with" and "Does not begin with" are changed to "Is" and "Is not". Searching in the BASIC pseudo field (Title plus Keywords) can only be done with "Includes" and "Does not include". Most of the functions of REFBASE can be applied to the selected records, such as saving, printing, deleting, etc. If you press CONTROL the F2 menu text will change from "Select" to "Repeat". Clicking on "Repeat" or pressing CONTROL-F2 allows you to repeat a search with the latest selection rule. _____________________________________________________________________ 14. TEXT MODE After starting REFBASE the default settings are to search and sort alphabetically, i.e. no distinction is made between upper case and lower case characters. By clicking on "Alpha" or pressing SHIFT-F5 you can activate the "ASCII" search mode, in which upper and lower case characters are treated differently during a "Select" operation. (This switch is also available in the Chain Search and Keywords menus; see below). If you want to sort your records by ASCII-code, you must activate this option separately via the "Mode" menu. This automatically implies that a number of other options ("GOTO", and "Find Duplicates") also will distinguish between upper and lower case. "Search and Replace" (see below) only works in ASCII mode. NOTE: only the text mode for sorting is stored with the mode preferences. The default text mode for searching is always set to alphabetical. _____________________________________________________________________ 15. TAGGING In "Display" mode records can be tagged by pressing "T". The tagged records are marked with a "grey colour". From the main menu, you can display the tagged records by pressing "D" or clicking on "Display tagged records". To release a record tag simply press "T" again. (Un)tagging of records can also be done with the RIGHT mouse button. By keeping the button depressed, multiple records can be (un)tagged during table view. With "TagSel" (SHIFT-F9) you can tag all currently selected records. and with "ClrTags" (SHIFT-F10) all current tags are erased. In addition the "Records" menu has the options "Untag selected records", "Invert tags", and "Tag all records". Most of the functions of REFBASE can be applied to the selection of tagged records, such as saving, printing, deleting, etc. _____________________________________________________________________ 16. LOADING FILES By clicking on "Open" (SHIFT-F1) you enter the FILE menu, and the directory of the current drive is searched for REFBASE files ending with ".REF". You can also ask to display all files by clicking on the box with " * ". Use the mouse to select one or more files to be loaded. By keeping the mouse button depressed, you can select multiple files at once. Also you can select them all, by clicking on "ALL". You can cancel a selection by clicking on a file name a second time. Cancel multiple selections by keeping the mouse button depressed. UNDO deselects all files. To load a selection of files click on LOAD. If you already have loaded a file, this will be erased and replaced by the new file(s). Alternatively, you can choose to load extra files by clicking on MERGE. If multiple files are loaded, each new file will be placed at the "bottom" of the previously loaded file(s), and all loaded files will be treated as a single large file. The "window" in the main menu shows which files are loaded. After each load or merge operation any stored sort orders are erased, and the GOTO facility becomes inactive until you have sorted the file again. You can interrupt the loading of files by pressing ESC. Folders are marked with a "*" before their name. Open them by clicking on their name. To close a folder, click in the box showing the drive path. You can switch between drives by clicking on the drive buttons. Drives "C" to "P" are also selectable via the keyboard by pressing the corresponding drive letter. If you select drive B, for security you will be asked once whether this drive is really switched on. You can also specify the drive for loading files in the main menu, by clicking on "Read drive" and typing in the drive letter. Read only files are marked with a "triangle" before their name (similar to TOS 2.06 and TOS 3.06). Hidden files are marked with a "#" before their name. The filename extension button ".ISS" is meant for issues files which were created with CC31HELP.PRG. By clicking on "???" you can enter a directory file-extension yourself. This extension will then become selectable under the left most "extension button". In the FILE menu a maximum of 68 files and folders can be displayed. If the number of files/folders exceeds 34, their names will automatically be printed in small text. If a directory contains more than 68 files or folders that match a given search extension, the reading of this directory is stopped and a warning "incomplete directory" is given. (In TT-medium and TT-high resolution, the maximum number of file-names in the directory is increased). Finally, the FILE menu offers some extra options: * With "NEW" you can erase the current file(s) from memory and start typing in a new file (this is equivalent to quitting and starting REFBASE) * With "DEL" you can delete a selection of files, provided that they are not write-protected. * With "RENAME" you can rename a series of selected files. One by one you can edit their names. Only the letters A to Z, the numbers 0 to 9, the dot (.) and the underscore (_) are accepted as valid characters. To skip a name, simply press RETURN, or enter an empty name. * With "ATTR" you can modify the file attributes of the selected files. "Hiding" a file makes it invisible in the normal GEM-Desktop. For the rest, hidden files can be read normally by REFBASE. (For obscure reasons, changing file attributes does not work if the data of REFBASE are stored in TT-RAM (GEMDOS returns an error code to REFBASE)). Pressing CONTROL + "P" will print the current (sub)directory. Pressing CONTROL + "S" writes the current (sub)directory to a disk file. For NeoDesk users, multiple files can be loaded automatically from the Desktop by dragging them on the REFBASE icon. The maximum number of files that can be loaded in this way is limited by the amount of space that GEMDOS reserves for storing the file names with their drive paths: their total length should not exceed 127 characters. With TOS 2.06 and TOS 3.06 only a single file can be loaded this way. You can "autoload" only .REF or .ISS files. A mixture of .REF and .ISS files is not allowed: if the first file in the sequence is a .REF file, any following .ISS files will be ignored, and vice versa. (With TOS versions 1.0x this autoload facility does not work). REFBASE assumes that the files to be loaded, either in the FILE menu, or in the keywords menu, are text files. If you try to load any other type of file errors may occur, and garbage will be displayed on the screen. You can leave the FILE menu by pressing ESCAPE or clicking on EXIT. _____________________________________________________________________ 17. MEMORY MANAGEMENT The maximum number of records that can be loaded in REFBASE is shown by the "Space" indicator in the main menu, directly after starting the program. If you load a file, the number of loaded records is shown by "Loaded", and "Space" will show the record space left. If during a load operation the maximum number of records is reached, loading will be stopped. REFBASE adjusts the amount of reserved record space to the amount of RAM available in the computer. In doing so, the program assumes an average record size of 400 characters (=bytes). This is the typical size of records with a reasonable amount of keywords and without abstracts. Therefore the maximum number of records that REFBASE will load is about 600 with 1 Mb of RAM, 2300 with 2 Mb RAM, and 5800 with 4 Mb RAM (ST- High Res). Records with abstracts consume much more memory space (up to 3000 bytes per record). If such records are loaded, the "space" indicator is unreliable, and will over-estimate the record space. For this reason REFBASE will also check if the size of files to be loaded or merged does not exceed the available amount of RAM, and a warning will be given if this is the case. This check for sufficient RAM will also include the size of any keywords files already loaded or deleted records still stored in memory, and you may need to erase a large keyword file or do a garbage removal first, before you can load a large data-file. You can ask for the average record size in a file by clicking on "File size" in the main menu. In TT-Medium and TT-High resolution, REFBASE consumes about 500 kilobytes more memory space compared to the ST-High resolution (due to the enlarged screen-buffers). Switching to these resolutions will therefore reduce the loading capacity of REFBASE. _____________________________________________________________________ 18. SAVING FILES Click on "Save" (SHIFT-F2) to save records to disk. If selected or tagged records are available, you can choose to save only these records. If you save the records to a file that already exists, a warning will be given, and you will be offered three options: overwrite the file ("replace"), add the records to the end of file ("append") or stop the save operation ("cancel"). If you append records to a file on disk, be sure that this file does not become too large for loading by REFBASE. If this should happen anyway, you can use REFSPLIT.PRG to recover the file (see 32. SUPPORTING PROGRAMS) You can specify the drive for saving record files in the main menu, by clicking on "Write drive" and typing in the drive letter. This drive selection is also valid for other save operations such as export, or printing to disk. During all save operations there is NO CHECK FOR SUFFICIENT DISK SPACE. You can do this yourself by clicking on "Disk space" in the main menu, and typing in the letter of the drive. Clicking of "File size" will give the size of the file that you want to save. During a save operation, the normal screen disappears, and a "snow storm" appears. This is the file, which is being written to disk in blocks of nearly one screen full. (If a save operation ends with a block of about one fifth of a screen full of "snow", then for unknown reasons REFBASE pauses for a moment, before writing the information to disk. This is probably a "bug" in GFA- Basic, for which I know no remedy). _____________________________________________________________________ 19. DELETING RECORDS Records can be deleted manually by pressing DELETE. Also it is possible to delete selected or tagged records via the "Records" menu. Deleted records are not erased from memory: they keep occupying space until a new file is loaded. If you have deleted a large number of records, you can permanently erase them from memory by choosing the "Garbage removal" in the "Records" menu. The space which they occupied then becomes available again, for instance for loading extra files with MERGE. Use "Undo record deletions" in the "Records" menu to retrieve all deleted records or the latest deleted record. These records will then be placed at the bottom of the file, and they are accessible by displaying all records. If by any chance a deleted record was tagged or selected, this will no longer be the case. _____________________________________________________________________ 20. FIND DUPLICATES After sorting on the "Journal" field you can look for duplicate records by choosing "Find duplicates" in the "Records" menu. REFBASE will then check if there are references of which the journal fields are EXACTLY the same, in which case they are scored as "duplicates". The duplicate records are stored as "selected records", which can be displayed by pressing "S", or clicking on "Display selected records". Also, of each set of N duplicate records, N-1 are tagged. In this way deleting selected records will delete all duplicates, whereas deleting tagged records will retain one copy of each duplicate record in the file. Searching for duplicates will erase all current record tags. Note that this duplicate finding routine will fail if multiple references occur on the same page of the journal (e.g. abstracts from symposia, or book reviews). ____________________________________________________________________ 21. CASE CONVERSION In the "Records" menu the references can be converted to upper case or lower case by clicking on "case conversion". During the case conversions the special characters "" are changed to "" and vice versa. The "Fields" menu also offers the possibility of case conversion, with the difference that this time the conversion can be applied to a single field. By pressing CONTROL and clicking on a record field during card-view, a menu pops up in which it is possible to select for lower-case conversion of this field. The fields menu also offers the possibility to "decapitalize" the journal names (see 23. FIELDS MENU). _____________________________________________________________________ 22. RECORDS MENU The options of the Records menu have already been discussed in the other sections of the manual: "Untag selected records" see 15. TAGGING "Invert tags" see 15. TAGGING "Tag all records" see 15. TAGGING "Delete selected records" see 19. DELETING RECORDS "Delete tagged records" see 19. DELETING RECORDS "Undo record deletions" see 19. DELETING RECORDS "Find duplicates" see 20. FIND DUPLICATES "Case conversion" see 21. CASE CONVERSION "Garbage removal" see 17. MEMORY MANAGEMENT and 19. DELETING RECORDS _____________________________________________________________________ 23. FIELDS MENU "Fields" menu has the following options, which can be applied to either all records, or a selection of records: With "Export field" the contents of a record field can be written to a file on disk. The most useful application is exporting the keywords field for generating a keyword list with KEYWORDS.PRG. With "Search and Replace" you can search for a text string in a field, and replace it by another text string. "Search and Replace" only works in ASCII-mode, i.e. upper case and lower case characters are treated differently. With "Erase field" you can erase its contents. With "Paste block..." you can choose to paste the block buffer to the end of a field, to the start of a field, or to fill the field with the block text and thus completely replace its contents. See also 9. BLOCK FUNCTIONS. For "Case conversion" see 21. CASE CONVERSION. With "Remove marks" you can remove all text placed in {}-brackets from the remarks field. With "Remove abstracts" you can remove any abstracts that are stored in the remarks field. The abstracts that are stored in the remarks field by the conversion program CC31HELP.PRG will always start with "---". The "Remove abstracts" option simply searches for "---" in the remarks field and then removes all text including and after this separating character sequence. If you wish you can enter a different start text string to search for. If you enter an empty string, the search will be cancelled. With "Remove issues" you can remove all issue numbers that are placed in ()-brackets at the end of the journal field. With "Import ... " you can import a field in the currently loaded REFBASE file. The import file must be a text file in which the number of lines is equal to the number of records in the REFBASE file. The import facility will then place each line of the import file in the selected field of the REFBASE file, starting with the first record. With "Decapitalize journals ..." you can convert journal-names from uppercase to lowercase, with the first character of each word remaining in uppercase. This option is meant for export files from the "Current Contents on Diskette V3.1" which sometimes contain records in which the journal names are left in upper-case. (In version 3.2 of the CCoD program, this bug has been repaired). _____________________________________________________________________ 24. MODE MENU The mode menu is activated by Shift-F10 in the main menu. Most of its options have already been discussed in the other sections of the manual: "Cursor blink" with this option you can specify whether or not the cursor should blink during data entry "Use wildcards" see 13. SEARCHING/SELECTION "Recall previous sorts" see 11. SORTING "Sort/Goto/FindDupl by ASCII" see 14. TEXT MODE "Partial equation" see 13. SEARCHING/SELECTION "Use quickfind algorithm" see 13. SEARCHING/SELECTION "Mouse delay time" with this option you can enter the value (0-9) of a short time pause to be given after each mouse function (e.g. mouse click, change from arrow to bee etc) in the program. The default value is 5. See also 25. THE MOUSE. "Soft scroll pause units:" see 6. DISPLAY "Use VDI 8*16 font" With this option you can specify whether the VDI-font (instead of the TOS-font) should be used for displaying records with the standard 8*16 pixel character set. This increases the scrolling speed if a VDI screen output accelerator such as NVDI is installed. (without such an accelerator installed choosing the VDI-font will have the opposite effect, i.e. slow down scrolling). In the main menu you can save the MODE configuration by clicking on "Save MODE preferences ... " or pressing "M". This will create a file "REFBASE.MOD" in the same (sub)directory that REFBASE was started from. Whenever REFBASE is loaded, this file will now be automatically read and the preferences set accordingly. _____________________________________________________________________ 25. THE MOUSE Programs written in GFA-Basic often have difficulties with the standard GEM alert boxes: the default button becomes black as soon as you move the mouse above it, you may need to click twice before the alert box responds, and sometimes pressing RETURN even selects the non-default option instead. For this reason REFBASE uses its own alert box, which can be operated with both the left and right mouse button. In fact, all mouse-selectable functions in REFBASE, except for the GEM-fileselect box, respond to the right mouse button as well. Users of TOS version 1.04 may have installed the button fix accessory (BUTTNFIX.ACC) to overcome some problems with the mouse-click in GEM- programs. Unfortunately, using BUTTNFIX.ACC affects the mouse functions in REFBASE. Examples are sudden pauses or halts in the program (which can be overcome with an extra click of the mouse), erratic and unwanted selections in the GEM-fileselect boxes, or difficulties in returning to the Desktop after quitting. These errors can be prevented reasonably well by introducing a small mouse delay time. The length of this time pause can be set in the mode menu. The alternative is not to use BUTTNFIX.ACC together with REFBASE, or to use the right mouse button for selecting the various functions instead. In the latter case the mouse errors will not occur. _____________________________________________________________________ 26. KEYWORDS You can enter the keywords menu from the main menu by clicking on "Keywrds" (SHIFT-F3), or pressing "K". You can also enter the keywords menu during "Display" or during data entry ("Input"/"Amend") by pressing "K" or CONTROL-K respectively. From the keywords menu you can load a file with keywords (or if necessary any other text file) by pressing or clicking on F3. You can scroll through the file by pressing the CURSOR UP and CURSOR DOWN keys. With CONTROL-CURSOR UP/DOWN you can scroll by page. CONTROL-CLRHOME and CONTROL-Z jump to the top and bottom of the file respectively. Each line is numbered to give an indication of the current position in the keywords file. The numeric keypad can also be used to scroll through the keywords (see 6. DISPLAY). If your keywords are sorted, you can jump through the file by binary search with the GOTO command (F7). GOTO normally works in alphabetical mode; if your keywords are sorted by ASCII-code, you must first activate the ASCII sort option in the mode menu, otherwise GOTO will not work correctly. With "Select" (F2) you can search for all keywords that contain a specified text string. You are allowed to make one combination of search terms by typing in "AND", "OR", or "NOT". Start the search by pressing RETURN. If no matching keywords are found, you return to the main list; otherwise the selected keywords are shown, and you can return to the main list by pressing ESC. The "Select" option can be set in alphabetical or ASCII mode by pressing F4. (This is the same switch as SHIFT-F5 in the main menu). With Find (F5) you can search for the first keyword that includes a specified text string. The cursor will then move to this position in the keywords file. You can repeat this search by pressing F6. With "Erase" the loaded keywords file is erased and the memory used is available again. Also when a new keywords file is loaded, the preceding one is erased first. You can quit the keywords menu by pressing ESC or "Exit" (F8). With TT-high resolution, pressing TAB will display the keywords in the centre of the screen for easy viewing. Pressing TAB again restores the default display (i.e. starting at the left of the screen). While entering or editing records, keywords can automatically be inserted at the cursor position. To do this, you must press CONTROL-K to enter the keywords menu, move to the desired keyword, and then press RETURN. Repeat this sequence if you want to collect more keywords. Each inserted keyword will be terminated with "; " as a separator. It is advised that you do this also when you type in the keywords yourself. Only the last keyword in the keywords field should be free of this separator sequence. In this way you can use keywords which actually consist of two or more words separated by spaces, e.g. "polyacrylamide gel electrophoresis". (With KEYWORDS.PRG you can make a sorted list of your exported keywords, which can be loaded into REFBASE. This program has a special facility for recognizing keywords that are separated by "; "). Keywords can also be entered with the mouse: (1) select the keyword with the left mouse button, and (2) press the right mouse button to insert it in the record. NOTE: keywords containing a double space (" ") will be inserted incompletely when pressing RETURN, since all text on the right side of the most right double space will be removed. This enables you to load keyword files in which each keyword is provided with its word frequency, separated by a double space. For instance, the keyword "monoclonal antibody 10" indicates that this occurred 10 times in the extracted keyword file; if you press RETURN, the "10" will be stripped off since it is preceded by a double space, and only "monoclonal antibody" will be inserted into the record. KEYWORDS.PRG offers you the option to make such keyword files with word frequencies. (Normally, keywords entered in REFBASE will never contain double spaces, since they are filtered out after data entry). The keyword files use memory space that is shared with the records. Therefore, if large literature files are loaded the keywords may be overwritten by the records. The user is notified when this occurs, and the use of the loaded keywords is blocked. Loading of keyword files is cancelled if there turns out to be insufficient space or RAM. Loading of keyword files will never lead to overwriting of records in memory. ______________________________________________________________________ 27. VIDEO-RECORDER BUTTONS During record display and in the keyword menu a series of video-recorder like buttons appear at the bottom of the screen. These buttons give direct mouse-access to a number of functions that are also available via the keyboard. DEL = Delete record (same als pressing [DELETE]) TOP = Goto TOP of file (same as CONTROL + CLRHOME, or 7 on numeric key- pad) BOT = Goto BOTTOM of file (same as CONTROL + Z, or 1 on numeric keypad) P=? = Enter soft scroll pause time (Same as pressing "P" during title view) SFT = Not used: reserved for future use << = Same as CONTROL + cursor up < = Same as cursor up > = Same as cursor down << = Same as CONTROL + cursor down REM = Show/Exit remarks field (Same as HELP) <= = Cursor left (switch between tables; soft scroll) => = Cursor right ( ,, ) INV = invert screen (same as "I") FNT = switch between fonts in table view (same as "F") KWD = enter/exit keywords menu (same as "K") ______________________________________________________________________ 28. PRINTING Clicking on "Print" (SHIFT-F4) gives the print menu. You can leave this menu again by pressing RETURN or ESCAPE, or clicking on EXIT. To activate the functions in the print menu simply click on them with the mouse. With the print menu, reports can be generated from either all, selected of tagged records. These reports can be sent to printers connected to the parallel port (= printer port) or the serial port (= modem port), written to disk, or shown on the screen. The layout of the reports is essentially the same for each of the four "print directions". You can choose between the following report types: 1. Reference = author + year + title + journal. In addition to this short format, you can also select a medium format (including the File and the Subject fields as well), a large format (to which the keywords and the marks in the remarks field are added) and finally the full format (which includes the remarks field in full). 2. Card - all fields are printed including labels, with each field starting on a new line. 3. Author Table - A table with authors + year + subject + journal + date + read + file. If you choose a column width of 136 (17 characters per inch) instead of 160 (20 c.p.i) then the date field is omitted. 4. Title table - Here you can choose for titles only, or for a more complete table with (very short) authors, year, subject, journal, and file as well. 5. Journal table - This will only print journal + year + file. If you choose to print in pages, the table will be printed in two columns. Start printing with "Print Report". Stop printing by pressing ESCAPE. By clicking on "Continuous Print"/"Pages + formfeeds" you can indicate whether or not you want to print in pages. If you print in pages, (1) each page can be printed with a header, (2) between pages the printer is instructed to move to a new sheet of paper (= form feed), (3) Journal tables are printed in two columns, (4) it is possible to print only even or uneven pages, thus facilitating double- sided printing, and (5) you can also choose to pause printing between pages. Furthermore, if the last reference or card of a page does not fit completely at the bottom of the paper, it will be printed at the start of the next page. With continuous print, no form feeds are given and the records are sent "straight" to the printer. Click on "No header"/"Print header" to indicate if you want page headers to be printed. With continuous print, only one header will be printed. Click on "Show header..." to enter or modify the page header. Each header will automatically contain the system date and the page number, and the user can specify any additional information. Click on "Print margins/No margins" to indicate if you want a margin to be printed. This margin will allow sufficient space for a paper perforator. You can place the margin either on the left side or the right side, or if desired left on the uneven pages, and right on the even pages. With "card print" you can select the label-text that will be printed for field 4: "DOCU" or "READ". You can choose between three printer types: 1) The standard 9-pin matrix printer (24-pin will probably also work properly although this has not been tested) For this printer type you may choose between 10, 12, 17 and 20 characters per inch (= pica, elite, condensed, and elite condensed respectively). Furthermore you can choose between 7 and 12 lines per inch; in the latter case the text will be printed in superscript. Other selectable options are Draft/N.L.Q and the paper height (11 or 12 inch). To prevent the columns in the tables from being printed too irregularly, an alert box will offered you the possibility of unidirectional print as well. 2) The HP-Deskjet printer. The following fonts are selectable: (cpi = characters per inch; lpi = lines per inch) Cour 10 cpi 6 lpi - standard Courier Pres 12 cpi 6 lpi - standard Prestige Pres 12 cpi 7 lpi - standard Prestige, reduced line spacing Pres 16 cpi 8 lpi - small Prestige Pres 16 cpi 10 lpi - small Prestige, reduced line spacing Cour 20 cpi 12 lpi - tiny Courier Cour 16 cpi 6 lpi - condensed Courier Cour 16 cpi 8 lpi - small Courier Cour 16 cpi 10 lpi - small Courier, narrow line spacing Goth 12 cpi 6 lpi - normal size Gothic Goth 16 cpi 8 lpi - small Gothic For the Prestige fonts you will need to install the Prestige font cartridge in your printer. The Gothic font is internal in recent Deskjet printers (e.g. HP-Deskjet-500), but requires a font cartridge in older HP-Deskjet models. 3) The HP-LaserJet4 printer. Both in Courier and Gothic scalable font a series of character sizes (measured in cpi) are selectable, all provided with a suitable line- spacing. For printing tables, you are obliged to choose a character pitch of 16, 17 or 20 cpi, even if you only want to print to disk, or to the screen. For printing cards or references, you are free to choose any character pitch you want. If you want to export references to a file, it is best to choose 10 cpi with a right margin. The references will then become about 75 characters wide, and they will fit nicely in your word processor documents. If you load reference files in 1ST Word Plus, you must first activate the WP- mode (if it was inactive) and then replace every space (" ") by a space (" "). This will convert the references to the Word Plus format, and they will now respond to the "reformat" key. When printing references, the journal field is printed in boldface (matrix printer) or underlined (Deskjet/HP-Laserjet4). If you switch on your HP-Deskjet printer with the computer already running, the printer will not respond to print commands. To correct this, click on "awaken printer" in the print options box. The current print settings (e.g. page print, printer, font) can be saved to disk by clicking on "save print defaults". These settings are stored in a file REFBASE.PRN and are automatically loaded at program startup. If you print to a printer connected to the serial port, you must first make sure that the "RS232 PORT CONFIGURATION" is properly installed with the control panel accessory. For the HP-Deskjet the following settings will work OK: Baud Rate "19200", Parity "None", Duplex "Full", Bits/Char "8", Strip Bit "Off", Xon/Xoff "On", and Rts/Cts "Off". ______________________________________________________________________ 29. CHAIN SEARCH You can enter the Chain search menu from the main menu by pressing "C" or clicking on "Chain search ...". You leave the chain search menu by pressing "E" or ESC, or by clicking on "Exit chain search ..." With the chain search multiple files on disk can be searched for records that match a given selection rule. This search facility only makes sense if you have more records than can be loaded in the memory of the computer, and if you have a hard disk. By clicking on "File" (F1) you enter the chain search file-select menu. Select the files you want to search as described in Section 16 (LOADING FILES). Accept a selection by clicking on CHAIN. Note that all files to be searched must be in the same (sub)directory, and that each separate file must fit in the ST's memory. A warning is given if any of the files is too large to be loaded. The maximum number of files in the directory (and thus for the chain search) varies from 68 for ST-high screen resolution to 188 for TT-high screen resolution. Use F2 to choose a selection rule as described in Section 13 (SEARCHING/SELECTION). With F4 ("Alpha"/"ASCII") you can choose whether or not distinction between upper and lower case characters must be made during the search (See 14. TEXT MODE). The selection rule remains active until replaced by another, and is not affected by any selection rules that are entered in the main menu. To start a chain search press or click on F3 ("Search"). Choose "Count selected records" if you only want to count how many records match the selection rule; choose "Fetch selected records" if you want to fetch and see them. During the chain search the selected files are loaded one after the other, and the number of records matching the selection rule (hits) are displayed for each file on the screen. After the chain search the total number of hits is shown in an alert box, and if you had chosen to fetch the selected records, they can be displayed. If records are fetched during the chain search, they are first stored in a RAM-buffer, the size of which is indicated in the chain search menu. If this buffer becomes full, REFBASE will start writing the search results to a separate file on disk. The maximum size of this file is indicated by the "Fetch limits" in the chain search menu, and depends on the amount of memory in your computer. As soon as this maximum file size is reached, the chain search will be terminated. You can modify the drive path for saving the chain search results by clicking on "Write drive", and alter the name of the search results file by clicking on "Save overflow as...". After the chain search, the selected records are displayed either after reading from the RAM-buffer, or after loading from disk. If during a chain search a loaded file turns out to have too many records, and thus does not fit in memory, the chain search will be stopped. Pressing/clicking on F5 ("Hitlist") will show the selection rule of the latest run, and the number of hits in each of the searched files. You can scroll the list with the cursor keys. Exit with ESC or a mouse-click. _____________________________________________________________________ 30. PROFILE SEARCH Enter the Profile Search menu from the main menu by pressing "P" or by clicking on "Profile Search" with the mouse. The Profile Search offers search facilities very similar to the "Current Contents on Diskette" program for DOS and Apple computers. With the profile search a series of search commands can be executed in a single run. The search commands can be stored on disk in a "search profile", which can be reloaded for repeated use. To enter a search profile press F5 (Enter). Select the field that you want to search on, and type in a search text. Press [RETURN], and the first profile line is displayed on the screen. To enter more profile lines repeat this sequence. The maximum number of profile lines that can be entered is 64. Individual search commands can be executed by placing the cursor on them (cursor up/down keys) and pressing F2 (Find). You can also "run" the profile with F1: all profile lines will then be executed. If the cursor is not at the start of the profile, you can choose to run the profile from the first line or from current cursor position downwards. After searching, the number of records found is shown on each profile line. You can interrupt a profile search by pressing ESCAPE (if no response, press ESCAPE again). You can examine the records found by pressing F3 (Display) or by double- clicking with the mouse on the profile line. Exit display with ESCAPE to return to the profile search. Multiple search keywords can be combined in a single search command. These must be separated by either AND or OR. For example: TITLE ____ PROTEASE OR PROTEINASE OR PEPTIDASE will search for records that contain either of these three words in the title. Alternatively: TITLE ____ PROTEASE AND PROTEINASE AND PEPTIDASE will search for records that contain all three search terms in the title. NOT may be used instead of AND: TITLE ____ PROTEASE NOT PROTEINASE AND PEPTIDASE will search for records that have PROTEASE and PEPTIDASE and not PROTEINASE in the title. Note that AND, NOT, and OR must be entered in uppercase characters. REFBASE will automatically indicate which of these operators are recognized: in the cursor-line they are shown in normal colours instead of inverted colours. If AND and OR occur in the same line, OR will be used and AND is ignored. The case sensitivity of the search terms in the profile depends on whether the search text mode (section 14) is set to ASCII or Alpha (F5 in the main menu): in the former case there is, in the latter case there is not a distinction between upper- and lower case characters. Brackets are not supported during entry of profile lines. Nor is it (yet) possible to combine the search results of different profile lines (and create a "Set_no." field similar to the Current Contents on Diskette). Note that with the profile search, you can only search whether a field includes or does not include a given search term. In fact, all search commands of the profile search are internally converted by REFBASE to search commands of the SELECT MENU (Section 13), after which an "includes" or a "does not include" search is performed for each keyword in the profile line. Wild-card search is also supported in the profile search menu. For instance: TITLE ____ intest*cel will find records that include "intestine cells" or "intestinal cellulose" in the title. Note that REFBASE treats the asterisk (*) differently compared with the Current Contents on Diskette software: in the latter program you would have to type in "*intest*cel*" to get the same result as "intest*cell" in REFBASE. With the wildcard search it is possible to make more complex search statements which can alleviate the lack of brackets, such as: TITLE ____ cell*intest OR intest*cell OR cellu*digest OR digest*cellul This will find records that contain ("intestine" AND "cell") OR ("cellulose" AND "digestion"). For more information about the use wildcards see section 13 (SEARCHING/SELECTION). To edit a profile, you may press F4 (Edit) to change a profile line (either its field, its text or both), or you may press DELETE or INSERT to remove or add profile lines at the cursor position. After having inserted or deleted a profile line, any search results in following profile lines are lost (to restore them, you must run the profile again, starting from the current cursor position). F6 (New) erases the current profile from memory. Use F8 and F7 to save and load your profile to and from disk. It is advised to give your SELection profiles the extension *.SEL, in order to distinguish them from search profiles (*.PRO) from the Current Contents on Diskette. F9 (Help) is still unavailable. Exit the profile search with ESCAPE or F10 (EXIT). During DISPLAY of profile search records it is not allowed to edit records, to edit block text, or to go to the keywords menu. The functions F2 (Help), F4 (TagSet), and F5 (Clrtags) are not yet available. _____________________________________________________________________ 31. FILE FORMAT / DATA EXCHANGE REFBASE stores its records as plain text files, with each field occupying a single line, and each record consisting of 10 lines. REFBASE files can therefore be loaded in every text editor, or word processor. A problem may arise though with large multi-line fields. If their length exceeds the maximum line length of the text editor (or word processor), they will be cut off and the remainder of the field is placed in the next line. For example: in the text editor TEMPUS the maximum line length is 255 characters, and in 1st Word Plus 3.2 it is 150. Loading REFBASE files in these programs may therefore damage their structure, and if you save the files again they may become useless for REFBASE. If you want to import REFBASE files in other databases, these programs must be able to read text fields that are longer than 255 characters. For those who want to write conversion programs in GFA-Basic V3, be sure to load the REFBASE files with the "RECALL" function. If you use the "LINE INPUT" function, long fields will as yet be truncated at 255 characters, and their remainder passed on to the next line that is to be read from disk. ____________________________________________________________________ 32. SUPPORTING PROGRAMS With this release of REFBASE three supporting programs are provided as well: 1) KEYWORDS.PRG - With this program you can create a sorted list of keywords from your references, which you can subsequently load in the keywords menu of REFBASE. First export the contents of the keywords fields to a file on disk. Then read this file with KEYWORDS.PRG to make the list. If you have separated your keywords with a semicolon + space ("; ") you must indicate this in the menu of KEYWORDS.PRG before you start the extraction. Otherwise, by default, the space will be interpreted as the keyword separator. 2) CC31HELP.PRG - with this program you can convert export files from the Current Contents on Diskette Version 3.1 (and 3.2) into files that can be read by REFBASE. To do this, you must export your CCoD search results in the "Comma-Delimited" file format using one of the two user defined record formats as specified CC31HELP.PRG. These CCoD record export formats are stored in the files CD_SHORT.CUS and CD_LONG.CUS. Load either of these files in the CCoD program, before exporting your records. Give the export files an extension *.CDS (comma delimited short) or *.CDL (comma delimited long) depending on the type of record format that was used. During conversion of the CCoD export files, the fields of the REFBASE records will be filled with the following information: SUBJECT = Discipline (abbreviated according to internal tables in the conversion program; if disciplines in an export file do not match any of the preset values it will be reported in an alert box, and their names will be truncated at 8 characters). READ/DOCUMENT = Document/Language in abbreviated form FILE = The first few characters of the name of the export file (see CC31HELP.PRG) JOURNAL = journal (source) + volume + pages + issue. (a standard format is used as explained in CC31HELP.PRG) DATE = The date of the journal issue (if given in the export file) REMARKS = The address of the author to whom reprint requests should be sent. (This address is always terminated with a "|", to facilitate its recognition by any "reprint request programs" that the user may wish to write). The other fields need no explanation If records are exported in the "long" format (*.CDL), any additional book information with be placed in the Title field, preceded by a "---" separator string. Furthermore, abstracts will be placed in the remarks field, also preceded by a "---" separator string CC31HELP.PRG also offers the option to load and print your CCoD search profiles. If you intend to routinely collect the full contents of your favourite journals, it is advised to create a separate profile with only "Journal" (or "Source") fields. After exporting records from CCoD with this profile, and converting them to a REFBASE file, you can use the issue extraction facility of CC31HELP.PRG to collect the issue numbers in this REF-file. Issue files are recognized by REFBASE from their extension ".ISS". When they are loaded in REFBASE, the "Expand" option of the table view is inactive, and only a single screen table with an adjusted selection of fields is shown. Also sorting on the journal field will go differently. For instance issue "(9)" will now be sorted before issue "(10)", and "(JAN)" will be sorted before "(FEB)". 3) REFSPLIT.PRG - Use this program to recover REFBASE files that have accidentally become too large to load in the computer's memory (e.g. due to a save + append operation). REFSPLIT.PRG splits the file in two or more smaller parts, which can then be loaded separately again. ______________________________________________________________________ 33. LIMITS OF REFBASE The maximum record size is 5000 characters. With larger records errors may occur during saving. When references from the Current Contents on Diskette are converted to REF_BASE format with CC31HELP.PRG their size will be tested, and they will be shortened if they have more than 4500 characters. (REFBASE itself does not yet check whether records exceed the maximum size). The maximum number of records that REFBASE can display is 32750. This limit is expected to be reached only on Atari-ST compatible computers with more than 20 Mb of RAM. In practice the maximum number of records that will be loaded (= "record space") ranges from about 600 for a 1 Mb ST to 5800 for a 4 Mb ST. The maximum number of files and folders that can be displayed in the load menu is 68. (88 in TT-medium resolution; 188 in TT-High resolution). This is also the maximum number of files for a chain-search. Assuming that on average 1000 records are stored per file, this means that a chain search is capable of handling 68000 to 188000 records in a single run. The maximum number of keywords that can be loaded is 10 times the record space; the maximum number of selected keywords that can be displayed as a subset is equal to the record space. The sorting algorithm has been programmed recursively. I have no idea how many levels of recursion are allowed on the Atari ST, nor do I know how many levels or recursion normally occur during a sort. It may be possible that this recursion poses a limit on the maximum number of records that can be sorted. However, I have experienced no difficulties in sorting 5000 records on a Mega ST4. REFBASE was written in BASIC. This implies that from time to time the user may expect short pauses or response delays in the program, which are caused by an automatic memory cleanup operation called the "string garbage collection". This phenomenon passes almost unnoticed with 1 or 2 Mb machines, but on 4 Mb machines with only a few hundred kilobytes of memory space left it may take one or two seconds before such a "freeze" of the program stops and action is resumed. _____________________________________________________________________ End of text Changes made in REFBASE Version 2.1 compared with Version 1.4: ================================================================= * Both REFBASE and its utility programs support the Atari TT in the medium and high screen resolutions. * The RIGHT mouse button can be used to (un)tag records. Keeping it depressed will (un)tag multiple records in table view. * In the load menu, de-selection of (multiple) files is now done by clicking on their name a second time. READ ONLY files are now marked with a triangle. * During data entry CONTROL + "=" produces a box with special characters (ASCII > 127) * You can switch between card view and table view by double clicking once on the current record with the LEFT mouse button. * In card view, pop-up menus are now accessed by pressing CONTROL and clicking with the LEFT mouse button on the desired field. The pop-up menu now also offers lower-case conversion. * The fields menu offers the possiblitiy to "decapitalize" the journal field. Upper case journal names are converted to lower case, with the first character of each word remaining in upper case. * REFBASE is now equipped with a series of mouse selectable videorecorder-like buttons for keyboard functions that are frequently used. * You can now use a PROFILE SEARCH facility similar to that available on the "Current Contents on Diskette". * Exported references with abstracts from "Current Contents on Diskette" versions 3.1 and 3.2 can now be directly converted into REFBASE records. * Two keys have swapped function during data entry: [TAB] is now used to move between fields (= similar to Phoenix 2.0), while [INSERT] is now used to add the (changed) record to the data- file. * The print menu supports the HP Laserjet4 printer. ==================================================================== PLANS AND IDEAS FOR FURTHER IMPROVEMENTS: * Import/export facility for single fields or block buffer. * Keyboard equivalents for ALL mouse functions. * Support of more color screen resolutions. * Conversion of CD-ROM export files into REFBASE format. * Set-number combination in the profile-search. * User definable table and report layout * User definable key-functions ==================================================================== End of text