GENEUS, a computer system for DNA and protein sequence analysis containing an information retrieval system for the EMBL data library.

We describe a comprehensive computer system, GENEUS, for extensive DNA, RNA and protein sequence analysis. The analysis system is developed for the DEC VAX/VMS computer and uses the EMBL Nucleic Acid Sequence Data Library. Help information is available on-line on terminal screen. To speed up system handling, a qualifier oriented user communication is employed. All results are stored on files making them accessible to the computer editor. An information retrieval system for the EMBL Nucleotide Sequence Data Library is also described. A defined data-base interface allows connection to other analysis programs.+     

GenBank.

The GenBank (Registered Trademark symbol) sequence database incorporates DNA sequences from all available public sources, primarily through the direct submission of sequence data from individual laboratories and from large-scale sequencing projects. Most submitters use the BankIt (Web) or Sequin programs to format and send sequence data. Data exchange with the EMBL Data Library and the DNA Data Bank of Japan helps ensure comprehensive worldwide coverage. GenBank data is accessible through NCBI's integrated retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome and protein structure information. MEDLINE (Registered Trademark symbol) s from published articles describing the sequences are included as an additional source of biological annotation through the PubMed search system. Sequence similarity searching is offered through the BLAST series of database search programs. In addition to FTP, Email, and server/client versions of Entrez and BLAST, NCBI offers a wide range of World Wide Web retrieval and analysis services based on GenBank data. The GenBank database and related resources are freely accessible via the URL: http://www.ncbi.nlm.nih.gov     

Use of a computer and mathematical methods in epidemiological work. Report 3. Experience with the operational tracing of infectious morbidity using an automic self-service information unit]

The authors describe their experience in the elaboration and introduction into practice of epidemiological service of the system of operative tracing of infectious morbidity at the level of the central sanitary-epidemiological station under conditions of automatic control system. Data on improvement of information supply and logic analysis of the information with the aid of Minsk-22 computer are presented. Forms of documents are considered. Experience in the use of this system for two years pointed to its expediency.     

Molecular and cellular interactions responsible for intrasegmental patterning during Drosophila embryogenesis

The elaboration of pattern within insect segments is a well-studied example of cellular patterning during development. This process requires that each cell develop appropriately for its position. Experimental embryology suggests that intercellular communication plays a key role in imparting positional information to cells. Drosophila genetics has identified numerous genes whose activity is required for patterning within segments, and whose molecular genetic analyses suggest they constitute and control cell communication circuits. Particular genes are expressed or required by cells that will follow distinct developmental pathways, and some appear to confer or interpret intercellular signals. Other patterning genes are ubiquitously required and may provide the machinery through which the signals are transmitted.     

Clinical data evaluation and the PL health control information system.

In a health control service environment, that is, a periodic, membership AMHTS type of comprehensive health check-up system, where clinical data evaluation especially an evaluation in terms of subject-specific normal ranges, is most important, the medical information system is required to handle: (1) Various network types files; (2) real-time immediacy; (3) an asserted reliability to meet personal health control purposes. As in other computer applications already successfully used, an indexed direct assess method (IDAM) developed is our solution. It allows us to provide multiple indices for the file network, instead of inverted files, a unique index-to-record relationship, preventing any unrecoverable chaining destruction and, thereby, provides any network type access a stable access time. Furthermore, for research purposes, a data integrity for on-line access and batch access was attained as well as a retrieval language system with a multiple key retrieval function.     

Computer Simulation of Fermentation Systems

Results of batch fermentation of gluconic acid by Pseudomonas ovalis were graphically analyzed to obtain a kinetic model to represent the data. Since gluconic acid was produced by the hydrolysis of a lactone intermediate, the model was necessarily represented by a set of kinetic equations. A computer simulation technique involving the use of the MIDAS program was developed to solve the system of nonlinear equations and to check the appropriateness of the model. Since the maximal specific growth rate and the rate constant for the production of the lactone intermediate varied with time, function generators were used to simulate these system parameters. The merit of using the MIDAS program was considered in relation to analysis and model testing in microbiological processes of similar types.     

Mating Systems and Distribution in some Tropical Ferns

Applying mating system genetics as the tool, three tropicalferns, namely, Ceratopteris thalictroides, Pseudodrynaria coronansand Pityrogramma calomelanos were examined for their distributionalpatterns. Absence of recessive lethals in the sporophytes ofP. colomelanos allows its spores to function as a single propagulein the colonization of open habitats through intra-gametophyticselfing and it is widely distributed. The phenomenon of leakylethality and ultimately recessive sporophytic lethality inP. coronans is associated with a restricted distribution ofthe species in the forest. Ecological specialization in thecase of C. thalictroides also renders it a poor colonizer thoughits mating system is directed towards intergemetophytic selfingwith capacity in time for intra-gametophytic selfing.     

Developmental genes and the reconstruction of metazoan evolution--implications of evolutionary loss, limits on inference of ancestry and type 2 errors

We consider three issues that appear to be important in theinterpretation of developmental genetics in an evolutionarycontext. The three issues under discussion are 1) evolutionaryloss as applied to evo-devo data; 2) the limits on our abilityto infer ancestry based on tree reconstruction; and 3) "type2" errors in the assessment of homology of developmental geneexpression data. Lack of consideration of any or all of thesedisparate issues narrows the set of hypotheses under consideration.We examine these issues through examples drawing on new dataon POU domain genes as well as through reference to publishedwork on Distal-less, engrailed and Nk2 genes.     

Randomised trial of personalised computer based information for cancer patients

ObjectiveTo compare the use and effect of a computer based information system for cancer patients that is personalised using each patient''s medical record with a system providing only general information and with information provided in booklets.DesignRandomised trial with three groups. Data collected at start of radiotherapy, one week later (when information provided), three weeks later, and three months later.Participants525 patients started radical radiotherapy; 438 completed follow up.InterventionsTwo groups were offered information via computer (personalised or general information, or both) with open access to computer thereafter; the third group was offered a selection of information booklets.OutcomesPatients'' views and preferences, use of computer and information, and psychological status; doctors'' perceptions; cost of interventions.ResultsMore patients offered the personalised information said that they had learnt something new, thought the information was relevant, used the computer again, and showed their computer printouts to others. There were no major differences in doctors'' perceptions of patients. More of the general computer group were anxious at three months. With an electronic patient record system, in the long run the personalised information system would cost no more than the general system. Full access to booklets cost twice as much as the general system.ConclusionsPatients preferred computer systems that provided information from their medical records to systems that just provided general information. This has implications for the design and implementation of electronic patient record systems and reliance on general sources of patient information.     

Using medical genetics applications to educate for computer competence.

This article proposes specific areas of computing competence and illustrates how these skills can be acquired as an integral part of the curriculum of medical genetics. Geneticists are at the forefront in the use of computers for medical care, because of the driving force of the Human Genome Project. Computer searching of international data bases is the most efficient method to keep current with the explosion in molecular genetics data and with its immediate relevance to clinical care. The use of computers in genetics education could go far beyond the use of computer-assisted instruction (CAI) to show how to use computer systems to assist with clinical decisions. The proposed basic computer skills can be obtained using genetics software. The six proposed skills include the use of (1) microcomputers, (2) productivity software, (3) CAI, patient simulations and specific application programs, (4) remote computers, (5) data bases and knowledge bases, and (6) computers to improve the clinical care of patients.     

Genetic Analysis of Growth in Tomato: the F1 generation

Some aspects of the genetic control of plant development wereinvestigated by combining the methods of growth analysis withthose of quantitative genetics. Four varieties of Lycopersiconesculentum and one of L. pimpinellifolium were included in adiallel cross and the growth of parents and hybrids were followedover a IO-week period. Whole plants and plants with side-shootsremoved were studied. Significant differences in growth-ratewere found between varieties and between the reciprocal inter-specifichybrids; the latter difference followed from the maternal variationin seed size. The growth-rate was reduced by removing the side-shoots.A diallel analysis showed that the control of log fruit weightand number was largely additive but similar analysis of dryweight and leaf-area data showed considerable variation withtime. Extreme caution is, therefore, necessary in generalizingfrom a genetic analysis made at only one point of time. Thisdifficulty was largely overcome and much more information concerningthe inheritance of factors influencing plant development providedby carrying out a genetic analysis of the measured growth-rates.     

Early diagnostic esophagoscopy in the management of corrosive burns of the esophagus

Effective methods developed to review and study the care of patients in hospital have not been applicable to ambulatory care, in which definitive diagnosis is the exception rather than the rule. A reasonable alternative to using diagnosis as the basis for assessing ambulatory care is to use the problems or requests presented by the patients themselves. A system has been developed for classifying and coding this information for flexible computer retrieval. Testing indicates that the system is simple in design, easily mastered by nonphysicians and provides reliable, useful data at a low cost.     

GenBank

The GenBank((R))sequence database incorporates publicly available DNA sequences of >55 000 different organisms, primarily through direct submission of sequence data from individual laboratories and large-scale sequencing projects. Most submissions are made using the BankIt (Web) or Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Data exchange with the EMBL Data Library and the DNA Data Bank of Japan helps ensure comprehensive worldwide coverage. GenBank data is accessible through NCBI's integrated retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping and protein structure information, plus the biomedical literature via PubMed. Sequence similarity searching is provided by the BLAST family of programs. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. NCBI also offers a wide range of WWW retrieval and analysis services based on GenBank data. The GenBank database and related resources are freely accessible via the NCBI home page at http://www.ncbi.nlm.nih.gov     

Reference master: A microcomputer-based storage and retrieval system for bibliographic references

A complete system for housekeeping and retrieval of bibliographic references managing individual reprint collections is described. By the use of special hardware and individual data base software even large reprint collections in the range up to 65 000 papers are handled economically. A fast 8-bit microprocessor (HD 64180) in combination with a Winchester hard disk drive serves as the basis for rapid access to the desired information. An efficient string search algorithm written in assembly language guarantees a fast operation with a search speed of more than 6,000 entries/ minute. The system cannot only prepare reference lists and reference files, but also incorporates an editor and maintains the control whether reprints are already on file or requested. The implementation of back-up schemes assure against data losses. Using a state of the art design single board computer and the most recent mass storage device technology, the system is as well small and cost effective, and thus suitable for personal use. In addition, some general questions and pitfalls concerning the management of scientific literature collections are touched upon.     

GenBank

The GenBank sequence database incorporates publicly available DNA sequences of more than 105 000 different organisms, primarily through direct submission of sequence data from individual laboratories and large-scale sequencing projects. Most submissions are made using the BankIt (web) or Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Data exchange with the EMBL Data Library and the DNA Data Bank of Japan helps ensure comprehensive worldwide coverage. GenBank data is accessible through NCBI’s integrated retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical literature via PubMed. Sequence similarity searching is provided by the BLAST family of programs. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. NCBI also offers a wide range of World Wide Web retrieval and analysis services based on GenBank data. The GenBank database and related resources are freely accessible via the NCBI home page at http://www.ncbi.nlm.nih.gov.     

The case against HIV antibody testing of refugees and immigrants.

Computers are now widely used in medical practice for accounting and secretarial tasks. However, it has been much more difficult to use computers in more physician-related activities of daily practice. I investigated the Desqview multitasking system on a 386 computer as a solution to this problem. Physician-directed tasks of management of patient charts, retrieval of reference information, word processing, appointment scheduling and office organization were each managed by separate programs. Desqview allowed instantaneous switching back and forth between the various programs. I compared the time and cost savings and the need for physician input between Desqview 386, a 386 computer alone and an older, XT computer. Desqview significantly simplified the use of computer programs for medical information management and minimized the necessity for physician intervention. The time saved was 15 minutes per day; the costs saved were estimated to be $5000 annually.     

Ectopic Hoxa2 induction after neural crest migration results in homeosis of jaw elements in Xenopus

Hox genes are required to pattern neural crest (NC) derived craniofacial and visceral skeletal structures. However, the temporal requirement of Hox patterning activity is not known. Here, we use an inducible system to establish Hoxa2 activity at distinct NC migratory stages in Xenopus embryos. We uncover stage-specific effects of Hoxa2 gain-of-function suggesting a multistep patterning process for hindbrain NC. Most interestingly, we show that Hoxa2 induction at postmigratory stages results in mirror image homeotic transformation of a subset of jaw elements, normally devoid of Hox expression, towards hyoid morphology. This is the reverse phenotype to that observed in the Hoxa2 knockout. These data demonstrate that the skeletal pattern of rhombomeric mandibular crest is not committed before migration and further implicate Hoxa2 as a true selector of hyoid fate. Moreover, the demonstration that the expression of Hoxa2 alone is sufficient to transform the upper jaw and its joint selectively may have implications for the evolution of jaws.     

Epidermal Patterning in Seedling Roots of Eudicotyledons

Three types of epidermal patterning occur in roots of angiosperms:in Type 1, all the epidermal cells can potentially produce roothairs (hair cells); in Type 2, asymmetric cell divisions produceshort cells that develop into hair cells and larger cells thatdo not (non-hair cells); and in Type 3, hair cells occur infiles separated by one to three files of non-hair cells. Inthe present study we examined the epidermal patternings of seedlingroots of 77 eudicotyledonous species from 43 families. We foundthat Type 1 patterning was the most common and no species hadType 2 patterning. Previously, Type 3 epidermal patterning hadbeen described only in the family Brassicaceae. In additionto the Brassicaceae (including the Capparaceae), we found Type3 patterning in the Brassicales families Limnanthaceae and Resedaceae,whereas the other Brassicales families we examined, Caricaceaeand Tropaeolaceae, had Type 1 patterning. We also found Type3 patterning in six families of the Caryophyllales sensu lato:Amaranthaceae, Basellaceae, Caryophyllaceae, Plumbaginaceae,Polygonaceae and Portulacaceae. However, the family Cactaceae,which is also in this order, had Type 1 patterning. Only oneother species, Nemophila maculata(Boraginaceae), had Type 3patterning; the other two species that we examined in this familyhad Type 1 patterning. Type 3 patterning thus occurs more widelyin the eudicotyledons than was previously thought. Copyright2001 Annals of Botany Company Brassicales, Caryophyllales, eudicotyledons, epidermal patterning, phylogeny, root hairs, roots, seedlings     

Feeding rate of Diaptomus sicilis and its relation to selectivity and effective food concentration in algal mixtures and in Lake Michigan

The concept of effective food concentration (EFC), a means ofpredicting food consumption from selectivity and food concentrationdata, is explained, tested, and applied to understanding foodconsumption by the freshwater copepod Diaptomus sicilis on mixturesof algae of different sizes and on Lake Michigan seston. Experimentson mixtures of different sized Chlamydomonas spp. showed thatselection (W') was an invariant function of particle size whenthe algae were counted microscopically. When the Coulter counterwas used, a more variable pattern of selectivity — similarto the peak tracking response reported by some investigators- was obtained. This was due to bias of zooplankton-producedparticles. Size-selective selectivity coefficients (W') wereused to weight the food concentration in each size categoryand the weighted values summed to give EFC. Food consumptionin experiments with seston and with cultured algae was betterdescribed by EFC than by total food concentration (TFC), theunweighted sum. Moreover, use of EFC diminished the magnitudeof the apparent threshold concentration required for feedingto commence. Although selectivity in algal mixtures and lakeseston was approximately the same, the food consumption versusEFC curve saturated more quickly for the algal mixtures thanfor the lake seston. Since expression of food concentrationas EFC allowed direct comparison of experiments having differentparticle-size spectra of food, we concluded the difference resultedfrom the lower food quality of lake seston, that is, its lowerdigestibility and sensory quality for zooplankton capture. ¹GLERL Contribution No. 368 ²Also Division of Biological Sciences, University of Michigan,Michigan, USA