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PubMed1991

SESAM: a relational database for structure and sequence of macromolecules.

A system is described that provides ways of integrating data on protein structure, sequence, and survey results, with molecular graphics and molecular mechanics software. Its major component is the relational database SESAM, presently implemented under the commercial package SYBASE. By design, the database allows full integration--within the same data organization--of raw data on protein structure, sequence, ligands, and heterogroups, obtained from the Brookhaven Protein Databank, with pure sequence information available from other databanks such as SWISS-PROT. It contains in addition higher level descriptions of structural and topological properties, as well as survey results, obtained by executing specialized computer programs. Aside from the very useful attribute of closely combining structural and nonstructural information, other important features distinguish it from analogous systems developed elsewhere. It includes a molecular dictionary with complete description of geometric properties and energy parameters used in modeling and conformational energy calculations. Using this dictionary, structural data are validated by checking for localized inconsistencies in atomic coordinates, atomic symbols, chirality definitions, and flagging errors and incomplete entries. Because of both the dictionary and the validation procedures, SESAM can be readily interfaced with conventional molecular graphics and mechanics software packages, or with other specialized application programs. With the aid of appropriate interfaces, data access is sufficiently fast for SESAM to be interrogated interactively. Prototypes of user interfaces, as well as an interface with the molecular graphics package BRUGEL, are described and the power of the system is illustrated in applications such as homology-based protein modeling, computer-aided protein design, protein structure predictions, analysis of local structure motifs, and of relationships between protein sequence and structure.

Amino Acid Sequence↗

PubMed1997

Design considerations for small, special-system developmental databases

Small developmental databases, devoted to special systems and run by a normal research laboratory, differ qualitatively as well as quantitatively from larger databases described elsewhere in this volume. Resource limits set different optimum balances between computing elegance and ease of construction, while flexibility of design and semantics often assume greatest importance because specialist research databases are most useful when understanding of the biology is partial and still evolving. In this article we discuss the main considerations when building a small database-scope, access, data input, storage, searching and semantics-and illustrate them with examples of real working databases.Copyright 1997 Academic Press Limited Copyright 1997Academic Press Limited

Journal Article↗

PubMed1975

A method for the identification and quantitative investigation of denatured proteins in mixtures based on computer comparison of amino-acid patterns.

A procedure is described in which stepwise regression is adapted to permit comparison of the amino-acid pattern from a composite sample with those of simple substances arranged in an easily accessible data bank. The computer program automatically selects from the bank those proteins whose amino-acid patterns best correspond to that of the sample, and calculates the proportion of the proteins contained in the mixture. The procedure is applicable to food analytical problems that involve the identification and determination of proteins in mixtures, and also to situations in which the properties of the proteins have been altered by denaturation or enzymatic degradation. The determination is limited to 3-4 proteins in the mixture.

Amino Acids↗

PubMed1995

A managed care workstation for support of ambulatory care in Veterans Health Administration medical centers.

This paper describes the development of a Managed Care Workstation for implementation in a Department of Veterans Affairs hospital. Each VA hospital information system contains a wealth of information in a comprehensive and well integrated M database, however, a clinician's access to the information is hampered by a lack of usable database tools. The Managed Care Workstation is designed to enhance access to VA databases. The workstation uses M (Mumps) and SQL to present the VA's M hierarchical database as relational tables on the workstation. This work reveals the benefits of using a SQL-M workstation to access data contained in an M based hospital information system and demonstrates how the workstation architecture supports the information model necessary for management of patient care outcomes.

Ambulatory Care Information Systems↗

PubMed2002

Systematic comparison of different algorithms for apnoea detection based on electrocardiogram recordings.

Sleep apnoea is a common disorder that is usually diagnosed through expensive studies conducted in sleep laboratories. Sleep apnoea is accompanied by a characteristic cyclic variation in heart rate or other changes in the waveform of the electrocardiogram (ECG). If sleep apnoea could be diagnosed using only the ECG, it could be possible to diagnose sleep apnoea automatically and inexpensively from ECG recordings acquired in the patient's home. This study had two parts. The first was to assess the ability of an overnight ECG recording to distinguish between patients with and without apnoea. The second was to assess whether the ECG could detect apnoea during each minute of the recording. An expert, who used additional physiological signals, assessed each of the recordings for apnoea. Research groups were invited to access data via the world-wide web and submit algorithm results to an international challenge linked to a conference. A training set of 35 recordings was made available for algorithm development, and results from a test set of 35 different recordings were made available for independent scoring. Thirteen algorithms were compared. The best algorithms made use of frequency-domain features to estimate changes in heart rate and the effect of respiration on the ECG waveform. Four of these algorithms achieved perfect scores of 100% in the first part of the study, and two achieved an accuracy of over 90% in the second part of the study.

Algorithms↗

PubMed2002

Incidence and determinants of migraine prophylactic medication in the Netherlands.

OBJECTIVE: To estimate and examine the incidence and determinants of initiation of migraine-prophylactic therapy as well as the corresponding drug of choice over a period of 5 years following the use of specific abortive migraine drugs. METHODS: By accessing data from a large prescription database, an identification of patients treated with ergotamine or a triptan from 1 January 1994 to 31 December 1998 was made. The cumulative incidence of initiation of migraine-prophylactic drugs (beta-blockers, serotonin antagonists, specific calcium antagonists, amitriptyline, clonidine and valproic acid) was estimated in patients following the use of ergotamine or a triptan. An assessment of the migraine-prophylactic drug of first choice was also performed. A few baseline determinants were analysed to highlight a possible association with the initiation of prophylactic therapy: age, gender, type of abortive migraine drug use and year of prophylaxis. Additional determinants included the analysis of drug-utilisation patterns, such as the consumption and switch patterns of abortive migraine drug use as well as co-medication use prior to prophylaxis. For this particular analysis a reference group (patients not having commenced prophylaxis) was selected from the initial study population. RESULTS: After having satisfied eligibility criteria, a total of 3999 first-time users of ergotamine and triptans were included of whom 479 (12%) had initiated migraine-prophylactic therapy. This corresponded to an incidence density of 6.0 per 100 person-years and was highest for patients younger than 45 years and for multiple abortive migraine drug users. The incidence fell considerably from 12.0 person-years in 1994 to 5.1 person-years in 1998. More than half of the patients had been prescribed a beta-blocker as the migraine-prophylactic drug of first choice by both general practitioners and neurologists. The use of antidepressants and/or benzodiazepines and oral contraceptives was significantly higher in patients starting prophylaxis compared with those who did not. The consumption of abortive migraine drug use (4.0 defined daily doses per month vs 3.7 defined daily doses per month), and switch patterns (27.1% vs 30.9%) were similar for patients starting and not starting prophylaxis. CONCLUSION: The overall incidence of initiation of migraine-prophylactic therapy following the use of abortive migraine analgesics was 6.0% per year and fell considerably during 5 years of the study. Beta-blockers were the migraine-prophylactic drugs of first choice for general practitioners and neurologists. In our study we could not determine any factors clearly associated with the initiation of migraine prophylaxis besides prior use of antidepressants and benzodiazepines. A future assessment of the usage patterns of migraine-prophylactic drugs may provide detailed information concerning the effectiveness and tolerability.

Adrenergic beta-Antagonists↗

PubMed2001

[Electronic versus paper-based patient records: a cost-benefit analysis].

BACKGROUND: The aim of this study is to compare the costs and benefits of electronic, paperless patient records with the conventional paper-based charts. METHODS: Costs and benefits of planned electronic patient records are calculated for a University eye hospital with 140 beds. Benefit is determined by direct costs saved by electronic records. RESULTS: In the example shown, the additional benefits of electronic patient records, as far as they can be quantified total 192,000 DM per year. The costs of the necessary investments are 234,000 DM per year when using a linear depreciation over 4 years. In total, there are additional annual costs for electronic patient records of 42,000 DM. Different scenarios were analyzed. By increasing the time of depreciation to 6 years, the cost deficit reduces to only approximately 9,000 DM. Increased wages reduce the deficit further while the deficit increases with a loss of functions of the electronic patient record. However, several benefits of electronic records regarding research, teaching, quality control and better data access cannot be easily quantified and would greatly increase the benefit to cost ratio. CONCLUSION: Only part of the advantages of electronic patient records can easily be quantified in terms of directly saved costs. The small cost deficit calculated in this example is overcompensated by several benefits, which can only be enumerated qualitatively due to problems in quantification.

Cost-Benefit Analysis↗

PubMed2002

Workflow optimization: current trends and future directions.

In an attempt to maximize productivity within the medical imaging department, increasing importance and attention is being placed on workflow. Workflow is the process of analyzing individual steps that occur during a single event, such as the performance of an MRI exam. The primary focus of workflow optimization within the imaging department is automation and task consolidation, however, a number of other factors should be considered including the stochastic nature of the workload, availability of human resources, and the specific technologies being employed. The purpose of this paper is to determine the complex relationship that exists between information technology and the radiologic technologist, in an attempt to determine how workflow can be optimized to improve technologist productivity. This relationship takes on greater importance as more imaging departments are undergoing the transition from film-based to filmless operation. A nationwide survey was conducted to compare technologist workflow in film-based and filmless operations, for all imaging modalities. The individual tasks performed by technologists were defined, along with the amount of time allocated to these tasks. The index of workflow efficiency was determined to be the percentage of overall technologist time allocated to image acquisition, since this is the primary responsibility of the radiologic technologist. Preliminary analysis indicates technologist workflow in filmless operation is enhanced when compared with film-based operation, for all imaging modalities. The specific tasks that require less technologist time in filmless operation are accessing data and retake rates (due to both technical factors and lost exams). Surprisingly, no significant differences were reported for the task of image processing, when comparing technologist workflow in film-based and filmless operations. Additional research is planned to evaluate the potential workflow gains achievable through workflow optimization software, improved systems integration, and automation of advanced image processing techniques.

Efficiency, Organizational↗

PubMed2005

The impact of landsat satellite monitoring on conservation biology.

Landsat 7's recent malfunctioning will result in significant gaps in long-term satellite monitoring of Earth, affecting not only the research of the Earth science community but also conservation users of these data. To determine whether or how important Landsat monitoring is for conservation and natural resource management, we reviewed the Landsat program's history with special emphasis on the development of user groups. We also conducted a bibliographic search to determine the extent to which conservation research has been based on Landsat data. Conservation biologists were not an early user group of Landsat data because a) biologists lacked technical capacity--computers and software--to analyze these data; b) Landsat's 1980s commercialization rendered images too costly for biologists' budgets; and c) the broad-scale disciplines of conservation biology and landscape ecology did not develop until the mid-to-late 1980s. All these conditions had changed by the 1990s and Landsat imagery became an important tool for conservation biology. Satellite monitoring and Landsat continuity are mandated by the Land Remote Sensing Act of 1992. This legislation leaves open commercial options. However, past experiments with commercial operations were neither viable nor economical, and severely reduced the quality of monitoring, archiving and data access for academia and the public. Future satellite monitoring programs are essential for conservation and natural resource management, must provide continuity with Landsat, and should be government operated.

Biology↗

PubMed1992

The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding.

The theory, assumptions and limitations are outlined for a simple protein engineering approach to the problem of the stability and pathway of protein folding. It is a general procedure for analysing structure-activity relationships in non-covalent bonding, including enzyme catalysis, that relates experimentally accessible data to changes in non-covalent bonding. Kinetic and equilibrium measurements on the unfolding and refolding of mutant proteins can be used to map the formation of structure in transition states and folding intermediates. For example, the ratio of the changes in the activation energy of unfolding and the free energy of unfolding on mutation is measured to give a parameter phi. There are two extreme values of phi that are often found in practice and may be interpreted in a simple manner. A value of phi = 0 implies that the structure at the site of mutation is as folded in the transition state as it is in the folded state. Conversely, phi = 1 shows that the structure at the site of mutation is as unfolded in the transition state as it is in the unfolded structure. Fractional values of phi are more difficult to interpret and require a more sophisticated approach. The most suitable mutations involve truncation of side-chains to remove moieties that preferably make few interactions with the rest of the protein and do not pair with buried charges. Fractional values of phi found for this type of mutation may imply that there is partial non-covalent bond formation or a mixture of states. The major assumptions of the method are: (1) mutation does not alter the pathway of folding; (2) mutation does not significantly change the structure of the folded state; (3) mutation does not perturb the structure of the unfolded state; and (4) the target groups do not make new interactions with new partners during the course of reaction energy. Assumptions (2) and (3) are not necessarily essential for the simple cases of phi = 0 or 1, the most common values, since effects of disruption of structure can cancel out. Assumption (4) may be checked by the double-mutant cycle procedure, which may be analysed to isolate the effects of just a pair of interactions against a complicated background. This analysis provides the formal basis of the accompanying studies on the stability and pathway of folding of barnase, where it is seen that the theory holds very well in practice.

Bacterial Proteins↗

PubMed1980

The measurement of distortion: concluding remarks.

The means by which fine measurements can be made and distortions computed have been discussed in this series. However, the fact remains that research of this nature is time consuming and demanding. At every step, and in all machined components, care must be taken to eliminate local inaccuracies. Precalibration, postcalibration, and an ongoing program of maintenance are essential if quality results are to be anticipated. An attempt has been made to introduce automatic reading devices with the ability to compute distortions by having the raw data sent directly to a computer. This latter step can be highly dangerous unless at least one "test case" can be programmed into the system as a check on the data access and computational procedures. These test cases should simulate as closely as possible the actual computational requirements of the system, in order that all program "bugs" be corrected before the research is run. In this area, the GIGO rule, "Garbage in-Garbage out," holds true. Unfortunately, if the computational errors are small and of the order of magnitude of the measured distortions the researcher can accept the results without realizing there is a computational problem.

Chemical Phenomena↗

PubMed1987

A device for spike train sampling with built-in memory.

The described interface to a digital computer measures interspike interval durations with a resolution of 10 microseconds. A built-in first-in first-out (FIFO) memory relieves the host computer from frequent I/O intensive tasks. The internal FIFO buffer can store up to 512 data words (wordlength is 16 bit) and works on the dual-port principle. This way the acquisition of a neuronal spike train is completely independent of the computer's simultaneously ongoing data access. A simple handshake protocol between the interface and the computer prevents any overhead communication. The buffer architecture of the instrument releases the host computer from high speed I/O handling schemes like real-time, clock-controlled, polling or interrupt procedures, that would request assembly language support. The body of two software, driver routines in the BASIC and the PASCAL language is presented. A complete and detailed schematic diagram of the circuitry is included.

Computer Literacy↗

PubMed1990

A workstation interface for measuring interspike intervals.

A method is presented for collecting and storing, singly or in parallel, interspike intervals to a DOS-based workstation as a background process. The method comprises digital electronics and low-level software effecting an interface mechanism from the receipt of digital spike pulses to the recording of user-accessible data arrays readily manipulable by high-level software. Functional details, requirements, and application to parital cortex single unit physiology are discussed.

Action Potentials↗

PubMed1984

A computerized record and verify system for radiation treatments.

We have developed a general purpose, comprehensive, and highly reliable computerized Record and Verify System to detect and prevent mistakes in the delivery of external beam radiation therapy. This system helps prevent accidental delivery of dangerous dose, improves quality control, and provides invaluable record keeping and report generating capabilities. Currently, treatment machine and couch parameter settings of four different machines are monitored by the system and compared with prescribed values. The system inhibits a machine from being turned on if the settings do not agree with the prescribed values to within specified maximum permissible deviations. The system is user-friendly and provides useful, complete, and easily accessible data. We describe many aspects of the system including hardware, software, data, and operation, and we conclude with a brief discussion of clinical experience and preliminary data.

Computers↗

PubMedDate not supplied

Approaching the millennium: perinatal problems and software solutions.

Strategic planning for rational development of perinatal computing capabilities for the year 2000 should be driven by anticipated trends in (1) the health care business, (2) computer technology and (3) medicine, as well as (4) the needs of perinatal practitioners. In the USA, health care is the fastest growing segment of the economy. This will produce increasing attention from hardware and software developers, and vendors, and will lead to a proliferation of computing platforms, operating systems and specific medical application software. Desktop computers, already capable of 20 million instructions per second (MIPS) with massive storage capacities, will continue to evolve and fall in price. Increasingly, perinatologists will develop software packages to facilitate patient care in their own environments. All of these trends will lead to severe fragmentation in medical computing. Simultaneously, however, the need for integrated institutional computer-based data access for quality assurance and fiscal and operations management will increase. Perinatal care will be more regionalized, complex and rigorous with new clinical trial- and effectiveness research-based interventions, as well as molecular diagnosis and therapy. To practice appropriately, clinicians will need to be familiar with computer capabilities. Having been exposed to computer-aided instruction (CAI) at the undergraduate and postgraduate levels, they will except on-line access to detailed and accurate patient information with linkage to laboratory, radiology and other medical databases, as well as to reference databases, such as Medlines and the Oxford Database of Perinatal Trials. Artificial intelligence (AI) software may support perinatal decision making; computerized professional and facility billing will be available.

Forecasting↗

PubMed1987

Human leukocyte differentiation antigens: monoclonal antibody computer databases as a tool for the future.

The immunofluorescence results of the Third International Workshop on Human Leukocyte Antigens have been used as the basis of a microcomputer database system. As well as providing a convenient means to access data on individual antibodies and the antigens identified by the Workshop (designated as 'clusters of differentiation' or CD antigens), it can be used to help characterize and identify new monoclonal antibodies. The ability to continue adding to this database means that it should become an increasingly powerful tool for both immunologists and haematologists. The philosophy behind the methods described should also be of interest to anyone making monoclonal antibodies to differentiation antigens.

Antibodies, Monoclonal↗

PubMed2026

The genomic landscape of HER2 negative metastatic breast cancer with loss of estrogen and progesterone receptors.

INTRODUCTION: Loss of estrogen receptor (ER) and/or progesterone receptor (PR) might occur during the metastatic progression of ER positive and HER2 negative (ER+/HER2-) breast cancer (BC), but the underpinning molecular alterations remain elusive. We explored the genomic context of HER2- tumors with ER and/or PR loss to investigate potential drivers and actionable alterations that might help personalize treatment of ER+/HER2- BC. METHODS: We accessed data from metastatic HER2- BC included in the MSK-2018 dataset to compare outcome, tumor characteristics and genomic alterations of BC with loss of ER (ER+/-, n = 66) to those maintaining ER positivity (ER+/+, n = 364) or ER negativity (ER-/-, n = 50). We also compared metastatic ER+/+ BC with loss of PR (PR+/-, n = 111) to those maintaining PR positivity (PR+/+, n = 192) or PR negativity (PR-/-, n = 41). RESULTS: In line with previous reports, ER+/- BC was associated with aggressive clinico-pathological characteristics and poor outcome. ER+/- BC showed significantly higher frequency of TP53 and RB1 mutations and lower frequency of PIK3CA and GATA3 mutations compared to ER+/+. ER+/- or PR+/- status was mutually exclusive with ESR1 mutations and was associated with a significantly higher tumor mutational burden. Moreover, ER+/- BC were enriched in driver alterations in the genes of the Notch and Retinoblastoma pathways and showed a significantly lower frequency of level 1 actionable alterations according to OncoKB. CONCLUSIONS: Loss of ER and/or PR may identify a distinct evolutionary trajectory of ER+/HER2- metastatic progression, largely non-overlapping with ESR1-mutant endocrine resistance. Further studies on matched primary and metastatic samples are warranted.

Humans↗

PubMed2026

Balancing growth and immunity of potato by humidity-dependent expression of a late blight resistance gene.

Inducible expression of resistance genes is an effective approach to balance plant growth and immunity, thus facilitating the development of disease-resistant crop cultivars. While pathogen-responsive and immunity-related promoters have been adopted for this purpose, alternative design strategies remain to be explored. High relative humidity (RH) has been recognized as a crucial permissive environmental condition for the occurrence of devastating plant diseases including tomato and potato late blight. Here, we identified humidity-activated cis-regulatory elements (HAEs) in Solanum lycopersicum through an integrative analysis of transcriptomics and chromatin accessibility data. Sequence homology-inferred HAEs in S. tuberosum can predict humidity-elicited changes in downstream gene expression. Transgenic S. tuberosum lines expressing a late blight resistance gene driven by an artificial humidity-inducible promoter containing a natural S. tuberosum HAE were generated. These transgenic lines exhibited comparable late blight resistance levels to the lines overexpressing the same resistance gene in controlled zoospore inoculation bioassays, while avoiding growth suppression and tuber yield penalties in common garden experiments. Our findings highlight the importance of plant cis-regulatory elements in the transcriptional responses to high RH and provide a proof-of-concept for a humidity-inducible environment-responsive resistance gene deployment strategy to engineer disease-resistant crop cultivars without compromising growth and yield.

Phytophthora infestans↗