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PubMed1994

An overview of software assessment.

Many engineering systems, especially those required to be particularly dependable, traditionally undergo inspections and assessments of safeness and fitness for purpose. Often some form of 'certificate' is provided by the assessment authority. To an increasing degree these systems are beginning to contain software components. The question naturally arises: how can the software component be assessed? This paper explores the feasibility and limitations of software assessment and the link between the process of developing the software and the quality of the resulting software product.

Europe↗
PubMed2026

A genome-wide coverage-based pipeline for the identification of host-derived candidate DNA biomarkers from cell-free blood.

We have created a new data-analysis pipeline for the discovery of host-specific candidate DNA biomarkers derived from sequencing data of cell-free blood. Unlike approaches that rely on specific molecular or genetic signatures, our method leverages the coverage distribution of cell-free DNA sequences mapped to a reference genome, applying statistical analyses to identify informative short genomic regions for biomarker discovery. The pipeline is applicable to diverse diseases and can be used to analyze cell-free DNA sequences from plasma or serum to identify candidate biomarkers that are characteristic of disease states in mammals. Core functionalities were developed in Java and integrated with open-source software tools for the preprocessing of raw sequencing data, complemented by Python scripts for the machine-learning analysis and statistical validation. The pipeline is designed for HPC use and users can access the pipeline through a Galaxy workflow, which offers a user-friendly web interface for input selection prior to execution and analysis progress monitoring. Performance tests, carried out using duplicate sets of COVID-19 samples and controls, showed linear scalability of execution time with an increasing dataset size, as well as a substantial reduction in execution time through parallelized computation, whereby each HPC node is used to process the data of one chromosome. Further statistical tests confirmed the quality of the pipeline's results by showing that the set of identified candidate biomarkers remained stable across varying dataset sizes.

Biomarkers↗
PubMed2002

Depression and somatization in patients with temporomandibular disorders.

STATEMENT OF PROBLEM: Psychological and behavioral traits may be important for the diagnosis and management of orofacial pain. PURPOSE: This study compared the levels of depression and somatization in patients in single and multiple research diagnostic criteria for temporomandibular disorders (RDC/TMD) diagnostic groups. MATERIAL AND METHODS: The RDC/TMD was established to allow standardization and replication of research into the most common forms of muscle- and joint-related research and is divided into 2 axes: axis I, clinical TMD, and axis II, pain-related disability and psychological status. One hundred seventeen patients (28 male and 89 female; mean age, 33.3 +/- 10.3 years) with RDC/TMD-defined clinical TMD were selected. The RDC/TMD history questionnaire and examination forms were input directly into computers with the use of a software program developed at the National University of Singapore (NUS TMDv1.1 software). Axis I and II variables were generated online and automatically archived for statistical analysis. Patients were subsequently classified into 7 groups based on the presence of the various RDC/TMD axis I diagnostic groups: group A, myofascial pain only (group I); group B, disk displacement only (group II); group C, other joint conditions such as arthralgia, osteoarthritis, and osteoarthrosis only (group III); group D, myofascial pain and disk displacement (groups I and II); group E, myofascial pain and other joint conditions (groups I and III); group F, disk displacement and other joint conditions (groups II and III); and group G, myofascial pain, disk displacement, and other joint conditions (groups I, II, and III). Differences in mean Symptom Checklist-90 scores between groups were compared by analysis of variance/Scheffé tests to contrast depression and somatization levels between the various axis I diagnostic groups (alpha=.05). RESULTS: The frequencies of the different groups were as follows: group A, 26.5%; group B, 29.9%; group C, 12.8%; group D, 6.0%; group E, 13.7%; group F, 4.3%; and group G, 6.8%. Approximately 39% of patients were clinically depressed, and 55% had moderate to severe somatization. Differences in mean depression and somatization with pain item scores were significant between groups (P<.05). CONCLUSION: Within the limitations of this study, patients diagnosed with myofascial pain and other joint conditions (group E) had significantly higher levels of depression (P=.03) and somatization (P=.03) than patients diagnosed with only disk displacements (group B).

Adult↗
PubMedDate not supplied

Modelling of age-related bone loss using cross-sectional data.

BACKGROUND: Current applications of bone mineral density (BMD) data in age studies are not free of certain drawbacks. Since it is well established that age-related patterns of BMD changes involve three distinct periods (bone acquisition in youth, stabilization at maturity, and decrease with ageing), adjusting for age via an inappropriate mathematical function may lead to inconsistencies and wrong conclusions. HYPOTHESIS: The piecewise model, which encompasses the above three periods, will accurately describe the BMD dependence on age. OBJECTIVE: To examine age-related patterns of BMD changes using a number of possible mathematical functions and to find among them the best-fitting function. Next, to test whether the chosen function is universally applicable or if there are diverse population-specific functions. MATERIAL AND METHODS: Thirteen ethnic samples from various regions of Europe and Asia, assigned into five ethnic-geographic groups, were examined. The total sample included 2430 males and 2515 females. Compact BMD of hand phalanges was measured by photodensitometry from plain radiographs of each individual studied. Statistical software was developed for the purposes of the present study; this software gave a maximum likelihood of the parameter estimates for various statistical models (functions). RESULTS: In all samples of sufficient size and representative age range, a two-interval function was found as the best fitting and most parsimonious model to describe the BMD age-related changes. This two-interval function was characterized by age-related bone mass increase, positive slope beta(1s) in young age or a plateau (beta(1s) = 0, i.e. no age-related changes) until a sex-specific age threshold, T(0), after which annual bone loss ensued with a slope coefficient beta(2s). Threshold of BMD loss in women of different ethnic groups ranged between 37.85 and 47.77 years, and roughly coincided with perimenopausal age. In males, the age T(0) varied between 27.85 and 49.07 years. The ensuing cortical bone loss appeared to be linear in both sexes, averaging between 0.51% and 1.15% in men and between 0.74% and 1.77% per year of young age BMD value in females. CONCLUSIONS: The change of phalangeal BMD with age may be best described by a two-interval function, regardless of sex and ethnic background. However, specific parameter estimates depend both on gender and ethnic affiliation. This study has yielded a well-fitted model of BMD dependence on age suitable for further use in population studies.

Adolescent↗
PubMed2006

GNU polyxmass: a software framework for mass spectrometric simulations of linear (bio-)polymeric analytes.

BACKGROUND: Nowadays, a variety of (bio-)polymers can be analyzed by mass spectrometry. The detailed interpretation of the spectra requires a huge number of "hypothesis cycles", comprising the following three actions 1) put forth a structural hypothesis, 2) test it, 3) (in)validate it. This time-consuming and painstaking data scrutiny is alleviated by using specialized software tools. However, all the software tools available to date are polymer chemistry-specific. This imposes a heavy overhead to researchers who do mass spectrometry on a variety of (bio-)polymers, as each polymer type will require a different software tool to perform data simulations and analyses. We developed a software to address the lack of an integrated software framework able to deal with different polymer chemistries. RESULTS: The GNU polyxmass software framework performs common (bio-)chemical simulations-along with simultaneous mass spectrometric calculations-for any kind of linear bio-polymeric analyte (DNA, RNA, saccharides or proteins). The framework is organized into three modules, all accessible from one single binary program. The modules let the user to 1) define brand new polymer chemistries, 2) perform quick mass calculations using a desktop calculator paradigm, 3) graphically edit polymer sequences and perform (bio-)chemical/mass spectrometric simulations. Any aspect of the mass calculations, polymer chemistry reactions or graphical polymer sequence editing is configurable. CONCLUSION: The scientist who uses mass spectrometry to characterize (bio-)polymeric analytes of different chemistries is provided with a single software framework for his data prediction/analysis needs, whatever the polymer chemistry being involved.

Biopolymers↗
PubMed2004

Tonal vocalizations in a noisy environment: an approach to their semi-automatic analysis and examples of its application.

Vocalizations with an emphasized fundamental are common in many species of animals. Such calls can presumably be sufficiently described by measures of their fundamental shape or 'contour'. Here we describe a software we developed to analyze such vocalizations semi-automatically. The software is particularly designed to cope with vocalizations recorded in a noisy environment. Some of the algorithms implemented (e.g. signal detection, contour detection, contour measurement, validation) and some preliminary applications dealing with calls of different species of birds are presented. Finally, we briefly discuss the possible significance of such vocalizations.

Animals↗
PubMed1995

MARIAN: an analysis tool for the assessment of left ventricular function measured by velocity encoding MRI.

Velocity encoding MRI is a new non-invasive technique for measuring cardiac blood flow velocities. Flow in the three directions of space can be measured during the entire heart cycle. However, the analysis of large amount of data obtained from this technique requires specialized computational software packages to provide physicians with efficient analysis tools. A data visualization software package named Magnetic Resonance Imaging Analyzer (MARIAN) was developed. This software package uses visualization, animation, analysis, and computational tools adapted to time series of cardiac MRI data files, all accessible through a sophisticated graphics user interface. MARIAN was used as a tool for the analysis of the left heart blood flow patterns in two groups of human subjects: ten volunteers and eight patients. The patients were diagnosed with incapacitating angina pectoris and previous left ventricular myocardial infarction. Vector plot animations of the left atrial flow were realized for all volunteer examinations. The temporal flow velocity profiles were sampled at the tips of the mitral leaflets and in the lumen of the right upper pulmonary vein, when possible. The isovolumic relaxation time (IVRT) was estimated. The following flow parameters were obtained from the velocity profiles: at the mitral valve, the early diastolic E-wave, the late diastolic A-wave, the time of occurrence of the E- and A- waves; at the right upper pulmonary vein, the systolic S-wave, the early diastolic D-wave and the reverse late diastolic R-wave. The results obtained were consistent with previous studies using similar MRI techniques. Compared to the control group, the patient group exhibited higher isovolumic relaxation time, a lower peak E-wave, and a lower D-wave. MARIAN thus provided a fast, efficient and accurate data visualization tool for the analysis of human data.

Adult↗
PubMed2002

HapScope: a software system for automated and visual analysis of functionally annotated haplotypes.

We have developed a software analysis package, HapScope, which includes a comprehensive analysis pipeline and a sophisticated visualization tool for analyzing functionally annotated haplotypes. The HapScope analysis pipeline supports: (i) computational haplotype construction with an expectation-maximization or Bayesian statistical algorithm; (ii) SNP classification by protein coding change, homology to model organisms or putative regulatory regions; and (iii) minimum SNP subset selection by either a Brute Force Algorithm or a Greedy Partition Algorithm. The HapScope viewer displays genomic structure with haplotype information in an integrated environment, providing eight alternative views for assessing genetic and functional correlation. It has a user-friendly interface for: (i) haplotype block visualization; (ii) SNP subset selection; (iii) haplotype consolidation with subset SNP markers; (iv) incorporation of both experimentally determined haplotypes and computational results; and (v) data export for additional analysis. Comparison of haplotypes constructed by the statistical algorithms with those determined experimentally shows variation in haplotype prediction accuracies in genomic regions with different levels of nucleotide diversity. We have applied HapScope in analyzing haplotypes for candidate genes and genomic regions with extensive SNP and genotype data. We envision that the systematic approach of integrating functional genomic analysis with population haplotypes, supported by HapScope, will greatly facilitate current genetic disease research.

Algorithms↗
PubMed1991

Microcomputer software simulating problems in Rh immune globulin prophylaxis and hemolytic disease of the newborn.

Our purpose was to develop educational software that would simulate laboratory investigation of problems in Rh immune globulin prophylaxis and hemolytic disease of the newborn. An interactive, branching style program was developed using a 256K Penonal Computer (International Business Machines, Boca Raton, FL). The software has been used in over 125 institutions for preprofessional and continuing professional education.

Journal Article↗
PubMed1995

A portable, GUI-based, object-oriented client-server architecture for computer-based patient record (CPR) systems.

Software applications for computer-based patient records require substantial development investments. Portable, open software architectures are one way to delay or avoid software application obsolescence. The Clinical Management System at Temple University School of Dentistry uses a portable, GUI-based, object-oriented client-server architecture. Two main criteria determined this approach: preservation of investment in software development and a smooth migration path to a Computer-based Patient Record. The application is separated into three layers: graphical user interface, database interface, and application functionality Implementation with generic cross-platform development tools ensures maximum portability.

Humans↗
PubMed2006

An extensible spatial and temporal epidemiological modelling system.

BACKGROUND: This paper describes the Spatiotemporal Epidemiological Modeller (STEM) which is an extensible software system and framework for modelling the spatial and temporal progression of multiple diseases affecting multiple populations in geographically distributed locations. STEM is an experiment in developing a software system that can model complex epidemiological scenarios while also being extensible by the research community. The ultimate goal of STEM is to provide a common modelling platform powerful enough to be sufficient for all modelling scenarios and extensible in a way that allows different researchers to combine their efforts in developing exceptionally good models. RESULTS: STEM is a powerful modelling system that allows researchers to model scenarios with unmixed populations that are not uniformly distributed and in which multiple populations exist that are being infected with multiple diseases. It's underlying representational framework, a graph, and its software architecture allow the system to be extended by incorporating software components developed by different researchers. CONCLUSION: This approach taken in the design of STEM creates a powerful platform for epidemiological research collaboration. Future versions of the system will make such collaborative efforts easy and common.

Animals↗
PubMed2001

Volumetric computerized tomography as a measurement of periprosthetic acetabular osteolysis and its correlation with wear.

Osteolysis, which is considered to be a major source of morbidity following total hip joint replacement, has been notoriously difficult to measure accurately, particularly in the acetabular area. In order to study periacetabular osteolysis, specialized software for computerized tomography (CT) scan image analysis has been developed. This software (3D-CT) eliminates metal artifacts, allows three-dimensional segmentation of the CT image, and reconstructs the segmented image to provide an accurate representation and measurement of volume for osteolytic lesions. In the present study, 20 patients underwent periacetabular osteolytic volume determination using 3D-CT, functional assessment (using the Harris Hip Scale, the Western Ontario and McMaster University Osteoarthritis Index, and the short form 36 questionnaire), and two-dimensional analysis of volumetic polyethylene wear using digitalized plain films. Periacetabular osteolysis correlated directly with the polyethylene wear rate (relative risk [RR] = 0.494, P = 0.027). If one patient with an acetabular revision, one patient with recurrent dislocation, and one patient with a Biomet prosthesis are excluded, then the correlation between wear and osteolysis is improved (RR = 0.685, P = 0.002). In summary, the current study demonstrates both the feasibility of CT imaging of periacetabular osteolysis and the correlation between polyethylene wear and osteolytic volume, providing a potential outcome measure for clinical trials that are designed to examine interventions in this complex disease process.

Acetabulum↗
PubMed2003

[Clinical application of a software for the analysis of arterial blood gases graph in 231 patients with chronic obstructive pulmonary disease].

OBJECTIVE: To evaluate the clinical significance of a computer software for the analysis of arterial blood gases graph (ABGG) in chronic obstructive pulmonary disease(COPD). METHODS: The software was developed with Win98 as the operating platform and the visual software Delphi 5.0 from Borland Company, and it was used for evaluation of the changes in arterial blood gases (ABG) of 231 COPD cases. RESULTS: (1) With the software it took only (4.7+/-0.5)s to draw and analyze an ABGG of COPD patients during oxygen inhalation; the time was much shorter than manual analysis (90.2+/-4.9)s, P<0.001. (2) During acute attack, the distributions of the arterial blood gases parameters on ABGG were as follows: 55.4% of cases in the area of insufficient ventilation and deranged gas exchange (area 5), 22.9% of cases in the area of compensated ventilation and deranged gas exchange (area 4), 21.6% of cases in the area of excessive ventilation and deranged gas exchange (area 6). (3) When the COPD patient's condition improved, the location of ABG in ABGG shifted from area 5 to area 4 or area 6. The distributions of the arterial blood gases parameters on ABGG of 106 cases on admission were significantly different from those at the time of discharge. (4) With deterioration of patient's condition, it shifted to area 5. Before death, the arterial blood gases parameters were exclusively in the area 5. CONCLUSION: The computer software for ABGG shortened the time to draw and evaluate ABG during oxygen inhalation, and it could reflect the changes in patient's condition promptly.

Aged↗
PubMed2002

[Expert systems in gastroenterology].

Expert systems are the software systems developed by the application of the various intelligence, which could successfully compete to peoples-experts, and have the consultant function with the characteristics of the explanations and the advices in some specific domain. These are, in essence, the intelligent information systems, which consists several thousands of the rules from the definite problem field and which are capable to explain their decisions. The knowledge systems are lesser software systems, also developed by means of the technique of the artificial intelligence which are usually less successful in some field of knowledge of the experts. In the paper are presented the basic characteristics three most often applied expert systems in gastroenterology: Quick Medical Reference (QMR), HEPAT, ILIAD.

Diagnosis, Computer-Assisted↗
PubMed1999

Ergonomic automated anesthesia recordkeeper using a mobile touch screen with voice navigtion.

OBJECTIVE: To develop an ergonomically designed computerized recordkeeping tool for anesthesiologists that allows the clinician to maintain visual contact with the patient while performing recordkeeping. METHODS: To simplify the human interface software, we developed two general use software components. All purpose menu type 1 (APM1) was used for entering events using a tree structured menu. APM1 was designed to adapt to the limits of human memory, by using Miller's rule of 7 to guide the input process. APM1 can be considered to be a three-dimensional table list consisting of 7 vertical and 7 horizontal choices, which has further 5 tree-structured divergences. APM1 is also completely configurable by the user. All purpose menu 2 (APM2) was used to implement the system-initiated human interface where the system will prompt the user by voice for each entry. When users touch a key on APM1 and APM2, the system was designed to respond with a voice prompt. A touch-screen was also utilized and designed to fit the anesthesia machine. The screen is equipped with a small speaker for voice response and a microphone for voice recognition. The positions of the screen are adjustable supported by a long flexible limb (85 cm). RESULTS: After improving the design, systems were assembled for 10 operating rooms. Of the multiple features of the VOCAAR user interface, the following were well accepted by users and employed daily: touch-screen input, and voice response. The noncompulsory use rate was 87% during the initial 2 weeks, increased to 94% after 2 weeks and 100% after two months. The mean sound emission by voice response (n = 10, mean +/- SD) was 8.2 +/- 2.3 dB at the main anesthetist site (35 cm from the speaker mounted on the touch-screen), 2.2 +/- 1.3 dB at the staff site (1.5 m from the touch-screen), which was only audible for anesthesiologist but for surgeon. DISCUSSION: An EARK system was designed to allow the user to maintain visual contact with the patient while performing recordkeeping tasks. The combination of a mobile touch screen and voice response/recognition facilitated the design goals of the system. Although the system has enjoyed universal clinical acceptance, the voice functions remain too limited to satisfy the needs of a completely handsfree user interface. Enhancements to voice recognition technology will offer the potential for improved functionality. Additional research is also needed to better define the relationship between vigilance and visual contact with the patient.

Anesthesiology↗
PubMedDate not supplied

A case study of the evolving software architecture for the FDA generic drug application process.

This primary goal of this project was to develop a software architecture to support the Food and Drug Administration (FDA) generic drug application process by making it more efficient and effective. The secondary goal was to produce a scalable, modular, and flexible architecture that could be generalized to other contexts in interorganizational health care communications. The system described here shows improvements over the old system for the generic drug application process for most of the defined design objectives. The modular, flexible design that produced this new system offers lessons for the general design of distributed health care information systems and points the way to robust application frameworks that will allow practical development and maintenance of a distributed infrastructure.

Drug Approval↗
PubMed2005

"Non-trivial pursuit of physiology".

This article describes a novel way to conduct a review session that combines interactivity, team learning, and peer-to-peer instruction. It uses the format of the familiar game "Trivial Pursuit." To facilitate the game process and to encourage its use by others, we have developed custom software. It allows an instructor to run the game from the podium and to input questions/answers for a particular block or other area to be reviewed. In addition to the software itself, the online supplement (http://advan.physiology.org/cgi/content/full/00031.2004/DC1) contains 100 sample questions and answers written for the cardiovascular physiology review session. The developed game format and its software add to the arsenal of educational tools that can be used to enrich students' learning experiences.

Cardiology↗