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PubMed1999

Genome analysis: Assigning protein coding regions to three-dimensional structures.

We describe the results of a procedure for maximizing the number of sequences that can be reliably linked to a protein of known three-dimensional structure. Unlike other methods, which try to increase sensitivity through the use of fold recognition software, we only use conventional sequence alignment tools, but apply them in a manner that significantly increases the number of relationships detected. We analyzed 11 genomes and found that, depending on the genome, between 23 and 32% of the ORFs had significant matches to proteins of known structure. In all cases, the aligned region consisted of either >100 residues or >50% of the smaller sequence. Slightly higher percentages could be attained if smaller motifs were also included. This is significantly higher than most previously reported methods, even those that have a fold-recognition component. We survey the biochemical and structural characteristics of the most frequently occurring proteins, and discuss the extent to which alignment methods can realistically assign function to gene products.

Algorithms↗
PubMed1999

Engineering aspects of hyperthermia therapy.

The continuing accrual of positive results in clinical cancer trials of adjunctive, synergistic hyperthermia therapy remains a strong motivation for the development of improved hyperthermia equipment and software. Indeed, the lack of needed engineering tools can be viewed as the major stumbling block to hyperthermia's effective clinical implementation. Developing clinically effective systems will be difficult, however, because (a) it requires solving several complex engineering problems, for which (b) setting appropriate design and evaluation goals is currently difficult owing to a lack of critical biological, physiological, and clinical knowledge, two tasks which must (c) be accomplished within a complicated social/political structure.

Biomedical Engineering↗
PubMed2000

Telepathology: design of a modular system.

Although telepathology systems have been developed for more than a decade, they are still not a widespread tool for routine diagnostic applications. Lacking interoperability, software that is not satisfying user needs as well as high costs have been identified as reasons. In this paper we would like to demonstrate that with a clear separation of the tasks required for a telepathology application, telepathology systems can be built in a modular way, where many modules can be implemented using standard software components. With such a modular design, systems can be easily adapted to changing user needs and new technological developments and it is easier to integrate modular systems into existing environments.

Computer Systems↗
PubMedDate not supplied

Image-guided conformal radiation therapy planning and delivery for non-small-cell lung cancer.

BACKGROUND: Our understanding of both the importance of local control for survival of patients with unresectable lung cancer and the inadequacy of conventional radiation therapy (RT) to provide this local control has undergone marked changes in the past 2 decades. METHODS: A review was conducted of recent studies and meta-analyses in the literature that have convincingly demonstrated the value of thoracic irradiation in increasing long-term survival in patients with both small-cell lung cancer and non-small-cell lung cancer (NSCLC). RESULTS: Large cooperative trials have shown long-term local control of only approximately 10% for NSCLC using conventionally planned radiation to doses of 60-64 Gy either as a single modality or when preceded by induction chemotherapy. Concurrent chemotherapy may modestly improve local control at the cost of greater acute esophageal toxicity. Simple escalation of radiation dose is limited by the tolerance of normal intrathoracic organs. Recent developments in anatomic and functional imaging, computerized RT planning, and RT delivery, as well as a reassessment of the appropriate target volumes for RT in the context of combined modality therapy, provide the capability to better conform regions of high dose to the target volume and test the hypothesis that increases in tumor dose will improve local control and survival. CONCLUSIONS: Encouraging phase II data have been reported from single institutions using individually developed software and hardware. The availability of commercial tools for planning and delivering such conformal treatment will allow prospective assessment of the true value of these technologies in the management of patients with lung cancer.

Carcinoma, Non-Small-Cell Lung↗
PubMed2003

Identification of adverse drug reactions in geriatric inpatients using a computerised drug database.

INTRODUCTION AND OBJECTIVE: Geriatric patients with multiple comorbidities are at high risk of experiencing an adverse drug reaction (ADR) during hospitalisation. The aim of the study was to compare the rate of ADRs as predicted by a computerised pharmacological database to the actual rate determined by direct observation in a sample of geriatric patients. STUDY DESIGN: During a 4-month period, geriatric patients were monitored using prospective observation. Patients were intensively screened for ADRs by a pharmacoepidemiological team (PET), consisting of two pharmacists and a physician. Actual ADRs detected by the PET were compared with those predicted by a computerised drug database. Furthermore, the set of actual ADRs, which resulted from drug-drug interactions (DDIs), were contrasted with potential DDIs signalled by the database. The main outcome measures were the incidence of actual ADRs. For the detection rate of the database we focused on frequent ADRs (>1% according to product information and database) and all DDIs indicated automatically by the database. RESULTS: 163 patients (121 female), mean age 79.8 +/- 7.1 years (range 60-98), were included in the study which was conducted on a geriatric rehabilitation hospital ward. The mean duration of hospitalisation was 24.3 +/- 8.4 days. Elderly patients received an average of 14.0 drugs (range 2-35) during their hospital stay. Of all patients, 60.7% experienced at least one ADR. The PET detected a total of 153 ADRs, with a mean of 0.9 ADRs per patient (range 0-5). The computerised drug database predicted an average of 309 potential ADRs for each patient; however, only 21 ADRs per patient were of high frequency. In 48% of ADR-positive patients (defined by PET) at least one of these frequent ADRs occurred.DDIs were detected by the PET in 14.7% of patients. Our database indicated a mean of 12 potential DDIs per patient. In 14 out of 24 DDI-positive patients, at least one signal indicated a real DDI. The database sensitivity was consequently 58.3%. CONCLUSION: In geriatric patients the incidence of ADRs is high. Computerised drug databases are a useful tool for detecting and avoiding ADRs. Our software, however, also produced a large number of signals that did not relate to actual ADRs found by the PET. The sheer number of these 'false' signals shows the need for refinement and optimisation of databases for daily clinical use.

Adverse Drug Reaction Reporting Systems↗
PubMed2002

Maximum a posteriori Bayesian estimation of oral cyclosporin pharmacokinetics in patients with stable renal transplants.

OBJECTIVE: To develop a maximum a posteriori probability (MAP) Bayesian estimator for the pharmacokinetics of oral cyclosporin, based on only three timepoints, and evaluate its performance with respect to a full-profile nonlinear regression approach. PATIENTS: 20 adult patients with stable renal transplants given orally administered microemulsified cyclosporin and mycophenolate. METHODS: Cyclosporin was assayed by liquid chromatography-mass spectrometry. Nonlinear regression and MAP Bayesian estimation were performed using a home-made program and a previously designed pharmacokinetic model including an S-shaped absorption profile described by a gamma distribution. OUTCOME MEASURES AND RESULTS: MAP Bayesian estimation using the best limited sampling strategy (before administration, and 1 and 3 hours after administration) was compared with nonlinear regression (taken as the reference method) for the prediction of the different pharmacokinetic parameters and exposure indices. Median relative prediction error was -0.49 and -3.42% for area under the concentration-time curve over the administration interval of 12 hours (AUC12) and estimated peak drug concentration (Cmax), respectively (nonsignificant). Relative precision was 2.00 and 4.32%, and correlation coefficient (r) was 0.985 and 0.955, for AUC12 and Cmax, respectively. CONCLUSION: This paper reports preliminary results in a stable renal transplant patient population, showing that MAP Bayesian estimation can allow accurate prediction of AUC12 and Cmax with only three samples (0, 1 and 3 hours). Although these results require confirmation by further studies in other clinical settings, using other drug combinations, other analytical methods and commercially available pharmacokinetic software, the method seems promising as a tool for the therapeutic drug monitoring of cyclosporin in clinical practice or for exposure-controlled studies.

Administration, Oral↗
PubMed1990

Tracking turns 19-month tide to hospital bottom.

When Saline Community Hospital, an 82-bed hospital in Saline Mich., saw its losses due to lower Medicare reimbursements mount, despite a review system already in place, administrators installed two intervention tools. The author discusses how an interactive software program and a plan to target "losing" DRGs can turn losses for any hospital.

Diagnosis-Related Groups↗
PubMed2000

CIM explorer--intelligent tool for exploring the ICD Romanian version.

The CIM Explorer software provides us with an intelligent interface for exploring the Romanian version of the International Classification of Diseases (in Romanian Clasificarea Internationala a Maladiilor-CIM). The ICD was transposed from its initial appearance as a printed document into a database. The classification can be accessed in two modes: "Navigation" and "Code" and queried in the "Key words" mode. In the last mode CIM Explorer program searches for the right content of the ICD records starting from naturally written expressions which it "understands". As a results it returns all the records containing the key words regardless their grammatical form. This program implements the specificity of the Romanian language where the words are made up from a root and a flexional termination.

Artificial Intelligence↗
PubMedDate not supplied

Oral health care practice and socio-demographic findings among the physicians in Ilorin, Nigeria.

BACKGROUND: In most developing countries, physicians attend to patients with oral health problems more than dentists usually because physicians are easily available. The aim of this study is to assess the level of practice of oral health care by physicians and make recommendations on how oral health care practice can be improved among the physicians. METHODS: This is a descriptive cross-sectional study carried out among 173 physicians who were randomly selected using their various health facilities. The study was carried out in Ilorin, the capital of Kwara State, Nigeria, over a period of six months. A well-structured questionnaire served as data collection tool while EPI-INFO version 6 software packages were used for analyzing data after being coded. RESULTS: There was a high level (74.1%) of practice of oral health care among the physicians and the major reasons for this were limited number of qualified dentists in the study area as well as lack of awareness by the patients concerning the treatment of oral health problems by dentists. Toothache and trauma were the most (68.2%) and least (2.3%) prevalent oral health problems respectively seen by physicians in this study. Antibiotics and analgesics were the medications used by the majority (58.1%) of the physicians to treat oral health problems. Almost all (97.7%) the respondents referred oral health problems to dentists while only 2.3% claimed never referred patients to a dentist. CONCLUSION: The available dental services in the study area cannot meet the oral health needs of the populace considering the fact that there are fewer dentists than physicians. Since this study showed a high level of practice of oral health care among the physicians, it is therefore necessary to include dentistry in the curricular of all medical schools in Nigeria and such curricula need to place more emphasis on promotive and preventive aspects of oral health as well as community participation.

Adult↗
PubMed2006

[Bioinformatic analysis of adenoma-normal mucosa SSH library of colon].

We established a colonic adenoma-normal mucosa suppressive subtraction hybridization (SSH) library in 1999. In this study, we wanted to explore the expression profile of all candidate genes in this library. We developed an EST pipeline which contained two in-house software packages, nucleic acid analytical software and GetUni. The nucleic acid analytical software, an integrator of the universal bioinformatics tools including phred, phd2fasta, cross_match, repeatmasker and blast2.0, can blast sequences of differential clones with the downloaded non-redundant nucleotide (NR) database. GetUni can cluster these NR sequences into Unigene via matching with the downloaded Homo Sapiens UniGene database. Sixty-two candidate genes in A-N library were obtained via the high throughput automatic gene expression bioinformatics pipeline. Gene Ontology online analysis revealed that ribosome genes and immunity-regulating genes were the two most common categories in the KEGG or Biocarta Pathway. We also detected the expression of 2 genes with highest hits, Reg4 and FAM46A, by semi-quantitative RT-PCR. Both genes were up-regulated in 10 or 9 out of 10 adenomas in comparison with the paired normal mucosa, respectively. The candidate genes in A-N library would be of great significance in disclosing the molecular mechanism underlying in colonic adenoma initiation and progression.

Adenoma↗
PubMed2006

Early childhood development project in Uganda as a strategy for reducing children's poor growth indicators: an explanatory study.

This study shall explore the activities of the Uganda nutrition and early childhood development project using explanatory program effects, qualitative research methods to determine the role/interplay of project factors and community dynamics in relation to poor growth and social indicators in Ugandan children. This project aimed to improve the quality of life for children age less than 6 years by improving their nutrition, health, cognitive and psychosocial development. The key concern remains how successful and sustainable are the outcomes? Data shall be collected using interviews, focus groups and document reviews. Data analysis shall employ the thematic networks analytical tool, which is aided by the ATLAS.ti software. The key hypotheses and recommendations from the analysis shall then be tested in a suitable community location and period in line with the research questions.

Child Development↗
PubMed1995

STUD2 system for computer assistance in oncology education.

In this paper, the application and use of microcomputers as an educational tool in oncology education is presented. The software packages of the system consists of two basic parts: exercises dealing with different subjects of oncology and a training module of diagnosis. The system STUD2 worked successfully in the Oncology Department of the Medical University of Lodz.

Computer Simulation↗
PubMed1996

Risk analysis in the valuation of medical practices.

Risk analysis techniques used in valuing medical practices are discussed. Employing these techniques provides superior information to the analyst than using a single estimate for uncertain variables. Examples of scenario analysis, sensitivity analysis, and simulation are presented. These tools can be easily implemented with spreadsheet software.

Computer Simulation↗
PubMed2004

Software approach to merging molecular with anatomic information.

Software image registration is a powerful and versatile tool that allows the fusion of molecular and anatomic information. Image registration can be applied to compare anatomic information with function, localize organs and lesions, and plan radiation therapy, biopsy, or surgery. Automatic volume-based image registration techniques have been devised for both linear and nonlinear image alignment. Challenges remain in the validation of the accuracy of software registration. Image registration has been applied clinically in neurology and oncology and may be particularly practical in radiotherapy applications. Potential new applications in cardiology could allow the combination of CT angiography with perfusion and viability images obtained by PET, SPECT, or MRI. Software methods allow versatility in the choice of modalities and facilitate retrospective and selective application. Fully automatic registration algorithms are needed for routine clinical applications. Connectivity, compatibility, and cooperation between various clinical departments are essential for the successful application of software-based image fusion in a hospital setting.

Algorithms↗
PubMed2005

SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments.

Footprinting is a powerful and widely used tool for characterizing the structure, thermodynamics, and kinetics of nucleic acid folding and ligand binding reactions. However, quantitative analysis of the gel images produced by footprinting experiments is tedious and time-consuming, due to the absence of informatics tools specifically designed for footprinting analysis. We have developed SAFA, a semi-automated footprinting analysis software package that achieves accurate gel quantification while reducing the time to analyze a gel from several hours to 15 min or less. The increase in analysis speed is achieved through a graphical user interface that implements a novel methodology for lane and band assignment, called "gel rectification," and an optimized band deconvolution algorithm. The SAFA software yields results that are consistent with published methodologies and reduces the investigator-dependent variability compared to less automated methods. These software developments simplify the analysis procedure for a footprinting gel and can therefore facilitate the use of quantitative footprinting techniques in nucleic acid laboratories that otherwise might not have considered their use. Further, the increased throughput provided by SAFA may allow a more comprehensive understanding of molecular interactions. The software and documentation are freely available for download at http://safa.stanford.edu.

Algorithms↗
PubMed2004

[Validation of a new in vivo measurement method to measure subsidence of a cemented Exeter femoral stem].

PURPOSE OF THE STUDY: Total hip arthroplasty has become one of the most common procedures in orthopedic surgery. These patients must nevertheless be followed with care due to the risk of instability. Knowledge of early migration behavior can provide an indirect assessment of implant fixation. The purpose of this work was to develop a new measurement tool for early assessment of the femoral component. MATERIAL AND METHODS: We analyzed the x-rays of ten Exeter stems (Stryker-Howmedica) implanted between 1996 and 2001 using a simple software designed to calculate the vertical subsidence of each implant. The technical precision and inter-observer reproducibility were checked. RESULTS: The software provided a precision of 0.14-0.3 millimeters. The overall precision of the technique was 1.2 millimeters. There was no statistically significant inter-observer variability. We observed a mean subsidence of 1.3+/-0.7 millimeters at six Months, followed by no further migration. DISCUSSION AND CONCLUSION: This new method was found to be reliable. It is useful for identifying implant migration at different bone-cement-implant interfaces. The time course of subsidence appears to be important to determine threshold values for failure. This tool provides an easy-to-use method for both retrospective and prospective analysis. With minor modifications of the software program, this tool can be used for other types of implants.

Adult↗
PubMed2001

Learning to consult with computers.

OBJECTIVE: To develop and evaluate a strategy to teach skills and issues associated with computers in the consultation. INTERVENTION: An overview lecture plus a workshop before and a workshop after practice placements, during the 10-week general practice (GP) term in the 5th year of the University of Melbourne medical course. DESIGN: Pre- and post-intervention study using a mix of qualitative and quantitative methods within a strategic evaluation framework. OUTCOME MEASURES: Self-reported attitudes and skills with clinical applications before, during and after the intervention. RESULTS: Most students had significant general computer experience but little in the medical area. They found the workshops relevant, interesting and easy to follow. The role-play approach facilitated students' learning of relevant communication and consulting skills and an appreciation of issues associated with using the information technology tools in simulated clinical situations to augment and complement their consulting skills. The workshops and exposure to GP systems were associated with an increase in the use of clinical software, more realistic expectations of existing clinical and medical record software and an understanding of the barriers to the use of computers in the consultation. CONCLUSIONS: The educational intervention assisted students to develop and express an understanding of the importance of consulting and communication skills in teaching and learning about medical informatics tools, hardware and software design, workplace issues and the impact of clinical computer systems on the consultation and patient care.

Attitude to Computers↗
PubMed2004

Towards a continuous evolution and adaptation of information systems in healthcare.

OBJECTIVES: To address the problem of alignment of health information systems to healthcare processes, which is a major challenge in healthcare organizations; to present a layered approach for system evolution and adaptation based on an application framework and rapid application development; to accomplish a demand-driven system evolution by embedding the software engineering process in business process optimization projects and by closely involving end users to improve their own work practices. METHODS: We have used a holistic health information system as a core application framework. System functionality is incrementally improved using an integrated "generator tool" for rapid application development. We have developed an iterative and participatory software engineering process, adapted to the conditions of the generator tool. The documentation techniques provided by the Unified Modeling Language (UML) were modified to achieve a straight forward documentation covering the whole development cycle from the business process model to generator-based computer applications. RESULTS AND CONCLUSION: The layered approach for system evolution did provide an environment in which a flexible and participatory software development process could be established. Today, generator-based applications are used in all clinical departments of our 1200-bed University Hospital. We expect that tools for rapid application development will be further improved and will play an increasingly important role to establish responsive IT-infrastructures where the application developer can concentrate on business process alignment instead of coding and debugging.

Academic Medical Centers↗