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PubMed1994

Finite-element method in electrical impedance tomography.

In electrical impedance tomography (EIT), current patterns are injected into a subject and boundary voltages are measured to reconstruct a cross-sectional image of resistivity distribution. Static EIT image reconstruction requires a computer model of a subject, an efficient data-collection method and robust and fast reconstruction algorithms. The finite-element method is used as the computer model. The paper describes the finite-element analysis software package developed, including an interactive graphical mesh generator and fast algorithms for solving linear systems of equations using sparse-matrix and vector techniques. Various models of irregularly shaped subjects are developed using mesh-design tools, including automatic mesh generation and optimisation using the Delaunay algorithm. Even though the software package is customised for use in electrical impedance tomography, it can be used for other biomedical research areas, such as impedance cardiography, cardiac defibrillation and impedance pneumography.

Algorithms↗
PubMed1997

Neutron Laue diffractometry with an imaging plate provides an effective data collection regime for neutron protein crystallography.

Neutron quasi-Laue diffraction data (2 A resolution) from tetragonal hen egg-white lysozyme were collected in ten days with neutron imaging plates. The data processing Laue software, LAUEGEN, developed for X-ray Laue diffractometry, was adapted for neutron diffractometry with a cylindrical detector. The data analysis software, X-PLOR, was modified and used for the refinement of hydrogen atoms, and the positions of 960 hydrogen atoms in the protein and 157 bound water molecules, were determined. Several examples are given of the methods used to identify hydrogen atoms and water molecules.

Animals↗
PubMed1993

Matching references with MEDLINE via TCP/IP.

Bibliographic references are an important part of databases and information resources used by clinicians and biomedical researchers. In addition to the obvious clerical advantages of standard references, bibliographic references can also be used as links to related items in different data sets. This paper describes an effort that involved matching references from a variety of disparate databases to canonical MEDLINE references. The references matched were those involved in a database unification project which is part of the Mouse Genome Informatics effort at The Jackson Laboratory. Software was developed to take advantage of a commercially available retrieval engine which accesses MEDLINE on CD-ROM disks. The software permits client programs on UNIX/C, and potentially other environments, to access unabridged MEDLINE via networks supporting the TCP/IP protocols. The matching process described can be used as a model for similar efforts with different research or clinical data sets, as well as different hardware or software environments.

Animals↗
PubMed2006

Predicting Caco-2 permeability using support vector machine and chemistry development kit.

PURPOSE: To predict Caco-2 permeability is a valuable target for pharmaceutical research. Most of the Caco-2 prediction models are based on commercial or special software which limited their practical value. This study represents the relationship between Caco-2 permeability and molecular descriptors totally based on open source software. METHODS: The Caco-2 prediction model was constructed based on descriptors generated by open source software Chemistry Development Kit (CDK) and a support vector machine (SVM) method. Number of H-bond donors and three molecular surface area descriptors constructed the prediction model. RESULTS: The correlation coefficients (r) of the experimental and predicted Caco-2 apparent permeability for the training set and the test set were 0.88 and 0.85, respectively. CONCLUSION: The results suggest that the SVM method is effective for predicting Caco-2 permeability. Membrane permeability of compounds is determined by number of H-bond donors and molecular surface area properties.

Caco-2 Cells↗
PubMed1989

A computer-assisted management information system for nutrition services.

A computer-assisted management information system was created to facilitate effective management of clinical nutrition services and labor resources in a 330-bed teaching and research hospital. Standards were developed for the quality and quantity of nutrition care, time required to provide nutrition care, and utilization of dietitians' time. Computer software was developed to report the volume of services provided, the need for services, and the utilization of labor hours. Data were evaluated to determine whether services were consistent with standards and to calculate a recommended number of clinical dietitian full-time equivalents for the hospital. Furthermore, the management information system was instrumental in developing a fee-for-service structure, for evenly distributing work loads among dietitians, and for monitoring adherence to standards of care.

Dietetics↗
PubMed1985

Application development approaches in a MUMPS environment.

A number of techniques exist to aid in the development of software applications. This paper briefly discusses the use of discrete, stand-alone packages written in MUMPS as tools for the efficient development and maintenance of applications packages. A preliminary set of requirements and a list of candidate functional clusters are included.

Computers↗
PubMed1999

staffTRAK-TB: software for surveillance of tuberculosis infection in healthcare workers.

The Centers for Disease Control and Prevention (CDC) recommends periodic tuberculin skin testing of healthcare workers with potential exposure to Mycobacterium tuberculosis. However, many healthcare facilities have neither a system to identify workers due for their skin test nor a means of analyzing aggregate data. To illustrate some of the complexities involved in tuberculin skin test (TST) tracking and analysis, and how these might be addressed, this report describes a software package called staffTRAK-TB, developed by the CDC to facilitate surveillance of tuberculosis infection in healthcare workers. staffTRAK-TB records data for each healthcare worker, including demographic information, occupation, work location, multiple TST results, and results of evaluations to determine if clinically active tuberculosis is present. Programmed reports include lists of workers due and overdue for skin tests, and skin test conversion rates by occupation or worksite. Standardization of types of occupations and locations allows data from multiple facilities to be aggregated and compared. Data transfer to the CDC can be performed via floppy diskettes. staffTRAK-TB illustrates important issues in software structure, standardization of occupation and work-location information, relevant data items, and reports and analyses that would be useful in practice. Developing software that adequately addresses the epidemiological issues is complex, and the lessons learned may serve as a model for hospital epidemiologists, infection control personnel, occupational health personnel, and computer programmers considering software development in this area or trying to optimize their facility's TST surveillance.

Adult↗
PubMedDate not supplied

[The information management of a radiology department: the development of a new type of software for the archiving of alphanumeric data and images].

The authors report the main characteristics and the goals of the development of the RIS of the II Chair of the Institute of Radiology, La Sapienza University, Rome. The system was developed with a commercial software (4th Dimension), for use with an Ethernet network and Macintosh Apple computers. One of the main problems was to obtain a user-friendly system. The main options of our system are: booking, registration, exam execution, reporting, archives and statistics and system administration. The main characteristics of our RIS is that it allows important images to be archived in limited number and at low resolution. The aim is to use images for consultation and teaching purposes, not for diagnosis which is made on the original images. Low resolution images permit to use limited storage space. Image quality is very similar to that of the original images for the equipment connected on line with the RIS--i.e., US and MR units in our institute. Conventional radiographic and CT images are digitalized by two scanners with maximum resolution of 4k x 4k x 11 bits. To date, good results have been obtained. Our RIS has been used by the medical and non-medical staffs, without any particular instruction and has allowed us to organize and make faster department management and reporting.

Computer Communication Networks↗
PubMed2002

Growth and remodelling of the autologous bone transplant used in a pediatric femoral reconstruction.

The aim of the present work was to assess how growth and remodelling changed the morphology of the transplanted fibula used to reconstruct the proximal femur of a 5 year old child affected by a Ewing's sarcoma during the first 3 years of follow-up. The morphological evolution of the transplant was quantitatively assessed on diagnostic images. Special software was developed to perform three-dimensional measurements on computed tomography (CT) datasets, while state-of-the-art image processing software was used for conventional radiography. The measurements were then correlated with the loads expected to act on the hip during the various stages of the rehabilitation protocol. A simple cantilever beam model was used for a gross estimate of the risk of fracture of the transplant. The results of the analysis showed that there is no clear correlation between the morphological changes of the autograft and the hip loading conditions experienced. Apart from a drastic increase in the periosteal radius in the frontal plane, occurring in the first 10 months after the operation, the growth of the transplanted fibula seems well within the ranges of the normal fibular growth. The cantilever beam model suggested that, although the autograft is currently subjected to subcritical stresses. morphological evolution could increase the risk of fracture in the next few years if a normal level of loading were allowed.

Bone Remodeling↗
PubMed2025

The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon.

The computational modeling of chromatin structure is highly complex due to the hierarchical organization of chromatin, which reflects its diverse biophysical principles, as well as inherent dynamism, which underlies its complexity. Chromatin structure modeling can be based on diverse approaches and assumptions, making it essential to determine how different methods influence the modeling outcomes. We conducted a project at the NIH-funded 4D Nucleome Hackathon on March 18-21, 2024, at The University of Washington in Seattle, USA. The hackathon provided an amazing opportunity to gather an international, multi-institutional and unbiased group of experts to discuss, understand and undertake the challenges of chromatin model comparison and validation. Here we give an overview of the current state of the 3D chromatin field and discuss our efforts to run and validate the models. We used distance matrices to represent chromatin models and we calculated Spearman correlation coefficients to estimate differences between models, as well as between models and experimental data. In addition, we discuss challenges in chromatin structure modeling that include: 1) different aspects of chromatin biophysics and scales complicate model comparisons, 2) large diversity of experimental data (e.g., population-based, single-cell, protein-specific) that differ in mathematical properties, heatmap smoothness, noise and resolutions complicates model validation, 3) expertise in biology, bioinformatics, and physics is necessary to conduct comprehensive research on chromatin structure, 4) bioinformatic software, which is often developed in academic settings, is characterized by insufficient support and documentation. We also emphasize the importance of establishing guidelines for software development and standardization.

Chromatin↗
PubMed2002

Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.).

A software tool was developed for the identification of simple sequence repeats (SSRs) in a barley ( Hordeum vulgare L.) EST (expressed sequence tag) database comprising 24,595 sequences. In total, 1,856 SSR-containing sequences were identified. Trimeric SSR repeat motifs appeared to be the most abundant type. A subset of 311 primer pairs flanking SSR loci have been used for screening polymorphisms among six barley cultivars, being parents of three mapping populations. As a result, 76 EST-derived SSR-markers were integrated into a barley genetic consensus map. A correlation between polymorphism and the number of repeats was observed for SSRs built of dimeric up to tetrameric units. 3'-ESTs yielded a higher portion of polymorphic SSRs (64%) than 5'-ESTs did. The estimated PIC (polymorphic information content) value was 0.45 +/- 0.03. Approximately 80% of the SSR-markers amplified DNA fragments in Hordeum bulbosum, followed by rye, wheat (both about 60%) and rice (40%). A subset of 38 EST-derived SSR-markers comprising 114 alleles were used to investigate genetic diversity among 54 barley cultivars. In accordance with a previous, RFLP-based, study, spring and winter cultivars, as well as two- and six-rowed barleys, formed separate clades upon PCoA analysis. The results show that: (1) with the software tool developed, EST databases can be efficiently exploited for the development of cDNA-SSRs, (2) EST-derived SSRs are significantly less polymorphic than those derived from genomic regions, (3) a considerable portion of the developed SSRs can be transferred to related species, and (4) compared to RFLP-markers, cDNA-SSRs yield similar patterns of genetic diversity.

DNA, Plant↗
PubMed2005

Software system for three-dimensional volumetric reconstruction of histological sections: a case study for the snake chondrocranium.

Volumetric digital computer-assisted reconstruction of histological sections is an attractive possibility for developmental studies. Commercial solutions are very expensive for many educational institutions. Therefore, we developed a software system for three-dimensional reconstruction of anatomical virtual models. The input data for the system are the digitized images from the histological samples of the chondrocranium of two crotalines, Bothrops jararaca and Crotalus durissus terrificus, and one colubrid, Philodryas olfersii, using a stereomicroscope connected to a digital camera. These images are then manually registered and segmented. We use computer graphics visualization algorithms such as marching cubes and ray casting to generate three-dimensional visualizations of the volumes. The results show that the digital reconstruction is as good as the manual reconstruction with the advantages of speed of reconstruction, accuracy, and flexibility to handle and study the volume. Compared with commercial options, our system has approximately the same features, and it is available free for the scientific community.

Animals↗
PubMed2007

Automated documentation error detection and notification improves anesthesia billing performance.

BACKGROUND: Documentation of key times and events is required to obtain reimbursement for anesthesia services. The authors installed an information management system to improve record keeping and billing performance but found that a significant number of their records still could not be billed in a timely manner, and some records were never billed at all because they contained documentation errors. METHODS: Computer software was developed that automatically examines electronic anesthetic records and alerts clinicians to documentation errors by alphanumeric page and e-mail. The software's efficacy was determined retrospectively by comparing billing performance before and after its implementation. Staff satisfaction with the software was assessed by survey. RESULTS: After implementation of this software, the percentage of anesthetic records that could never be billed declined from 1.31% to 0.04%, and the median time to correct documentation errors decreased from 33 days to 3 days. The average time to release an anesthetic record to the billing service decreased from 3.0+/-0.1 days to 1.1+/-0.2 days. More than 90% of staff found the system to be helpful and easier to use than the previous manual process for error detection and notification. CONCLUSION: This system allowed the authors to reduce the median time to correct documentation errors and the number of anesthetic records that were never billed by at least an order of magnitude. The authors estimate that these improvements increased their department's revenue by approximately $400,000 per year.

Anesthesia↗
PubMed1994

Population approaches in drug development. Report on an expert meeting to discuss population pharmacokinetic/pharmacodynamic software.

An expert meeting to discuss population pharmacokinetic/pharmacodynamic software was held in Brussels in November 1993 under the auspices of the European Co-operation in Science and Technology (COST), Medicine (B1) programme. Recently developed statistical methods offer the possibility of gaining integrated information on pharmacokinetics and response from relatively sparse observational data obtained directly in patients who are being treated with the drug under development. These methods can minimize the need to exclude patient groups and also allow analysis of a variety of unbalanced designs that frequently arise in the evaluation of the relationships between dose or concentration on the one hand and efficacy or safety on the other relationships that do not readily lend themselves to other forms of statistical analysis. The purpose of the Brussels meeting was to evaluate the state of both existing software and software under development, and to specify the needs and wishes of potential users of such software. It was apparent from the meeting that software development for population data analysis is currently a very active area of investigation and that several very good packages are already available, with more in development. The general consensus of the meeting was that well validated, easy to use software was essential to the implementation of the population approach to drug development.

Humans↗
PubMed2005

Navigation with electromagnetic tracking for interventional radiology procedures: a feasibility study.

PURPOSE: To assess the feasibility of the use of preprocedural imaging for guide wire, catheter, and needle navigation with electromagnetic tracking in phantom and animal models. MATERIALS AND METHODS: An image-guided intervention software system was developed based on open-source software components. Catheters, needles, and guide wires were constructed with small position and orientation sensors in the tips. A tetrahedral-shaped weak electromagnetic field generator was placed in proximity to an abdominal vascular phantom or three pigs on the angiography table. Preprocedural computed tomographic (CT) images of the phantom or pig were loaded into custom-developed tracking, registration, navigation, and rendering software. Devices were manipulated within the phantom or pig with guidance from the previously acquired CT scan and simultaneous real-time angiography. Navigation within positron emission tomography (PET) and magnetic resonance (MR) volumetric datasets was also performed. External and endovascular fiducials were used for registration in the phantom, and registration error and tracking error were estimated. RESULTS: The CT scan position of the devices within phantoms and pigs was accurately determined during angiography and biopsy procedures, with manageable error for some applications. Preprocedural CT depicted the anatomy in the region of the devices with real-time position updating and minimal registration error and tracking error (<5 mm). PET can also be used with this system to guide percutaneous biopsies to the most metabolically active region of a tumor. CONCLUSIONS: Previously acquired CT, MR, or PET data can be accurately codisplayed during procedures with reconstructed imaging based on the position and orientation of catheters, guide wires, or needles. Multimodality interventions are feasible by allowing the real-time updated display of previously acquired functional or morphologic imaging during angiography, biopsy, and ablation.

Angiography↗
PubMed1995

"Hyperstat": an educational and working tool in epidemiology.

The work of a researcher in epidemiology is based on studying literature, planning studies, gathering data, analyzing data and writing results. Therefore he has need for performing, more or less, simple calculations, the need for consulting or quoting literature, the need for consulting textbooks about certain issues or procedures, and the need for looking at a specific formula. There are no programs conceived as a workstation to assist the different aspects of researcher work in an integrated fashion. A hypertextual system was developed which supports different stages of the epidemiologist's work. It combines database management, statistical analysis or planning, and literature searches. The software was developed on Apple Macintosh by using Hypercard 2.1 as a database and HyperTalk as a programming language. The program is structured in 7 "stacks" or files: Procedures; Statistical Tables; Graphs; References; Text; Formulas; Help. Each stack has its own management system with an automated Table of Contents. Stacks contain "cards" which make up the databases and carry executable programs. The programs are of four kinds: association; statistical procedure; formatting (input/output); database management. The system performs general statistical procedures, procedures applicable to epidemiological studies only (follow-up and case-control), and procedures for clinical trials. All commands are given by clicking the mouse on self-explanatory "buttons". In order to perform calculations, the user only needs to enter the data into the appropriate cells and then click on the selected procedure's button. The system has a hypertextual structure. The user can go from a procedure to other cards following the preferred order of succession and according to built-in associations. The user can access different levels of knowledge or information from any stack he is consulting or operating. From every card, the user can go to a selected procedure to perform statistical calculations, to the reference database management system, to the textbook in which all procedures and issues are discussed in detail, to the database of statistical formulas with automated table of contents, to statistical tables with automated table of contents, or to the help module. he program has a very user-friendly interface and leaves the user free to use the same format he would use on paper. The interface does not require special skills. It reflects the Macintosh philosophy of using windows, buttons and mouse. This allows the user to perform complicated calculations without losing the "feel" of data, weight alternatives, and simulations. This program shares many features in common with hypertexts. It has an underlying network database where the nodes consist of text, graphics, executable procedures, and combinations of these; the nodes in the database correspond to windows on the screen; the links between the nodes in the database are visible as "active" text or icons in the windows; the text is read by following links and opening new windows. The program is especially useful as an educational tool, directed to medical and epidemiology students. The combination of computing capabilities with a textbook and databases of formulas and literature references, makes the program versatile and attractive as a learning tool. The program is also helpful in the work done at the desk, where the researcher examines results, consults literature, explores different analytic approaches, plans new studies, or writes grant proposals or scientific articles.

Computer-Assisted Instruction↗
PubMed2006

Detection of glaucoma using operator-dependent versus operator-independent classification in the Heidelberg retinal tomograph-III.

OBJECTIVE: To compare the abilities of a new Glaucoma Probability Scoring (GPS) system and Moorfields regression analysis (MRA) to differentiate between glaucomatous and normal eyes using Heidelberg retinal tomograph (HRT)-III software and race-specific databases. METHODS: In this prospective study, one eye (refractive error < or =5 D) each of consecutive normal patients and those with glaucoma was enrolled. All patients underwent a full eye examination, standard achromatic perimetry (Swedish Interactive Threshold Algorithm-standard automated perimetry (SITA-SAP), program 24-2) and confocal scanning laser ophthalmoscopy (HRT-II) within 1 month. Normal patients had two normal visual fields in both eyes (pattern standard deviation (PSD) >5% and Glaucoma Hemifield Test within 97% normal limits) and a normal clinical examination. Glaucoma was defined on the basis of SITA-SAP visual field loss (PSD<5% or Glaucoma Hemifield Test outside normal limits) on two consecutive visual fields. HRT-II examinations were exported to the HRT-III software (V.3.0), which uses an enlarged race-specific database, consisting of 733 eyes of white people and 215 eyes of black people. Race-adjusted MRA for the most abnormal sector (operator-dependent contour line placement) was compared with the global race-adjusted GPS (operator independent). MRA sectors outside the 99.9% confidence interval limits (outside normal limits) and GPS > or =0.64 were considered abnormal. RESULTS: 136 normal patients (72 black and 64 white patients) and 84 patients with glaucoma (52 black and 32 white patients) were enrolled (mean age 50.4 (SD 14.4) years). The average visual field mean deviation was (-)0.4 (SD 1.1) db for the normal group and (-)7.3 (SD 6.7) db for the glaucoma group (p<0.001). Mean GPS values were 0.21 (SD 0.23) and 0.73 (SD 0.27) for normal and glaucomatous eyes, respectively (p<0.001). Sensitivity and specificity values were 77.1% and 90.3% for GPS, and 71.4% and 91.9% for MRA, respectively. CONCLUSIONS: In this cohort, GPS software sensitivity and specificity values are similar to those of MRA, which requires placement of an operator-dependent contour line. The development of software to detect glaucoma without a contour line is critical to improving the potential use of HRT as a tool for glaucoma detection and screening.

Black People↗