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At least 307 records · Page 17Linked to original sources

PubMed2005

nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms.

Nonsynonymous single nucleotide polymorphisms (nsSNPs) are prevalent in genomes and are closely associated with inherited diseases. To facilitate identifying disease-associated nsSNPs from a large number of neutral nsSNPs, it is important to develop computational tools to predict the nsSNP's phenotypic effect (disease-associated versus neutral). nsSNPAnalyzer, a web-based software developed for this purpose, extracts structural and evolutionary information from a query nsSNP and uses a machine learning method called Random Forest to predict the nsSNP's phenotypic effect. nsSNPAnalyzer server is available at http://snpanalyzer.utmem.edu/.

Algorithms↗

PubMed1995

Neurosurgical robot Minerva: first results and current developments.

We describe the development and approach to clinical application of the neurosurgical robot Minerva, including the mechanical structure of the robot and the software developed to perform intracranial neurosurgical operations with accuracy, smoothness, and safety. The first eight operations have been undertaken on patients requiring stereotactic brain biopsy. We describe the ongoing developments, including improved sterilization features, force sensors, nonlinear electrostimulation probe, and implantation of living encapsulated cells, all of which have entered a test phase. The goals are increased safety and capability to perform simple three-dimensional operations. This research should ease the way for new complex operations that are difficult to perform manually today.

Biopsy↗

PubMed2003

Three-dimensional reconstruction of tubular structure of vacuolar membrane throughout mitosis in living tobacco cells.

Plant vacuoles are the largest of organelles, performing various functions in cellular metabolism, morphogenesis and cell division. Dynamic changes in vacuoles during mitosis were studied by monitoring tubular structure of vacuolar membrane (TVM) in living transgenic tobacco BY-2 cells stably expressing a GFP-AtVam3p fusion protein (BY-GV). Comprehensive images of the complicated TVM configurations were obtained by reconstructing three-dimensional (3-D) surface structures from sequential confocal sections, using newly developed software, SSR (stereo-structure reconstructor). Using the surface modeling technique, we succeeded for the first time in clarifying the development process of TVMs and the topological relationship between TVMs and large vacuoles. TVMs, initially organized from large vacuoles, elongated to encircle the spindle at metaphase. Subsequently, the TVMs invaded the equatorial region from anaphase to telophase, and then they were divided to the two daughter cells by the cell plate at cytokinesis. When the daughter nuclei were separating from the cell plate, some TVMs enlarged to form large vacuoles near the division site. Spatial analysis revealed that from anaphase until cytokinesis, TVMs connected the two large vacuoles and functioned as a route for inter-vacuolar transport. Furthermore, the experiments using the inhibitor for actin microfilaments indicated that the microfilaments were indispensable for the development and the maintenance of TVMs.

Agrobacterium tumefaciens↗

PubMed1995

Critical care medicine in cyperspace: Internet resources and techniques for the intensivist.

The internet, is an informational tool of impressive proportions and capabilities. New software developments puts the use of this informational technology into the hands of all physicians. The use of Internet informational resources allows the intensivist to stay abreast of new developments in critical care medicine, communicate in a matter of seconds with colleagues half a world away, acquire medically related software, access remote database structures, obtain continuing medical education, and in the near future to "see' patients and obtain physiological data in real time. This tutorial will introduce the Internet and it's current tool suite.

Computer Communication Networks↗

PubMed1989

Topographical brain electrical activity mapping on an IBM-compatible personal computer.

A new system for computing brain electrical activity maps on a standard IBM-compatible computer has been developed. The EEG is recorded using a CED1401 intelligent laboratory interface and stored in the computer; colour coded maps are generated using software developed in Turbo PASCAL and displayed on the EGA graphics screen. An acceptable computation time of 1.2 s for a 64 x 64 map displayed as a 128 x 128 pixel image has been achieved by incorporating assembly language routines and a maths coprocessor. The system may be readily upgraded as improved hardware becomes available and further software can be added. In addition to triggering auditory, visual and somatosensory stimulators, it provides the potential for the generation of complex stimuli for cognitive experiments by means of mass RAM and digital-to-analogue converters.

Brain Mapping↗

PubMed2003

Computer-aided placement of endosseous oral implants in patients after ablative tumour surgery: assessment of accuracy.

The objective of this study was to evaluate the feasibility and accuracy of a novel surgical computer-aided navigation system for the placement of endosseous implants in patients after ablative tumour surgery. Pre-operative planning was performed by developing a prosthetic concept and modifying the implant position according to surgical requirements after high-resolution computed tomography (HRCT) scans with VISIT, a surgical planning and navigation software developed at the Vienna General Hospital. The pre-operative plan was transferred to the patients intraoperatively using surgical navigation software and optical tracking technology. The patients were HRCT-scanned again to compare the position of the implants with the pre-operative plan on reformatted CT-slices after matching of the pre- and post-operative data sets using the mutual information-technique. A total of 32 implants was evaluated. The mean deviation was 1.1 mm (range: 0-3.5 mm). The mean angular deviation of the implants was 6.4 degrees (range: 0.4 degrees - 17.4 degrees, variance: 13.3 degrees ). The results demonstrate, that adequate accuracy in placing endosseous oral implants can be delivered to patients with most difficult implantologic situations.

Dental Implantation, Endosseous↗

PubMed2006

Model-driven user interfaces for bioinformatics data resources: regenerating the wheel as an alternative to reinventing it.

BACKGROUND: The proliferation of data repositories in bioinformatics has resulted in the development of numerous interfaces that allow scientists to browse, search and analyse the data that they contain. Interfaces typically support repository access by means of web pages, but other means are also used, such as desktop applications and command line tools. Interfaces often duplicate functionality amongst each other, and this implies that associated development activities are repeated in different laboratories. Interfaces developed by public laboratories are often created with limited developer resources. In such environments, reducing the time spent on creating user interfaces allows for a better deployment of resources for specialised tasks, such as data integration or analysis. Laboratories maintaining data resources are challenged to reconcile requirements for software that is reliable, functional and flexible with limitations on software development resources. RESULTS: This paper proposes a model-driven approach for the partial generation of user interfaces for searching and browsing bioinformatics data repositories. Inspired by the Model Driven Architecture (MDA) of the Object Management Group (OMG), we have developed a system that generates interfaces designed for use with bioinformatics resources. This approach helps laboratory domain experts decrease the amount of time they have to spend dealing with the repetitive aspects of user interface development. As a result, the amount of time they can spend on gathering requirements and helping develop specialised features increases. The resulting system is known as Pierre, and has been validated through its application to use cases in the life sciences, including the PEDRoDB proteomics database and the e-Fungi data warehouse. CONCLUSION: MDAs focus on generating software from models that describe aspects of service capabilities, and can be applied to support rapid development of repository interfaces in bioinformatics. The Pierre MDA is capable of supporting common database access requirements with a variety of auto-generated interfaces and across a variety of repositories. With Pierre, four kinds of interfaces are generated: web, stand-alone application, text-menu, and command line. The kinds of repositories with which Pierre interfaces have been used are relational, XML and object databases.

Computational Biology↗

PubMed2006

Improving retrospective sorting of 4D computed tomography data.

Respiratory correlated CT is commercially available, and we have implemented its routine clinical use in planning lung tumor patients. Its value is determined by the fidelity of the spatiotemporal data set after processing the acquired reconstructed slices. Retrospective sorting of reconstructed slices is based on respiratory phase. However, the existing commercial software inadequately models respiratory phase for about 30% of the patients, mainly due to irregularities in the respiratory cycle. We have developed software that improves phase determination and consequently leads to an improvement of retrospective data sorting to make 4DCT data acquisition feasible for routine clinical use. Peak inhalation and exhalation respiratory states are selected manually; intermediate phases are interpolated. Residual motion artifacts in the resulting 4DCT volumes are reduced and allow use of the 4D imaging studies for treatment planning.

Algorithms↗

PubMedDate not supplied

Andhra Pradesh cold chain system marching beyond routine to obtain WHO accreditation.

The GOAP-PATH partnership project provided an opportunity to carryout situational analysis of the cold chain system in the State of Andhra Pradesh. Apart from identifying areas of work many quality issues like freezing of vaccine were brought to light, which lead to development of a comprehensive plan of action for total overhauling of cold chain system. Introduction of new technologies, training, infrastructure and software development has reformed the cold chain system. The EVSM (Effective vaccine stores management initiative) self assessment was done recently for the Central vaccine stores at Hyderabad and the results of this self assessment has raised the confidence of health personnel to aim for WHO, EVSM accreditation for central vaccine store at Hyderabad.

Accreditation↗

PubMed2005

ArrayQuest: a web resource for the analysis of DNA microarray data.

BACKGROUND: Numerous microarray analysis programs have been created through the efforts of Open Source software development projects. Providing browser-based interfaces that allow these programs to be executed over the Internet enhances the applicability and utility of these analytic software tools. RESULTS: Here we present ArrayQuest, a web-based DNA microarray analysis process controller. Key features of ArrayQuest are that (1) it is capable of executing numerous analysis programs such as those written in R, BioPerl and C++; (2) new analysis programs can be added to ArrayQuest Methods Library at the request of users or developers; (3) input DNA microarray data can be selected from public databases (i.e., the Medical University of South Carolina (MUSC) DNA Microarray Database or Gene Expression Omnibus (GEO)) or it can be uploaded to the ArrayQuest center-point web server into a password-protected area; and (4) analysis jobs are distributed across computers configured in a backend cluster. To demonstrate the utility of ArrayQuest we have populated the methods library with methods for analysis of Affymetrix DNA microarray data. CONCLUSION: ArrayQuest enables browser-based implementation of DNA microarray data analysis programs that can be executed on a Linux-based platform. Importantly, ArrayQuest is a platform that will facilitate the distribution and implementation of new analysis algorithms and is therefore of use to both developers of analysis applications as well as users. ArrayQuest is freely available for use at http://proteogenomics.musc.edu/arrayquest.html.

Algorithms↗

PubMed2006

Computer-aided detection and evaluation of lipid-rich plaque on noncontrast cardiac CT.

OBJECTIVE: Noncontrast electron beam CT (EBCT) and MDCT are established for the assessment of calcified plaque, but not lipid-rich plaque. We developed software to identify lipid-rich plaque with noncontrast electron beam tomography (EBT) and MDCT. MATERIALS AND METHODS: A computer algorithm was developed to automatically find contiguous lipid-rich lesions with voxel intensities below a calculated patient-specific lipid threshold. Lipid density and lipid inhomogeneity in Hounsfield units were calculated in the proximal left coronaries of three populations: 34 low-risk patients (low-risk group < 6% Framingham risk score, no calcium), 31 high-risk patients (high-risk group > 20% Framingham risk score, no calcium), and 37 patients with calcified plaque (calcium group). RESULTS: The mean lipid density was -19.6 +/- 3.0 (SD) H in the low-risk group, -25.3 +/- 8.2 H in the high-risk group, and -34.3 +/- 13.0 H in the calcium group (p < 0.05). The mean lipid inhomogeneity was 17.7 +/- 3.6 H in the low-risk group, 21.5 +/- 5.5 H in the high-risk group, and 29.0 +/- 7.6 H in the calcium group (p < 0.05). The mean interscan variability in lipid density and lipid inhomogeneity were 2.0 +/- 3.3 H and 2.1 +/- 3.6 H, respectively. In five patients, the locations of lipid-rich plaque correlated well with available intravascular sonography findings. CONCLUSION: Our method may be able to identify lipid-rich plaque on noncontrast cardiac CT.

Adult↗

PubMed1994

Photo CD and medical archives.

Most people involved in medical photography and illustration are aware of the difficulties of efficient archiving and retrieval of picture information. The recent developments in Photo CD now enable cost effective storage of high resolution images. Applications already exist for easy archive management and new software developments make it simple to tailor standard systems for professional people in very specific fields without the necessity of commissioning programmers and system developers with the consequential cost implications.

Archives↗

PubMed2005

The shakedown.

Customer Strategy Solutions, a California-based developer of order-fulfillment systems, is facing a shakedown. Six months after the firm's CEO, Pavlo Zhuk, set up a software development center in Kiev, local bureaucrats say the company hasn't filed all the tax schedules it should have. Moreover, Ukrainian tax officials claim that the company owes the government tax arrears. Zhuk is shocked; he and his colleagues have done everything by the book. This isn't the first time Zhuk has encountered trouble in Ukraine. In the process of getting the development center up and running, a state-owned telecommunications utility had made it difficult for Zhuk to get the phone lines his company needed. Senior telecom manager Vasyl Feodorovych Mylofienko had told Zhuk it would take three years to install the lines in his office-but for a certain price, Mylofienko had added, the lines could be functioning the following week. Even as the picture of rampant bribery and corruption in Ukraine becomes clear, Zhuk still doesn't want to pull out of the country. Of Ukrainian descent, he has dreams of helping to modernize the country. By paying his programmers more than they could make at any local company, he hopes to raise their standard of living so they can afford three meals a day without having to barter, stand in queues for hours, or moonlight. And yet, he isn't sure he can keep compromising his principles for the sake of the greater good. Should Customer Strategy Solutions pay off the Ukrainian tax officials? Commenting on this fictional case study are Alan L. Boeckmann, the chairman and CEO of Fluor Corporation; Rafael Di Tella, a professor at Harvard Business School; Thomas W. Dunfee, the Kolodny Professor of Social Responsibility and a professor of legal studies at Wharton; and Bozidar Djelic, the former finance and economy minister of Serbia.

Commerce↗

PubMedDate not supplied

Automated identification by computer of the mass spectra of drugs in urine or serum extracts.

Gas chromatography/mass spectrometry (GC/MS) is the method of choice for confirming the presence of drugs tentatively identified in urine or serum by thin-layer chromatography, gas chromatography, or immunoassay. One of the most widely used GC/MS systems is the Hewlett-Packard (HP) Model 5970 mass selective detector equipped with a work station programmed in Pascal. Searching of mass spectra after a GC/MS run must be done manually, and this can take hours, especially when there are many peaks in a chromatogram to check. I have developed software that allows the unattended searching of all peaks in a run, using a forward search algorithm with a custom-made drug library developed over a period of 5 years, and a reverse search with a 1600+ drug library from HP or another in-house drug library. Using these libraries with the two algorithms maximizes the chances of finding a drug peak and identifying it correctly. Individual searches take about 5 seconds each. Overall search time of nearly 200 mass spectra per run takes about 40 minutes, including printing time. This software has proven to be both labor saving and effective in positively identifying drugs.

Electronic Data Processing↗

PubMed2002

Benchmarking HIPAA compliance.

One of the nation's largest academic medical centers is benchmarking its operations using internally developed software to improve privacy/confidentiality of protected health information (PHI) and to enhance data security to comply with HIPAA regulations. It is also coordinating the development of a web-based interactive product that can help hospitals, physician practices, and managed care organizations measure their compliance with HIPAA regulations.

Academic Medical Centers↗

PubMed2001

Potential technology for studying dosimetry and response to airborne chemical and biological pollutants.

Advances in computational, and imaging techniques have enabled the rapid development of three-dimensional (3-D) models of biological systems in unprecedented detail. Using these advances, 3-D models of the lungs and nasal passages of the rat and human are being developed to ultimately improve predictions of airborne pollutant dosimetry. Techniques for imaging the respiratory tract by magnetic resonance imaging (MRI) were developed to improve the speed and accuracy of geometric data collection for mesh reconstruction. The MRI resolution is comparable to that obtained by manual measurements but at much greater speed and accuracy. Newly developed software (NWGrid) was utilized to translate imaging data from MR into 3-D mesh structures. Together, these approaches significantly reduced the time to develop a 3-D model. This more robust airway structure will ultimately facilitate modeling gas or vapor exchange between the respiratory tract and vasculature as well as enable linkages of dosimetry with cell response models. The 3-D, finite volume, viscoelastic mesh structures form the geometric basis for computational fluid dynamics modeling of inhalation, exhalation and the delivery of individual particles (or concentrations of gas or vapors) to discrete regions of the respiratory tract. The ability of these 3-D models to resolve dosimetry at such a high level of detail will require new techniques to measure regional airflows and particulate deposition for model validation.

Air Movements↗

PubMed2001

Overview of the tunable beamlines for protein crystallography at the EMBL Hamburg Outstation; an analysis of current and future usage and developments.

The EMBL Hamburg Outstation currently operates two tunable protein crystallography beamlines suitable for single and multiple anomalous diffraction (SAD/MAD) experiments. The first beamline, designated X31, is located on a bending magnet of the DORIS III storage ring whereas the second beamline, BW7A, is positioned at a multipole wiggler at the same storage ring. X31 is equipped with an energy stabilization device to ensure constant wavelength during longer data-collection periods. The in-house built crystallographic end-station is now equipped with a Mar345 imaging-plate scanner as a detector. The wiggler beamline BW7A features a novel sagitally focusing monochromator. The end-station used here has also been developed and built in-house. The beamline is currently operated with a Mar 165 CCD detector. In this paper the hardware and software developments of the last years will be summarized and the outlook for substantial upgrades will be given. The future plans include the design and construction of a third tunable beamline, designated X12, for protein crystallography. The development of automated beamlines for protein crystallography is of particular importance with respect to structural genomics initiatives. The analysis of the projects of the last years shows the wide range of anomalous scatterer used on the tunable beamlines thus demonstrating the need of a wide range of accessible energies and fast and reliable energy changes.

Crystallography↗

PubMed2004

Feasibility of rapid and automated importation of 3D echocardiographic left ventricular (LV) geometry into a finite element (FEM) analysis model.

BACKGROUND: Finite element method (FEM) analysis for intraoperative modeling of the left ventricle (LV) is presently not possible. Since 3D structural data of the LV is now obtainable using standard transesophageal echocardiography (TEE) devices intraoperatively, the present study describes a method to transfer this data into a commercially available FEM analysis system: ABAQUS. METHODS: In this prospective study TomTec LV Analysis TEE Software was used for semi-automatic endocardial border detection, reconstruction, and volume-rendering of the clinical 3D echocardiographic data. A newly developed software program MVCP FemCoGen, written in Delphi, reformats the TomTec file structures in five patients for use in ABAQUS and allows visualization of regional deformation of the LV. RESULTS: This study demonstrates that a fully automated importation of 3D TEE data into FEM modeling is feasible and can be efficiently accomplished in the operating room. CONCLUSION: For complete intraoperative 3D LV finite element analysis, three input elements are necessary: 1. time-gaited, reality-based structural information, 2. continuous LV pressure and 3. instantaneous tissue elastance. The first of these elements is now available using the methods presented herein.

Echocardiography, Three-Dimensional↗