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At least 1,621 records · Page 90Linked to original sources
PubMed2005

ArrayCyGHt: a web application for analysis and visualization of array-CGH data.

UNLABELLED: ArrayCyGHt is a web-based application tool for analysis and visualization of microarray-comparative genomic hybridization (array-CGH) data. Full process of array-CGH data analysis, from normalization of raw data to the final visualization of copy number gain or loss, can be straightforwardly achieved on this arrayCyGHt system without the use of any further software. ArrayCyGHt, therefore, provides an easy and fast tool for the analysis of copy number aberrations in any kinds of data format. AVAILABILITY: ArrayCyGHt can be accessed at http://genomics.catholic.ac.kr/arrayCGH/

Algorithms↗
PubMed1995

Building and maintaining a library Gopher: traditional skills applied to emerging resources.

Gopher software has emerged rapidly as a powerful tool for providing library users with organized access to Internet resources. Building and maintaining Gophers is one way in which librarians' traditional knowledge and skills are being applied in a nontraditional area. In March 1992, the University of Michigan's ULibrary Gopher was created, mainly as a means of providing access to U.S. Census data and the U.S. Department of Commerce's Economic Bulletin Board. In an effort to broaden the scope of the Gopher, librarians were asked to submit ideas for new resources to access. The result was the ULibrary Gopher Working Group, a team of eighteen librarians from six libraries on campus. The Alfred Taubman Medical Library staff drafted a menu design for life sciences resources and received basic UNIX training. In March 1993, the life sciences section of ULibrary became fully operational and now is maintained by the Taubman staff. This paper describes the history of the ULibrary Gopher and the working group, the creation and ongoing maintenance of the life sciences area of the Gopher, staffing issues, and the relationship of Gopher building to traditional collection development.

Computer Communication Networks↗
PubMed2005

Sampling frequencies and measurement error for linear and temporal gait parameters in primate locomotion.

Quantitative analyses of animal motion are increasingly easy to conduct using simple video equipment and relatively inexpensive software packages. With careful use, such analytical tools have the potential to quantify differences in movement between individuals or species and to allow insights into the behavioral consequences of morphological differences between taxa. However, as with any other type of measurement, there are errors associated with kinematic measurements. Because normative kinematic data on human and nonhuman primate locomotion are used to model aspects of gait of fossil hominins, errors in the extant data influence the accuracy of fossil gait reconstructions. The principal goal of this paper is to illustrate the effect of camera speeds (frame rates) on kinematic measurement errors, and to demonstrate how these errors vary with subject size, movement velocity, and sample size. Kinematic data for human walking and running (240 Hz), as well as data for primate quadrupedal walking and running (180 Hz) were used as inputs for a simulation of the measurement errors associated with various linear and temporal kinematic variables. Measurement errors were shown to increase as camera speed, subject body size, and interval duration all decrease, and as movement velocity increases. These results have implications for the methods used to calculate subject velocity and suggest that using a moving marker to measure the linear displacements of the body is preferable to the use of a stationary marker. Finally, while slower camera speeds will always result in higher measurement errors than do faster camera speeds, this effect can be moderated to some extent by collecting sufficiently large samples of data.

Animals↗
PubMed1998

MoldaNet: a network distributed molecular graphics and modelling program that integrates secure signed applet and Java 3D technologies.

MoldaNet is a molecular graphics and modelling program that integrates several new Java technologies, including authentication as a Secure Signed Applet, and implementation of Java 3D classes to enable access to hardware graphics acceleration. It is the first example of a novel class of Internet-based distributed computational chemistry tool designed to eliminate the need for user pre-installation of software on their client computer other than a standard Internet browser. The creation of a properly authenticated tool using a signed digital X.509 certificate permits the user to employ MoldaNet to read and write the files to a local file store; actions that are normally disallowed in Java applets. The modularity of the Java language also allows straightforward inclusion of Java3D and Chemical Markup Language classes in MoldaNet to permit the user to filter their model into 3D model descriptors such as VRML97 or CML for saving on local disk. The implications for both distance-based training environments and chemical commerce are noted.

Computer Graphics↗
PubMed2000

Graphically-enabled integration of bioinformatics tools allowing parallel execution.

Rapid analysis of large amounts of genomic data is of great biological as well as medical interest. This type of analysis will greatly benefit from the ability to rapidly assemble a set of related analysis programs and to exploit the power of parallel computing. TurboGenomics, which is a software package currently in its alpha-testing phase, allows integration of heterogeneous software components to be done graphically. In addition, the tool is capable of making the integrated components run in parallel. To demonstrate these abilities, we use the tool to develop a Web-based application that allows integrated access to a set of large-scale sequence data analysis programs used by a transposon-insertion based yeast genome project. We also contrast the differences in building such an application with and without using the TurboGenomics software.

Computational Biology↗
PubMed2006

Modular neuropile organization in the Drosophila larval brain facilitates identification and mapping of central neurons.

Elucidating how neuronal networks process information requires identification of critical individual neurons and their connectivity patterns. For this purpose, we used the third-instar Drosophila larval brain and applied reverse-genetic tools, immunolabeling procedures, and 3D digital reconstruction software. Consistent topological definition of neuropile compartments in the larval brain can be obtained through simple fluorescence-immunolabeling methods. The modular neuropiles can be used as a fiducial framework for mapping the projection patterns of individual neurons labeled with green fluorescent protein (GFP). GFP-labeled neurons often exhibit dendrite-like arbors as well as clustered varicose terminals on neurite branches that innervate identifiable neuropile compartments. We identified candidate cholinergic interneurons in genetic mosaic brains that overlap with the larval optic nerve terminus. By using the neuropile framework, we demonstrate that the candidate visual interneurons are not a subset of the previously identified circadian pacemaker neurons that also contact the larval optic nerve terminus; they may represent parallel pathways in the processing of visual inputs. Thus, in the Drosophila larval brain, modular neuropiles can be used as a framework for systematically identifying, mapping, and classifying interneurons; understanding their roles in behavior can then be pursued further.

Animals↗
PubMed1998

Semi-automatic tool for segmentation and volumetric analysis of medical images.

Segmentation software is described, developed for medical image processing and run on Windows. The software applies basic image processing techniques through a graphical user interface. For particular applications, such as brain lesion segmentation, the software enables the combination of different segmentation techniques to improve its efficiency. The program is applied for magnetic resonance imaging, computed tomography and optical images of cryosections. The software can be utilised in numerous applications, including pre-processing for three-dimensional presentations, volumetric analysis and construction of volume conductor models.

Brain Ischemia↗
PubMed2006

Optimization of nutrient parameters for lovastatin production by Monascus purpureus MTCC 369 under submerged fermentation using response surface methodology.

Lovastatin, an inhibitor of HMG-CoA reductase, was produced by submerged fermentation using Monascus purpureus MTCC 369. Five nutritional parameters screened using Plackett-Burman experimental design were optimized by Box-Behnken factorial design of response surface methodology for lovastatin production in shake flask cultures. Maximum lovastatin production of 351 mg/l were predicted in medium containing 29.59 g/l dextrose, 3.86 g/l NH4Cl, 1.73 g/l KH2PO4, 0.86 g/l MgSO4 x 7H2O, and 0.19 g/l MnSO4 x H2O using response surface plots and point prediction tool of DESIGN EXPERT 7.0 (Statease, USA) software.

Culture Media↗
PubMed1995

New user interfaces.

Usability of a computer-based information system has three components: user-friendliness, acceptance and user-competence. These are important considerations in human-computer interface designs. So far, visual/manual interface techniques have dominated data-capture activities in hospital settings. Despite the improvements made in these areas, usability issues still remain over the use of such I/O devices like the computer keyboard, touch-sensitive screens, light pen and bar codes. This paper will examine two of the newer user interfaces that have emerged in recent years which can potentially improve computer usability in the healthcare setting. These are voice and pen technologies. Speech as a medium for communicating with computers has several advantages. It gives users freedom of movement away from a computer terminal. It further allows users to enter or receive data while engaged in other activities. For example, a doctor can simultaneously examine a patient and record his findings using voice input. The use of pen technology also liberates the physician and other healthcare workers from the keyboard and monitor. It gives them mobility, facilitates eye contact with patients and most importantly, allows them to tap the newest of computer hardware and software technology with the oldest of communication tools--the pen. Healthcare facilities are beginning to explore the use of these two technologies to improve on user-acceptance and user-competence. Some examples of their successful applications will be given.

Handwriting↗
PubMed1997

Finite element models in tissue mechanics and orthopaedic implant design.

This article attempts to review the literature on finite element modelling in three areas of biomechanics: (i) analysis of the skeleton, (ii) analysis and design of orthopaedic devices and (iii) analysis of tissue growth, remodelling and degeneration. It is shown that the method applied to bone and soft tissue has allowed researchers to predict the deformations of musculoskeletal structures and to explore biophysical stimuli within tissues at the cellular level. Next, the contribution of finite element modelling to the scientific understanding of joint replacement is reviewed. Finally, it is shown that, by incorporating finite element models into iterative computer procedures, adaptive biological processes can be simulated opening an exciting field of research by allowing scientists to test proposed 'rules' or 'algorithms' for tissue growth, adaptation and degeneration. These algorithms have been used to explore the mechanical basis of processes such as bone remodelling, fracture healing and osteoporosis. RELEVANCE: With faster computers and more reliable software, computer simulation is becoming an important tool of orthopaedic research. Future research programmes will use computer simulation to reduce the reliance on animal experimentation, and to complement clinical trials.

Journal Article↗
PubMed2001

Dynamic arc radiosurgery and radiotherapy: commissioning and verification of dose distributions.

PURPOSE: Conformal stereotactic radiosurgery and radiotherapy using a linear accelerator and a micromultileaf collimator (mMLC) offer the possibility of irradiating irregularly shaped target volumes. Dynamic arc radiosurgery and radiotherapy, i.e., stereotactic radiation therapy combining a moving gantry with a dynamic mMLC, enable the radiation even of lesions with concave structures. METHODS AND MATERIALS: The dynamic arc method requires additional tools for quality assurance (QA) and three-dimensional verification at a high spatial resolution. A QA program was developed. Dose distributions of planning target volumes with concavities were investigated in polymer gel phantoms. The radiation-induced change of the relaxation rate R(2) was measured by magnetic resonance imaging. The distributions were compared with image processing tools. RESULTS: Using the therapy-planning software BrainSCAN 4.0 (and 4.1 beta) in combination with the mMLC m3, deviations between the planned and measured 90% isodoses of about 2 mm were registered in the isocenter plane. Three-dimensional verification was feasible in the range of accuracy achieved in planning and dose measurement. CONCLUSIONS: Dynamic arc radiosurgery and radiotherapy offer excellent conformation even for complicated planning target volumes with concavities. The dose distribution calculated with the treatment-planning software used can be accomplished with the available equipment. Patients can be treated by dynamic arc radiosurgery and radiotherapy.

Calibration↗
PubMed2006

Tools for kinetic modeling of biochemical networks.

The number of software packages for kinetic modeling of biochemical networks continues to grow. Although most packages share a common core of functionality, the specific capabilities and user interfaces of different packages mean that choosing the best package for a given task is not trivial. We compare 12 software packages with respect to their functionality, reliability, efficiency, user-friendliness and compatibility. Although most programs performed reliably in all numerical tasks tested, SBML compatibility and the set-up of multicompartmentalization are problematic in many packages. For simple models, GEPASI seems the best choice for non-expert users. For large-scale models, environments such as Jarnac/JDesigner are preferable, because they allow modular implementation of models. Virtual Cell is the most versatile program and provides the simplest and clearest functionality for setting up multicompartmentalization.

Biochemistry↗
PubMed2006

Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser.

The Yeast Gene Order Browser (YGOB) is an online tool designed to facilitate the comparative genomic visualization and appraisal of synteny within and between the genomes of seven hemiascomycete yeast species. Three of these genomes are polyploid, and hence contain intra-genomic syntenic regions, the correct assembly of which is a particular success of YGOB. Designed to accurately assemble, display and score gene order relationships, YGOB is both an interactive tool for browsing genomic data, and a software engine now being used for evolutionary analyses on a whole-genome scale. Underlying the online interface is the YGOB database, which consists of homology assignments across the species, extensively curated based on sequence similarity and novelly, an appraisal of genomic context (synteny) in multiple genomes. Currently the YGOB database incorporates genome data from Saccharomyces cerevisiae, Candida glabrata, Saccharomyces castellii, Ashbya gossypii, Kluyveromyces lactis, Kluyveromyces waltii and Saccharomyces kluyveri, but the system is scaleable to accommodate additional genomes. This paper discusses the usage and utility of version 1.0 of YGOB, which is publicly available at http://wolfe.gen.tcd.ie/ygob.

Chromosomes, Fungal↗
PubMed2001

A dose reconstruction of 60Co-contaminated window frames in a Taiwanese school.

Since 1992, hundreds of buildings in Taiwan were discovered to have 60Co contamination in the structural rebar. The contamination resulted from improper handling of 60Co-contaminated scrap metal in 1982 and 1983, which subsequently was recycled and used throughout Taiwan. Hsin-hsin Kindergarten school enrolled about 600 students over the 10-y period before the contamination was discovered. Hsin-hsin Kindergarten had three 60Co-contaminated steel window frames with measured dose rates on contact up to 150 microSv h(-1). In this study, a range of potential doses received by the Hsin-hsin Kindergarten students were estimated using ISOSHLD dose modeling software. ISOSHLD is a rapid, inexpensive screening tool to reconstruct dose ranges. To assess the potential risks to habitants of the school for the first year after construction, calculated dose rate ranges of 0.08 microSv h(-1) to 75.38 microSv h(-1) were then applied to the International Commission [corrected] on Radiation Protection 60 nominal detriment coefficients for stochastic effects. Risk estimates ranged from 1.46 x 10(-4) to 7.42 x 10(-4) excess fatal cancers per lifetime.

Adolescent↗
PubMed2003

The role of certified nursing assistants in nursing homes.

UNLABELLED: OBJECTIVE Pilot study to examine the experiences of the certified nursing assistants (CNAs) in Colorado nursing homes. BACKGROUND DATA: CNAs provide 80% to 90% of the care to residents in nursing homes. Their reported turnover rate is as high as 400% in some studies, and the potential pool of CNAs is dwindling. As the demand for CNAs increases, their experiences must be understood to effectively address recruitment and retention issues. METHODS: Minimally structured interviews of 12 CNAs in 6 Colorado nursing homes and observations of care provided were conducted. Atlas/Ti software was used as a data management tool for analyzing and coding data. RESULTS: The overriding theme that emerged from the interviews was "we love our jobs." Three patterns of thought and behavior emerged: attributes of the CNA, working conditions of the CNA, and future success of the CNA and the nursing home. CONCLUSIONS: Issues important to CNAs revolved around basic motivational factors, such as job enrichment opportunities, personal growth opportunities, recognition, responsibility, and sense of achievement. Leadership must become creative and build on that base, providing CNAs with job mobility, job enrichment opportunities, recognition, and increased job responsibility, producing positive outcomes not only for the CNA but also for the resident and the facility.

Adult↗
PubMed2004

Bispectral Index monitoring correlates with sedation scales in brain-injured patients.

OBJECTIVE: Monitoring critically ill, brain-injured patients with a decreased level of consciousness is challenging. Our goal is to determine in this population the correlation between the Bispectral Index (BIS) and three commonly used sedation agitation scales: the Richmond Agitation-Sedation Scale (RASS), the Sedation-Agitation Scale (SAS) and the Glasgow Coma Scale (GCS) scores. DESIGN: Prospective, single-blinded observational study. SETTING: Eight-bed neurology-neurosurgery intensive care unit at the Cleveland Clinic Foundation. PATIENTS: Thirty critically ill patients admitted to the neurointensive care unit with primary brain injury and a decreased level of consciousness. MEASUREMENTS AND MAIN RESULTS: Patients were prospectively evaluated for level of consciousness using the RASS, SAS, and GCS every hour and simultaneously were monitored continuously with a BIS monitor for 6 hrs. A Spearman's correlation coefficient was used to correlate the BIS scores with clinical scales. In 15 patients monitored with the newer BIS XP version, the BIS values correlated significantly with the RASS (R2 = .810; p < .0001), SAS (R2 = .725; p < .0001), and GCS (R2 = .655; p < .0001). In 15 patients monitored with the older BIS 2.1.1 software, the correlation was as follows: for RASS, R2 = .30 (p < .008), for SAS: R2 = .376 (p < .001), and for GCS: R2 = .274 (p < .015). This correlation was maintained in patients who received sedative medications. CONCLUSIONS: A statistically significant correlation existed between BIS values and the RASS, SAS, and GCS scores in critically ill brain-injured patients, with and without sedation. The newer BIS XP software package may be a useful adjunctive tool in objective assessment of level of consciousness in brain-injured patients.

Aged↗
PubMed2024

De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes.

Three-dimensional genome organization plays a critical role in gene regulation, and disruptions can lead to developmental disorders by altering the contact between genes and their distal regulatory elements. Structural variants (SVs) can disturb local genome organization, such as the merging of topologically associating domains upon boundary deletion. Testing large numbers of SVs experimentally for their effects on chromatin structure and gene expression is time and cost prohibitive. To address this, we propose a computational approach to predict SV impacts on genome folding, which can help prioritize causal hypotheses for functional testing. We developed a weighted scoring method that measures chromatin contact changes specifically affecting regions of interest, such as regulatory elements or promoters, and implemented it in the SuPreMo-Akita software (Gjoni and Pollard 2024). With this tool, we ranked hundreds of de novo SVs (dnSVs) from autism spectrum disorder (ASD) individuals and their unaffected siblings based on predicted disruptions to nearby neuronal regulatory interactions. This revealed that putative cis-regulatory element interactions (CREints) are more disrupted by dnSVs from ASD probands versus unaffected siblings. We prioritized candidate variants that disrupt ASD CREints and validated our top-ranked locus using isogenic excitatory neurons with and without the dnSV, confirming accurate predictions of disrupted chromatin contacts. This study establishes disrupted genome folding as a potential genetic mechanism in ASD and provides a general strategy for prioritizing variants predicted to disrupt regulatory interactions across tissues.

Journal Article↗
PubMed2004

Distributed data mining on grids: services, tools, and applications.

Data mining algorithms are widely used today for the analysis of large corporate and scientific datasets stored in databases and data archives. Industry, science, and commerce fields often need to analyze very large datasets maintained over geographically distributed sites by using the computational power of distributed and parallel systems. The grid can play a significant role in providing an effective computational support for distributed knowledge discovery applications. For the development of data mining applications on grids we designed a system called Knowledge Grid. This paper describes the Knowledge Grid framework and presents the toolset provided by the Knowledge Grid for implementing distributed knowledge discovery. The paper discusses how to design and implement data mining applications by using the Knowledge Grid tools starting from searching grid resources, composing software and data components, and executing the resulting data mining process on a grid. Some performance results are also discussed.

Algorithms↗