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At least 577 records · Page 32Linked to original sources
PubMed2005

Role-tailored software systems for medical response to disasters: enhancing the capabilities of "mid-tier" responders.

WIISARD (Wireless Internet Information System for Medical Response in Disasters) is developing wireless technology to coordinate and enhance the care of mass casualties at disaster sites. Mid-tier personnel (area supervisors) play a critical role in disaster response, supervising care processes in the triage, Treatment and Transport areas of the attack site. The design of a software tool to support mid-tier activities focuses on providing supervisors aggregate information on patient conditions and needs, real-time data on ambulance availability and location, and hospital status and on coordinating care delivery among triage, treatment and transport areas.

Computer Systems↗
PubMed2004

The Swiss-Prot protein knowledgebase and ExPASy: providing the plant community with high quality proteomic data and tools.

The Swiss-Prot protein knowledgebase provides manually annotated entries for all species, but concentrates on the annotation of entries from model organisms to ensure the presence of high quality annotation of representative members of all protein families. A specific Plant Protein Annotation Program (PPAP) was started to cope with the increasing amount of data produced by the complete sequencing of plant genomes. Its main goal is the annotation of proteins from the model plant organism Arabidopsis thaliana. In addition to bibliographic references, experimental results, computed features and sometimes even contradictory conclusions, direct links to specialized databases connect amino acid sequences with the current knowledge in plant sciences. As protein families and groups of plant-specific proteins are regularly reviewed to keep up with current scientific findings, we hope that the wealth of information of Arabidopsis origin accumulated in our knowledgebase, and the numerous software tools provided on the Expert Protein Analysis System (ExPASy) web site might help to identify and reveal the function of proteins originating from other plants. Recently, a single, centralized, authoritative resource for protein sequences and functional information, UniProt, was created by joining the information contained in Swiss-Prot, Translation of the EMBL nucleotide sequence (TrEMBL), and the Protein Information Resource-Protein Sequence Database (PIR-PSD). A rising problem is that an increasing number of nucleotide sequences are not being submitted to the public databases, and thus the proteins inferred from such sequences will have difficulties finding their way to the Swiss-Prot or TrEMBL databases.

Arabidopsis↗
PubMedDate not supplied

Informatics in radiology (infoRAD): navigating the fifth dimension: innovative interface for multidimensional multimodality image navigation.

The display and interpretation of images obtained by combining three-dimensional data acquired with two different modalities (eg, positron emission tomography and computed tomography) in the same subject require complex software tools that allow the user to adjust the image parameters. With the current fast imaging systems, it is possible to acquire dynamic images of the beating heart, which add a fourth dimension of visual information-the temporal dimension. Moreover, images acquired at different points during the transit of a contrast agent or during different functional phases add a fifth dimension-functional data. To facilitate real-time image navigation in the resultant large multidimensional image data sets, the authors developed a Digital Imaging and Communications in Medicine-compliant software program. The open-source software, called OsiriX, allows the user to navigate through multidimensional image series while adjusting the blending of images from different modalities, image contrast and intensity, and the rate of cine display of dynamic images. The software is available for free download at http://homepage.mac.com/rossetantoine/osirix.

Humans↗
PubMed2007

Prediction of absorbed dose to normal organs in thyroid cancer patients treated with 131I by use of 124I PET and 3-dimensional internal dosimetry software.

UNLABELLED: The objective of this work was to determine normal organ (131)I dosimetry in patients undergoing radioiodide therapy for thyroid cancer by use of serial scanning with (124)I PET. METHODS: A total of 26 patients who had papillary and follicular metastatic thyroid cancer and who were already enrolled in a Memorial Sloan-Kettering Cancer Center (131)I thyroid cancer protocol were selected for this study. Imaging before (131)I therapy consisted of multiple, whole-body (124)I PET studies over a period of 2-8 d, an (18)F-FDG PET scan and, for some, a diagnostic CT scan. With a set of in-house-developed software tools (3-dimensional internal dosimetry [3D-ID] and Multiple Image Analysis Utility [MIAU]), the following procedures were performed: all PET emission and transmission and CT image sets were aligned; half-life-corrected tomographic images of (131)I activity were integrated voxel by voxel to produce cumulated (131)I activity images; and the latter images were, in turn, convolved with a (131)I electron-photon point kernel to produce images of (131)I dose distribution. Cumulated activity values and calculated residence times obtained from our patient-specific dosimetry software (3D-ID) were used as inputs to OLINDA, and volume difference-adjusted comparisons were made between the mean dose estimates. RESULTS: With 3D-ID, dose volume histograms and mean doses were calculated for 14 organs, and results were expressed in Gy/GBq. The highest mean dose, 0.26 Gy/GBq, was seen in the right submandibular gland, whereas the lowest mean dose, 0.029 Gy/GBq, was seen in the brain. CONCLUSION: This is the first comprehensive study of normal organ dosimetry in patients by use of a quantitative tomographic imaging modality.

Adult↗
PubMed2003

Locating sequence on FPC maps and selecting a minimal tiling path.

This study discusses three software tools, the first two aid in integrating sequence with an FPC physical map and the third automatically selects a minimal tiling path given genomic draft sequence and BAC end sequences. The first tool, FSD (FPC Simulated Digest), takes a sequenced clone and adds it back to the map based on a fingerprint generated by an in silico digest of the clone. This allows verification of sequenced clone positions and the integration of sequenced clones that were not originally part of the FPC map. The second tool, BSS (Blast Some Sequence), takes a query sequence and positions it on the map based on sequence associated with the clones in the map. BSS has multiple uses as follows: (1) When the query is a file of marker sequences, they can be added as electronic markers. (2) When the query is draft sequence, the results of BSS can be used to close gaps in a sequenced clone or the physical map. (3) When the query is a sequenced clone and the target is BAC end sequences, one may select the next clone for sequencing using both sequence comparison results and map location. (4) When the query is whole-genome draft sequence and the target is BAC end sequences, the results can be used to select many clones for a minimal tiling path at once. The third tool, pickMTP, automates the majority of this last usage of BSS. Results are presented using the rice FPC map, BAC end sequences, and whole-genome shotgun from Syngenta.

Chromosomes, Artificial, Bacterial↗
PubMed2001

XML documentation of biopathways and their simulations in Genomic Object Net.

Genomic Object Net is a software tool for modeling and simulating biopathways which employs the notion of hybrid functional net as its basic architechture. This paper shows how to integrate this basic architecture with XML documents for biopathway representations, simulations, and visualizations for creating a tailor-made simulation environment.

Bacteriophage lambda↗
PubMed1994

VISA: Visual Sequence Analysis for the comparison of multiple amino acid sequences.

VISA (VIsual Sequence Analysis) is a software package that displays global similarities within a set of related protein sequences. The program identifies amino acid patterns that are common to many members of the set of sequences and displays them as a series of histograms. Individual peaks on the display can be assigned a color and analogous peaks in the other sequences are then automatically marked in the same color. This can be repeated for each significant peak and leads to a display in which major matching segments of multiple amino acid sequences appear as dominant peaks of the histograms with matching colors. These peaks usually correspond to the conserved sequence motifs that are characteristic of particular proteins. An extensive set of software tools is included to help the localization, visualization and analysis of the global similarities displayed. VISA provides a graphic overview of the sequence similarity that can help to understand the architecture of the protein family and can be helpful while designing experiments to probe function.

Algorithms↗
PubMed2006

Mass analysis peptide sequence prediction (MAPSP).

UNLABELLED: The software tool MAPSP allows the combinatorial prediction of novel short peptides such as hormones with common sequence features. In addition, it assists in de novo sequencing in general. The tool was designed for use in conjunction with the analytical identification method of mass spectrometry (MS) and it can considerably speed-up the analysis of unknowns. AVAILABILITY: The web interface is freely available at http://mapsp.ifg.uni-muenster.de/

Algorithms↗
PubMed2001

A statistical framework for quantitative trait mapping.

We describe a general statistical framework for the genetic analysis of quantitative trait data in inbred line crosses. Our main result is based on the observation that, by conditioning on the unobserved QTL genotypes, the problem can be split into two statistically independent and manageable parts. The first part involves only the relationship between the QTL and the phenotype. The second part involves only the location of the QTL in the genome. We developed a simple Monte Carlo algorithm to implement Bayesian QTL analysis. This algorithm simulates multiple versions of complete genotype information on a genomewide grid of locations using information in the marker genotype data. Weights are assigned to the simulated genotypes to capture information in the phenotype data. The weighted complete genotypes are used to approximate quantities needed for statistical inference of QTL locations and effect sizes. One advantage of this approach is that only the weights are recomputed as the analyst considers different candidate models. This device allows the analyst to focus on modeling and model comparisons. The proposed framework can accommodate multiple interacting QTL, nonnormal and multivariate phenotypes, covariates, missing genotype data, and genotyping errors in any type of inbred line cross. A software tool implementing this procedure is available. We demonstrate our approach to QTL analysis using data from a mouse backcross population that is segregating multiple interacting QTL associated with salt-induced hypertension.

Algorithms↗
PubMed2006

A qualitative study of the implementation of a bioinformatics tool in a biological research laboratory.

OBJECTIVE: To explore how the implementation of a comprehensive new bioinformatics analysis system would affect workflow, collaboration and information management in a small genetic research lab. DESIGN: This was a longitudinal qualitative study of seven individuals involved in genomic and proteomic research. The study data were gathered using the illuminative/responsive approach of immersion in the environment. Additional qualitative data were gathered using informal semi-structured interviews, participant observation in lab meetings, and direct observation of lab researchers engaged in specific tasks. MEASUREMENTS: Interview, observation and field note data were coded and analyzed based on three analysis perspectives. A subset of the data was independently evaluated by an external researcher to enhance the trustworthiness of results. RESULTS: Three reoccurring themes were observed in the study. (1) Satisfaction and acceptance of software tools tended to be role and goal specific. (2) The system was seen primarily as a measurement system rather than a "total laboratory analysis system". (3) Lab meetings deemphasized the system, preferring more traditional data analysis techniques. These themes support the observations that the system was not used to its full potential in the lab. CONCLUSION: Themes identified in this study suggest that sophisticated genetic researchers face similar problems of technology implementation as do professionals in other fields. We recommend that leadership support and on-going training and evolution of academic curricula can improve chances of bioinformatics analysis systems becoming used more effectively.

Computational Biology↗
PubMed2004

Assessment of protein spot components applying correspondence analysis for peptide mass fingerprint data.

Proteins separated by two-dimensional gel electrophoresis (2-DE) may be distributed over several spots. Otherwise, one spot may contain more than one component. The same protein occurring in several spots supposedly represents differently modified protein species that might be of biological relevance. Identification of spots with peptide mass fingerprinting and database searching leads only to the detection of the major spot components. If a spot also contains additional minor protein components, quantitation of spots with protein staining techniques or antibody detection becomes misleading. In order to find spots containing minor components we applied correspondence analysis, a multivariate data exploration method, to peptide mass fingerprint data. Correspondence analysis using peak lists revealed groups of spots containing the same protein with their characteristic mass-to-charge ratio (m/z) values. In order to detect different protein spot components an interactive threshold setting and removal of m/z values with subsequent recalculation of the correspondence analysis using our software tool CorrAn are performed. The usefulness of this methodical approach was shown by a data set of peptide mass fingerprints of 284 spots of Helicobacter pylori 26695 separated by 2-DE.

Bacterial Proteins↗
PubMed2003

Inexpensive ethography using digital video.

We describe an inexpensive method for digital video recording of behavioral experiments and present a simple, freely-redistributable software tool enabling ethographic analysis of these recordings via classification of video frames into user-defined categories. While high-end commercial solutions already exist for these purposes, we focus on minimizing equipment expenses and complexity for research projects or undergraduate laboratory courses employing compatible behavioral paradigms.

Computer Graphics↗
PubMed2004

Standardized terminology for clinical trial protocols based on top-level ontological categories.

This paper describes a new method for the ontologically based standardization of concepts with regard to the quality assurance of clinical trial protocols. We developed a data dictionary for medical and trial-specific terms in which concepts and relations are defined context-dependently. The data dictionary is provided to different medical research networks by means of the software tool Onto-Builder via the internet. The data dictionary is based on domain-specific ontologies and the top-level ontology of GOL. The concepts and relations described in the data dictionary are represented in natural language, semi-formally or formally according to their use.

Clinical Trials as Topic↗
PubMed2006

A formal foundation for ICNP.

The International Classification for Nursing Practice (ICNP) has been developed as a 'unifying framework' for comparing and combining disparate nursing data from across the world. In order to meet the increasingly sophisticated needs of users of ICNP, substantial revision has been made to the Beta 2 version of ICNP, culminating in the launch of ICNP Version 1 in 2005. In its revision of ICNP, the development team has followed a rigorous development process using current best practice in ontology development. The core of ICNP Version 1 is represented in the Web Ontology Language, the de facto standard ontology representation language. An ontology editor, Protégé, and other software tools have been used to support the process. The result is a robust terminological resource that can accommodate existing and emerging nursing terminologies and allow comparisons to be made between disparate nursing data. The revision has provided ICNP with a sustainable foundation that will a) facilitate further development and maintenance of ICNP and b) extend significantly its functionality.

Internationality↗
PubMed2006

Digital tools for collecting data from cervigrams for research and training in colposcopy.

Colposcopy is a critical part of gynecologic practice but has documented deficiencies, including lack of correlation between the colposcopic appearance and the severity of underlying neoplasia, limited reproducibility, and difficulty in the optimal placement of colposcopically directed biopsies. In a collaborative effort to improve colposcopy, we are analyzing digitized cervigram images from National Cancer Institute-funded studies. Specifically, the National Cancer Institute has collected close to 100,000 cervigrams, digitized to create a database of images of the uterine cervix for research, training, and education. In addition to the cervigram images, this database contains clinical, cytologic, and molecular information at multiple examinations of 15,000 women, with password and ID labeling strategies to protect patient privacy. The National Library of Medicine has designed two web-accessible software tools. The Boundary Marking Tool allows experts on colposcopy to perform an evaluation of the pictures and to mark boundary regions of normal and abnormal regions of the uterine cervix; these evaluations are collected and saved in the database. The Multimedia Database Tool enables retrieval of test and image biomedical data according to specific queries, for example, all women with cervical intraepithelial neoplasia 3 whose cytologic results are atypical squamous cells of undetermined significance. The resource soon will be available as an open resource, via a teaching tool coordinated by a database manager, which will permit a variety of applications for teaching and research. In this article, we describe the perceived need for the resource and its components.

Biomedical Research↗
PubMed1992

Construction of simple pathways and simple cycles in ecosystems.

We present software tools for overcoming the problem of combinatorics in the enumeration of simple pathways and simple cycles in a first flow-through analysis of carbon transfer in large ecosystems. Rather than search through the very large number of potential routes in a reasonably sized ecosystem for the relatively small number of actual routes, our main algorithm performs an efficient rule-based construction of the actual routes. The enumeration of the unique pathways becomes tractable in terms of CPU time, which increases linearly with ecosystem size and connectedness. Networks of up to 80 entities can be evaluated using our software.

Algorithms↗
PubMed2001

Enhancing implant surgery planning via computerized image processing.

Computerized tomography (CT) and magnetic resolution imaging (MRI) are the medical imaging modalities to deliver cross-sectional images of the human body. In the last decade, CT has become the most frequently used imaging modality for the evaluation of the jaw for dental implants. Furthermore, image reformatting software has been developed in order to obtain a correct preoperative diagnosis and treatment planning regarding osseointegrated implants. Previous work has shown that CT images are affected by a distortion ration from 0% to 6%. This might be due to the alignment of the patient during scanning, to his/her movements, or possibly to the saturation of pixels composing the image. In order to solve the former problem, intraoral stents can be used to center the patient's head perpendicular to the axis of the implant to be inserted. However, if more than one implant must be placed - possibly with very different axes - it would be necessary to acquire the corresponding number of tomograms, each perpendicular to the axis of one planned tooth. Obviously, it would be better not to expose the patient to multiple CT scanning. In this work, we present a software approach for enhancing implants surgery planning in order to obtain exact morphological measurements of the bone and planned teeth with a single CT acquisition. This is achieved by applying image-processing techniques to the original CT images, in order to produce new Ct images lying on different planes, and possibly perpendicular to a different tooth. The resulting software system (Dental/Vox) has been implemented in C+ + and runs on Intel-based personal computers under the Windows operating systems. DentalVox ensures better mechanical results in the design and planning of a dental implant compared to other, similar software tools; it can reconstruct axial (and panorex and cross-sectional) images once any direction is chosen. This makes it possible to implant a mechanically and esthetically superior prothesis in the underlying gnathic morphology.

Dental Implantation, Endosseous↗
PubMed2001

Electronic collection of health-related quality of life data: validity, time benefits, and patient preference.

This study sought to validate World Wide Web-compliant software tools used to collect health-related quality of life (HRQOL) data, relative to pencil-and-paper collection. The RAND-36 general health survey and the Seattle Angina questionnaire (SAQ), a disease-specific functional status measure for patients with coronary artery disease, were each administered in paper and electronic format to 55 consecutive patients visiting the cardiology outpatient clinic of a public hospital. All eight sub-scale scores of the RAND-36 (interclass correlation coefficient range = 0.54-0.75, p < 0.01) and all five domains of the SAQ (interclass correlation coefficient range = 0.84-0.90, p < 0.01) collected using the software were significantly correlated with those collected using the paper version of questionnaires. Computer literacy, educational level, age, sex, and race were not significantly associated with the ability to successfully complete the computer-assisted questionnaire. Eighty-two percent of patients preferred the computer-assisted administration to paper, and 89% reported that they would feel comfortable using the software in the future without any technical assistance. This pilot study suggests that HRQOL measures can be reliably collected using software operating over the World Wide Web. Data collected in this manner are valid and of comparable quality to self-reported, HRQOL data obtained via paper survey.

Adult↗