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At least 1,261 records · Page 70Linked to original sources

PubMed2005

SNPdetector: a software tool for sensitive and accurate SNP detection.

Identification of single nucleotide polymorphisms (SNPs) and mutations is important for the discovery of genetic predisposition to complex diseases. PCR resequencing is the method of choice for de novo SNP discovery. However, manual curation of putative SNPs has been a major bottleneck in the application of this method to high-throughput screening. Therefore it is critical to develop a more sensitive and accurate computational method for automated SNP detection. We developed a software tool, SNPdetector, for automated identification of SNPs and mutations in fluorescence-based resequencing reads. SNPdetector was designed to model the process of human visual inspection and has a very low false positive and false negative rate. We demonstrate the superior performance of SNPdetector in SNP and mutation analysis by comparing its results with those derived by human inspection, PolyPhred (a popular SNP detection tool), and independent genotype assays in three large-scale investigations. The first study identified and validated inter- and intra-subspecies variations in 4,650 traces of 25 inbred mouse strains that belong to either the Mus musculus species or the M. spretus species. Unexpected heterozygosity in CAST/Ei strain was observed in two out of 1,167 mouse SNPs. The second study identified 11,241 candidate SNPs in five ENCODE regions of the human genome covering 2.5 Mb of genomic sequence. Approximately 50% of the candidate SNPs were selected for experimental genotyping; the validation rate exceeded 95%. The third study detected ENU-induced mutations (at 0.04% allele frequency) in 64,896 traces of 1,236 zebra fish. Our analysis of three large and diverse test datasets demonstrated that SNPdetector is an effective tool for genome-scale research and for large-sample clinical studies. SNPdetector runs on Unix/Linux platform and is available publicly (http://lpg.nci.nih.gov).

Algorithms↗

PubMed2000

The NCBI. Publicly available tools and resources on the Web.

As computing technology advances and new sources of valuable biological information are collected the numbers of database and the tools that are used to analyze the data they contain will change. From the time this article was originally written to the time (about 6 months) this summary was put together another 4 releases of Genbank have been made available, two new BLAST search engines, PHI-BLAST and organism-specific BLAST, a database of Human Genetic Variation (dbSNP), and a new version of Cn-3D. The NCBI will, for the forseeable future, provide the research community with a wealth of information and computing tools. made a number of other tools available for molecular biologists.

Animals↗

PubMed2004

Multi-colored simplified asthma guideline reminder: why pragmatic asthma tools are needed in real-world practice.

Asthma is a chronic disease that is highly prevalent around the world with increasing societal and economic burden. National Asthma Educational and Preventive Program (NAEPP) and Global Initiative for Asthma (GINA) are evidence-based documents designed to help clinicians make appropriate decisions for their patients and to reduce undesirable variation in the care of asthmatic patients. It is a generally accepted fact that asthma specialists achieved better and improved asthma outcomes for their patients when compared with primary care physicians (PCPs). These outcome differences are somewhat related to PCPs' poor adherence to published NAEPP guidelines. Multi-Colored Simplified Asthma Guideline Reminder (MSAGR) is the first user-friendly single-sheet convenient asthma tool designed for clinicians after barriers to the poor adherence to asthma guidelines in primary care settings were identified. Voluntary acceptance and utilization of MSAGR resulted in fewer emergency room visits and hospitalizations for their patients. General acceptance of MSAGR (more than 1 million copies requested by clinicians globally), and overwhelming positive comments by asthma care providers, strongly advocate a need for real-time, pragmatic clinical tools not only in asthma, but also in other chronic diseases such as chronic obstructive pulmonary disease, diabetes mellitus, hypertension, and depression, etc. In this brief review, we discuss how clinicians, patients, and payers are utilizing these simplified asthma tools to improve asthma care in their community.

Adult↗

PubMed2006

Diagnostic tools for early caries detection.

BACKGROUND: Management of dental caries demands early detection of carious lesions. This article provides an overview of the state-of-the-art methodologies for the detection and assessment of early carious lesions. TYPES OF STUDIES REVIEWED: The authors reviewed MEDLINE for available literature on new caries detection methodology and tools, using terms such as "early caries detection," "fluorescence" and "transillumination." Their review was not a systematic review of the literature. They included in their review in vitro, in situ, in vivo and clinical studies, as well as position papers, editorials and consensus conferences statements published in English. RESULTS: Each early caries detection tool has advantages and disadvantages; some perform better on certain surfaces than others. Therefore, their performance threshold and the operator's influence on performance must be considered. Not all methods accurately detect early lesions, and false positives and false negatives may occur. Detecting early lesions in combination with assessing activity status is essential for establishing the prognosis and threshold required for preventive intervention. Clinically useful tools to help make such decisions are under development. CLINICAL IMPLICATIONS: Early caries detection methods should be an adjunct to clinical decision making, supporting preventive treatment planning in conjunction with caries risk assessment but not justifying premature restorative intervention.

Dental Caries↗

PubMed2005

New bioinformatics tools for viral genome analyses at Viral Bioinformatics--Canada.

Viruses are much smaller than prokaryotes and eukaryotes, and it is now practical to sequence closely related members of virus families, strains, or even different isolates recovered during the course of an outbreak. However, comparative analysis of viral genomes requires the development of novel bioinformatics tools that allow us to align, edit, compare and interact with these genomes at all levels, from whole genome, to gene family, to single nucleotide polymorphisms. Comparative viral genomics can lead to the identification of the core characteristics that define a virus family, as well as the unique properties of viral species or isolates that contribute to variations in pathogenesis. This paper describes a number of tools, mainly developed for Viral Bioinformatics--Canada, that can be used for annotation and comparative genomic analysis of poxviruses. Nonetheless, these tools are also broadly applicable to other virus families.

Base Sequence↗

PubMed2003

Determining the effectiveness of the usability problem inspector: a theory-based model and tool for finding usability problems.

Despite the increased focus on usability and on the processes and methods used to increase usability, a substantial amount of software is unusable and poorly designed. Much of this is attributable to the lack of cost-effective usability evaluation tools that provide an interaction-based framework for identifying problems. We developed the user action framework and a corresponding evaluation tool, the usability problem inspector (UPI), to help organize usability concepts and issues into a knowledge base. We conducted a comprehensive comparison study to determine if our theory-based framework and tool could be effectively used to find important usability problems in an interface design, relative to two other established inspection methods (heuristic evaluation and cognitive walkthrough). Results showed that the UPI scored higher than heuristic evaluation in terms of thoroughness, validity, and effectiveness and was consistent with cognitive walkthrough for these same measures. We also discuss other potential advantages of the UPI over heuristic evaluation and cognitive walkthrough when applied in practice. Potential applications of this work include a cost-effective alternative or supplement to lab-based formative usability evaluation during any stage of development.

Adult↗

PubMed2001

Correctional officers' intention of accepting or refusing to make HIV preventive tools accessible to inmates.

The aim of this study was to identify the factors which explain correctional officers' intention of accepting or refusing to make HIV preventive tools (condoms, bleach, tattooing equipment, and syringes) accessible to inmates. A total of 957 officers completed a questionnaire that took into account determinants from several social-cognitive behavior theories. The results indicated that only 21.4% of officers were favorable toward making accessible all of the preventive tools. The theoretical model explained 87% of the intention variance, p < .0001. Self-efficacy (beta = .35), personal normative belief (beta = .29), social determinants (beta = .21) and the affective dimension of attitude (beta = .19) were significant determinants. Moreover, officers with a high level of intention differed from those with a low level of intention on several points of the theoretical model. In conclusion, the results clearly indicated that several difficulties must be overcome before HIV preventive tools as a whole can be made accessible to inmates.

Adult↗

PubMed1982

[Studies of peripheral nerve conduction velocities in vibrating tool operators].

Vibrating tools such as chain-saws, rock-drills, grinders and tie-tampers have been widely used in many kinds of industries in Japan, causing vibration syndrome among the operators. As is well-known, the syndrome includes disorders of the peripheral circulation in the hands, e.g. Raynaud's phenomenon, and of the peripheral and central nervous systems. As the result of preventive countermeasures to the syndrome during the last decade, the picture of the syndrome has been partly changing especially for the patients among the state forestry workers; for example, the prevalence of the peripheral nerve disorders has been relatively increasing compared with that of Raynaud's phenomenon. Peripheral nerve disorders such as numbness, paresthesia and hypesthesia in the upper limbs tend to be usually cumulative and irreversible. The disorders are very important problem of vibration syndrome from the standpoint of treatment and prevention, though there are only a few reports of the study on the disorders using electrophysiological methods. In order to make objectively clear the peripheral nerve disorders, 236 male vibrating tool operators (= Group V) were examined. The following nerve conduction velocities were measured: (1) Maximal motor nerve conduction velocities (MCV) of the median and ulnar nerves in the forearm. (2) Sensory nerve conduction velocities (SCV) of the median and ulnar nerves in the forearm and palm. (3) Residual latency (RL) of the median and ulnar nerves. Besides, working conditions and complaints relevant to vibration syndrome were examined by using questionnaires. MCVs, SCVs and RLs that were outside of mean +/- 2 S.D. of the control group (= Group C), consisting of 30 healthy men, were evaluated as abnormal. The obtained results led to the following conclusions: (1) All MCVs, SCVs and RLs of Group V were significantly less than those of the control group. In Group V, prevalence of the abnormality in each of forearm SCVs was higher than that in each of MCVs of the corresponding nerves. (2) The difference between the median and ulnar SCV in the palm and the respective SCV in the forearm of each subject was significantly greater for Group V than Group C. (Palm-forearm difference) (3) The difference between the forearm and palmar SCV of the ulnar nerve and the respective velocities of the median nerve was statistically greater for Group V than for Group C. (Ulnar-median difference) (4) Ulnar SCV in the palm of Group V was significantly related to the total operating hours of vibrating tools. (5) There was no significant relation between all the nerve conduction velocities and the white finger attack. But a significant relation was noticed between the prevalence of the abnormal values of ulnar SCV in the palm and the peripheral circulatory function score computed from the data of nail press test and cold immersion test.

Adult↗

PubMed2006

Assessment and optimization of mortality prediction tools for admissions to pediatric intensive care in the United kingdom.

OBJECTIVE: To assess the Pediatric Risk of Mortality (PRISM, PRISM III-12, and PRISM III-24) systems and the Pediatric Index of Mortality (PIM and PIM2) systems for use in comparing the risk-adjusted mortality of children after admission for pediatric intensive care in the United Kingdom. METHODS: All PICUs in the United Kingdom were invited to participate. Predicted probability of PICU mortality was calculated using the published algorithms for PIM, PIM2, and PRISM and compared with observed mortality. These scores, along with PRISM III-12 and PRISM III-24, whose algorithms are not published, were optimized for the United Kingdom. RESULTS: Of 26 PICUs in the United Kingdom, 22 (85%) were recruited, and sufficient prospective data were collected from 18 (69%) units on 10,197 (98%) of 10,385 admissions between March 2001 and February 2002. All published tools were found to have poor calibration but provided good discriminatory power. After estimation of UK-specific coefficients, only PIM2, PRISM III-12, and PRISM III-24 had satisfactory calibration. All models provided good discriminatory power. Funnel plots for all of the recalibrated models indicated that the risk-adjusted mortality for all units was consistent with random variation. CONCLUSIONS: PIM2, PRISM III-12, and PRISM III-24 all were found to be suitable for use in a UK PICU setting. All tools provided similar conclusions in assessing the distribution of risk-adjusted mortality in UK PICUs. It now is important that these tools be used to monitor outcome and improve the quality of pediatric intensive care within the United Kingdom.

Child↗

PubMed2003

Two-dimensional gap analysis: a tool for efficient conservation planning and biodiversity policy implementation.

The maintenance of biodiversity by securing representative and well-connected habitat networks in managed landscapes requires a wise combination of protection, management, and restoration of habitats at several scales. We suggest that the integration of natural and social sciences in the form of "Two-dimensional gap analysis" is an efficient tool for the implementation of biodiversity policies. The tool links biologically relevant "horizontal" ecological issues with "vertical" issues related to institutions and other societal issues. Using forest biodiversity as an example, we illustrate how one can combine ecological and institutional aspects of biodiversity conservation, thus facilitating environmentally sustainable regional development. In particular, we use regional gap analysis for identification of focal forest types, habitat modelling for ascertaining the functional connectivity of "green infrastructures", as tools for the horizontal gap analysis. For the vertical dimension we suggest how the social sciences can be used for assessing the success in the implementation of biodiversity policies in real landscapes by identifying institutional obstacles while implementing policies. We argue that this interdisciplinary approach could be applied in a whole range of other environments including other terrestrial biota and aquatic ecosystems where functional habitat connectivity, nonlinear response to habitat loss and a multitude of economic and social interests co-occur in the same landscape.

Conservation of Natural Resources↗

PubMed2004

A front-end automation tool supporting design, verification and reuse of SOC.

This paper describes an in-house developed language tool called VPerl used in developing a 250 MHz 32-bit high-performance low power embedded CPU core. The authors showed that use of this tool can compress the Verilog code by more than a factor of 5, increase the efficiency of the front-end design, reduce the bug rate significantly. This tool can be used to enhance the reusability of an intellectual property model, and facilitate porting design for different platforms.

Algorithms↗

PubMed2005

Use of a content analysis procedure for the development of a Falls Management Audit Tool.

The Falls Management Audit Tool (FMAT) was developed to assess the documentation of the falls management process in nursing homes. The multistep content analysis procedure was used to guide tool development and obtain reliability and validity of the FMAT. Established fall guidelines and national experts were used for item development. Trained gerontological nurse practitioners conducted chart audits in nursing home residents with a fall history. Adequate content validity (content validity index > .88) and interrater and intrarater reliability were established (kappas > .78) in the final version of the 57-item FMAT and pilot testing demonstrated feasibility. This study provided evidence that the FMAT is a reliable and valid tool, which can be used to assess the documentation of the falls management process and for measuring the effect of research or quality improvement interventions.

Accidental Falls↗

PubMed1995

Risk analysis systems for veterinary biologicals: a regulator's tool box.

Recent advances in biology and technology have significantly improved our ability to produce veterinary biologicals of high purity, efficacy and safety, virtually anywhere in the world. At the same time, increasing trade and comprehensive trade agreements, such as the Uruguay Round of the General Agreement on Tariffs and Trade (GATT: now the World Trade Organisation [WTO]), have put pressure on governments to use scientific principles in the regulation of trade for a wide range of products, including veterinary biologicals. In many cases, however, nations have been reluctant to allow the movement of veterinary biologicals, due to the perceived threat of importing an exotic disease. This paper discusses the history of risk analysis as a decision support tool and provides examples of how this tool may be used in a science-based regulatory system for veterinary biologicals. A wide variety of tools are described, including qualitative, semi-quantitative and quantitative methods, most with a long history of use in engineering and the health and environmental sciences.

Animals↗

PubMedDate not supplied

Accelerated deployment of an agricultural nutrient management tool: the Maryland Phosphorus Site Index.

In 1998, the Maryland legislature mandated nitrogen (N) and phosphorus (P) nutrient management planning for nearly all of Maryland's commercial agricultural operations. State regulations required that a phosphorus indexing tool (P Index) be used for determining the potential for P losses from agricultural land, even though a reliable P Index did not exist. The development and assessment of the P Index as a dependable tool for the evaluation of the potential for P losses was constrained by a very aggressive implementation schedule imposed by state regulations. The Maryland Phosphorus Site Index (PSI) was evaluated on 646 state-representative field sites beginning in the spring of 1999 and continuing through the spring of 2000. Of the representative fields, 69% were determined to have a "low" P loss rating, 19% were in the "medium" P loss rating category, 8% were determined to be a "high" risk for P loss, and 4% rated as "very high" P loss potential. Fifty-five percent of the fields evaluated had soil test phosphorus (STP) levels less than the 75 mg kg-1 Mehlich-1 P environmental threshold established by state regulations. The frequency distribution of PSI performance was evaluated for several subcategories of the statewide data set. The Maryland PSI will be deployed for use in constructing farm nutrient management plans well before its predictive capabilities can be objectively and rigorously validated. Field validation is essential. In the meantime, the Maryland PSI should function adequately as a tool to assist in the prioritization of field P loss risk potential.

Agriculture↗

PubMed2002

MarC-V: a spreadsheet-based tool for analysis, normalization, and visualization of single cDNA microarray experiments.

The comprehensive analysis and visualization of data extracted from cDNA microarrays can be a time-consuming and error-prone process that becomes increasingly tedious with increased number of gene elements on a particular microarray. With the increasingly large number of gene elements on today's microarrays, analysis tools must be developed to meet this challenge. Here, we present MarC-V, a Microsoft Excel spreadsheet tool with Visual Basic macros to automate much of the visualization and calculation involved in the analysis process while providing the familiarity and flexibility of Excel. Automated features of this tool include (i) lower-bound thresholding, (ii) data normalization, (iii) generation of ratio frequency distribution plots, (iv) generation of scatter plots color-coded by expression level, (v) ratio scoring based on intensity measurements, (vi) filtering of data based on expression level or specific gene interests, and (vii) exporting data for subsequent multi-array analysis. MarC-V also has an importing function included for GenePix results (GPR) raw data files.

DNA, Complementary↗

PubMed2002

Performance evaluation of swimmers: scientific tools.

The purpose of this article is to provide a critical commentary of the physiological and psychological tools used in the evaluation of swimmers. The first-level evaluation should be the competitive performance itself, since it is at this juncture that all elements interplay and provide the 'highest form' of assessment. Competition video analysis of major swimming events has progressed to the point where it has become an indispensable tool for coaches, athletes, sport scientists, equipment manufacturers, and even the media. The breakdown of each swimming performance at the individual level to its constituent parts allows for comparison with the predicted or sought after execution, as well as allowing for comparison with identified world competition levels. The use of other 'on-going' monitoring protocols to evaluate training efficacy typically involves criterion 'effort' swims and specific training sets where certain aspects are scrutinised in depth. Physiological parameters that are often examined alongside swimming speed and technical aspects include oxygen uptake, heart rate, blood lactate concentration, blood lactate accumulation and clearance rates. Simple and more complex procedures are available for in-training examination of technical issues. Strength and power may be quantified via several modalities although, typically, tethered swimming and dry-land isokinetic devices are used. The availability of a 'swimming flume' does afford coaches and sport scientists a higher degree of flexibility in the type of monitoring and evaluation that can be undertaken. There is convincing evidence that athletes can be distinguished on the basis of their psychological skills and emotional competencies and that these differences become further accentuated as the athlete improves. No matter what test format is used (physiological, biomechanical or psychological), similar criteria of validity must be ensured so that the test provides useful and associative information concerning current or future performance. The practical worth of any proposed testing or monitoring protocol should be carefully evaluated. In addition, the developmental stage of the athlete(s) in question should be reflected in the testing/monitoring programme. Finally, increasing technological innovations will bring to the pool deck or dry-land training area simple, fast and advanced diagnostic tools, particularly in the areas of blood-borne markers of training response and neuromuscular excitability.

Heart Rate↗

PubMed2003

Integer/linear mathematical programming models: a tool for allocating healthcare resources.

In today's environment, the demand for efficient healthcare resource allocation is increasing. As new technologies become available, allocation decisions become more complex and tools to assist decision makers in determining efficient allocations of healthcare resources are encouraged. Mathematical programs have multiple properties that are desirable for healthcare decision makers such as the simultaneous consideration of multiple constraints and a built-in sensitivity analysis. These models have been well researched and are considered invaluable in other industries. Mathematical programming has also become increasingly visible in facilitating the allocation of healthcare resources in the health services research sector. However, the use of mathematical programming tools has been limited in economic evaluations of new technologies. Budget allocations, such as formulary, drug development, and pricing decisions may benefit greatly from the use of mathematical programs. As an increasing number of expensive new technologies become available and pressure grows to contain healthcare costs, these tools may help guide a more efficient allocation of resources for technologies under budgetary and other constraints.

Decision Making↗

PubMed2001

Information technology tools for efficient SNP studies.

We are currently facing a new era of studies involving single nucleotide polymorphisms (SNPs). This increased attention is stimulated by interest in individual differences in disease susceptibility as well as individual responses to drug treatment and the falling cost of genotyping. This review is a guide to the numerous public data repositories and Information Technology (IT) tools that may aid planning, preparation, running and analysis of studies involving SNPs. I will also highlight areas where researchers will have to resort to home-made IT solutions. Unfortunately, both information and IT tools are scattered throughout the internet and a lack of data exchange conventions can hamper the efficient use of these existing resources. This can lead to situations where the planning, preparation and analysis of a SNP study can actually cost more than the actual genotyping. We propose that only a customizable backbone IT infrastructure for SNP studies can help reduce costs associated with SNP data handling and tool launching.

Genetic Diseases, Inborn↗