SEARCH · PubMed Health

Results for “Tools”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 649 records · Page 36Linked to original sources

PubMed2006

The national continuous quality improvement tool for mental health education: results of targeted and supported implementation in England.

The national continuous quality assurance tool for mental health education and training has recently been developed. This paper describes the planned implementation of the tool across NHS Workforce Development Confederations (WDCs) in England. Large stakeholder groups in 15 WDCS were convened. The groups rated 29 programmes across a range of provisions including pre-qualifying programmes (social work and mental health nursing), post-qualifying programmes, new graduate mental health worker programmes and programmes run within NHS Trusts. Overall, the results indicate that the majority of rated programmes are relevant to the policy agenda and involve service users in a meaningful way. However, courses are less likely to engage with carers and to assess the impact of the programmes. Key factors are identified that promote the implementation of the new quality assurance tool and key barriers to implementation are also elicited. The paper concludes that the tool can provide a useful framework to assess the quality of a broad range of mental health education, furthermore, that it should be incorporated into existing quality assurance systems.

Curriculum↗

PubMed2002

Manual asymmetries in tool-use: implications for apraxia.

Previous examinations of manual performance asymmetries have utilised relatively simple movements such as goal-directed aiming and rapid finger-tapping. In the present research, three-dimensional kinematic analyses were employed to examine manual asymmetries in the production of transitive limb gestures. Transitive limb gestures involve the use of tools and/or objects and are complex movements used in the evaluation of limb apraxia. Ten healthy right hand dominant participants produced two transitive limb gestures in response to verbal command both with (tool-use) and without (pantomime) the appropriate tool. Analyses revealed a dominant (right) hand advantage, although the magnitude of this advantage was influenced by movement context (pantomime vs tool-use). This study provides the first evidence that manual asymmetries are elicited during the production of transitive limb gestures, and mandates that future kinematic analyses of limb apraxia consider the impact of pre-morbid manual asymmetries when contrasting the performance of left and right hemisphere damaged patients.

Journal Article↗

PubMedDate not supplied

A tool for designing digital test objects for module performance evaluation in medical digital imaging.

Currently, medical digital imaging systems are characterized by the introduction of additional modules such as digital display, image compression and image processing, as well as film printing and digitization. These additional modules require performance evaluation to ensure high image quality. A tool for designing computer-generated test objects applicable to performance evaluation of these modules is presented. The test objects can be directly used as digital images in the case of film printing, display, compression and image processing, or indirectly as images on film in the case of digitization. The performance evaluation approach is quality control protocol based. Digital test object design is user-driven according to specifications related to the requirements of the modules being tested. The available quality control parameters include input/output response curve, high contrast resolution, low contrast discrimination, noise, geometric distortion and field uniformity. The tool has been designed and implemented according to an object oriented approach in Visual C++ 5.0, and its user interface is based on the Microsoft Foundation Class Library version 4.2, which provides interface items such as windows, dialog boxes, lists, buttons, etc. The compatibility with DICOM 3.0 part 10 image formats specifications allows the integration of the tool in the existing software framework for medical digital imaging systems. The capability of the tool is demonstrated by direct use of the test objects in case of image processing, and indirect use of the test objects in case of film digitization.

Algorithms↗

PubMedDate not supplied

Quantitative exposure assessment for shipyard workers exposed to hand-transmitted vibration from a variety of vibration tools.

The quantitative exposure to vibration for shipyard workers who have used several kinds of vibratory tools was studied. The dose-response relationship between lifetime exposure dose and hand-arm vibration syndrome also was studied. The study included 344 workers who were exposed to vibration in one shipyard and 53 unexposed workers in the same company. Vibration measurements were made on several vibratory tools according to the international standard, ISO 5349. The actual exposure times for the vibratory tools were measured. Questionnaires for demographics, exposure to vibration, and confounding factors were completed. A lifetime vibration dose was calculated for each worker using job categories, usage pattern of vibratory tools, and the measured vibration acceleration magnitude. Each worker was asked about vascular and neurological symptoms, and symptoms were classified according to the Stockholm workshop scale. The prevalence of vascular and sensorineural symptoms for workers exposed to vibration was 22.7 and 78.2%, which were significantly higher than 0 and 34.0% obtained in the nonexposed workers, respectively. The prevalence and severity of the hand-arm vibration syndrome was increased with an increased lifetime vibration dose. The lifetime vibration dose showed a significant association with both vascular and sensorineural symptoms. In conclusion, the lifetime vibration dose was a useful parameter for quantitative exposure assessment and showed a dose-response relationship between exposure and symptoms when adjusted for confounding factors.

Adult↗

PubMed1998

The effectiveness of local exhaust-ventilated (shrouded) hand power tools used for grinding/sanding composite materials.

The effectiveness of one particular shrouded tool type in capturing composite dust generated during dry machining operations was tested. The effectiveness of the shrouded tool was measured by comparing exposures during identical operations done by the same workers. The operation was conducted by dividing the time into two equal portions, one using an unshrouded tool and the other with same tool shrouded. The operations included sanding and grinding operations of fibrous glass/epoxy composite materials. Unshrouded short-term exposures ranged from 2.17 mg/m3 to 50.81 mg/m3. There was a significant reduction in exposure using the shroud (paired t-test, p = 0.005). The effect of a shroud on respirable dust exposures was inconclusive, because of the limited amount of respirable dust collected in these short-term samples.

Aerosols↗

PubMed1997

Manual specialisation and tool use in captive chimpanzees (Pan troglodytes): the effect of unimanual and bimanual strategies on hand preference.

Hand preference for tool use was assessed in a sample of captive chimpanzees (Pan troglodytes). Whether the subjects solved the tool task using either a unimanual or coordinated bimanual strategy was manipulated in the chimpanzees. No population-level hand preference was found for tool use when unimanual strategies were used by the chimpanzees. However, a population-level right-hand bias was found when coordinated bimanual actions were required of the chimpanzees. A significant correlation was found in hand use for the two hand preference testing conditions. Neither sex nor rearing was found to significantly affect the direction or strength in hand preference. These results may explain discrepancies in hand preference reported in captive and wild chimpanzees with regard to tool use and other manual activities.

Journal Article↗

PubMed2006

Dose response explorer: an integrated open-source tool for exploring and modelling radiotherapy dose-volume outcome relationships.

Radiotherapy treatment outcome models are a complicated function of treatment, clinical and biological factors. Our objective is to provide clinicians and scientists with an accurate, flexible and user-friendly software tool to explore radiotherapy outcomes data and build statistical tumour control or normal tissue complications models. The software tool, called the dose response explorer system (DREES), is based on Matlab, and uses a named-field structure array data type. DREES/Matlab in combination with another open-source tool (CERR) provides an environment for analysing treatment outcomes. DREES provides many radiotherapy outcome modelling features, including (1) fitting of analytical normal tissue complication probability (NTCP) and tumour control probability (TCP) models, (2) combined modelling of multiple dose-volume variables (e.g., mean dose, max dose, etc) and clinical factors (age, gender, stage, etc) using multi-term regression modelling, (3) manual or automated selection of logistic or actuarial model variables using bootstrap statistical resampling, (4) estimation of uncertainty in model parameters, (5) performance assessment of univariate and multivariate analyses using Spearman's rank correlation and chi-square statistics, boxplots, nomograms, Kaplan-Meier survival plots, and receiver operating characteristics curves, and (6) graphical capabilities to visualize NTCP or TCP prediction versus selected variable models using various plots. DREES provides clinical researchers with a tool customized for radiotherapy outcome modelling. DREES is freely distributed. We expect to continue developing DREES based on user feedback.

Computer Simulation↗

PubMed2003

PAINT: a promoter analysis and interaction network generation tool for gene regulatory network identification.

We have developed a bioinformatics tool named PAINT that automates the promoter analysis of a given set of genes for the presence of transcription factor binding sites. Based on coincidence of regulatory sites, this tool produces an interaction matrix that represents a candidate transcriptional regulatory network. This tool currently consists of (1) a database of promoter sequences of known or predicted genes in the Ensembl annotated mouse genome database, (2) various modules that can retrieve and process the promoter sequences for binding sites of known transcription factors, and (3) modules for visualization and analysis of the resulting set of candidate network connections. This information provides a substantially pruned list of genes and transcription factors that can be examined in detail in further experimental studies on gene regulation. Also, the candidate network can be incorporated into network identification methods in the form of constraints on feasible structures in order to render the algorithms tractable for large-scale systems. The tool can also produce output in various formats suitable for use in external visualization and analysis software. In this manuscript, PAINT is demonstrated in two case studies involving analysis of differentially regulated genes chosen from two microarray data sets. The first set is from a neuroblastoma N1E-115 cell differentiation experiment, and the second set is from neuroblastoma N1E-115 cells at different time intervals following exposure to neuropeptide angiotensin II. PAINT is available for use as an agent in BioSPICE simulation and analysis framework (www.biospice.org), and can also be accessed via a WWW interface at www.dbi.tju.edu/dbi/tools/paint/.

Angiotensin II↗

PubMed2003

An applications-focused review of comparative genomics tools: capabilities, limitations and future challenges.

A team at the Lawrence Livermore National Laboratory (LLNL) was given the task of using computational tools to speed up the development of DNA diagnostics for pathogen detection. This work will be described in another paper in this issue (see pages 133-149). To achieve this goal it was necessary to understand the merits and limitations of the various available comparative genomics tools. A review of some recent tools for multisequence/genome alignment and substring comparison is presented, within the general framework of applicability to a large-scale application. We note that genome alignments are important for many things, only one of which is pathogen detection. Understanding gene function, gene regulation, gene networks, phylogenetic studies and other aspects of evolution all depend on accurate nucleic acid and protein sequence alignment. Selecting appropriate tools can make a large difference in the quality of results obtained and the effort required.

Algorithms↗

PubMed2026

Phage bioinformatics tools: a review of computational approaches for bacteriophage research.

Rising clinical interest in phage therapy and the exponential growth of metagenomic sequence catalogues have driven a rapid expansion of bacteriophage bioinformatics. More than 80 dedicated tools, mostly published since 2020, now span identification, assembly, annotation, taxonomy, lifestyle prediction, defence-system detection, and host prediction. Aimed at experienced practitioners and developers, this review synthesizes the field through the lens of three successive computational paradigms: sequence homology, bounded by database completeness; machine learning, constrained by labelled training data; and foundation models, which now achieve Matthews correlation coefficients above 0.95 in identification tasks and, through structure-informed prediction, raise functional annotation to over half of phage genes. Furthermore, we map the upstream components, namely, gene callers, homology engines, protein language models, and structural search tools, that underpin most downstream pipelines, exposing shared infrastructure and ecosystem-level fragility when dependencies change. To translate this into practice, we propose web-based and command-line reference workflows calibrated to user expertise and sample types. Finally, we set an agenda for the next wave of tool development. Roughly half of phage genes still resist functional annotation despite structural methods; no broadly generalizable strain-level host predictor exists for phage therapy; varying true-positive rates (0%-97%) underscore the absence of standardized community benchmarks analogous to Critical Assessment of Structure Prediction or Critical Assessment of Metagenome Interpretation. As generative genome models begin designing synthetic phages, progress will depend less on producing standalone tools than on rigorous evaluation, interoperable infrastructure, and clinically meaningful prediction targets.

Computational Biology↗

PubMed2026

OmniExtract: an automatic data extraction tool based on large language model and prompt engineering.

Extracting structured information from documents or scientific papers is crucial for data sharing and retrieval. Recent advances in large language models (LLMs) have demonstrated strong capabilities in language understanding, and a number of LLM-based tools have been developed for extraction-oriented tasks. However, it's still difficult to find a universal and user-friendly tool for various practical extraction tasks. To address this challenge, we propose OmniExtract, an automatic data extraction tool with user-friendly configuration files that can adapt to various data extraction tasks. OmniExtract employs a prompt optimization method to refine task-specific prompts and achieve high extraction performance. It also supports comprehensive data extraction from both documents and tables, making it applicable to a broad range of data sources. Evaluation results show that OmniExtract obtains a high accuracy ~90% for three datasets. Furthermore, two additional data extraction applications of OmniExtract in real-world scenarios have been presented, achieving an accuracy of 92.21% and ~90% precision and recall, respectively. Specifically, OmniExtract can handle tabular files of various sizes and formats, and achieve over 99% precision and recall on table information extraction tasks. The data reliability performance shows that OmniExtract is a valuable tool for database updating. An online testing service is available at https://ngdc.cncb.ac.cn/omniextract/. The service can be deployed locally with the code in https://github.com/wyb39/OmniExtract.

Large Language Models↗

PubMed2026

CHITRA: an interactive visualization tool for comparative genomic rearrangement analysis.

MOTIVATION: The increasing availability of chromosome-scale genome assemblies has fuelled a renewed interest in studying chromosomal evolution and rearrangements. Synteny visualization plays a critical role in understanding genome organization, structural variations, and evolutionary relationships. However, existing tools often have steep learning curves, produce static plots, or are limited in their ability to analyse multiple genomes simultaneously. There is a growing need for an intuitive and interactive visualization tool that can effectively explore syntenic relationships and chromosomal rearrangements. RESULTS: Here, we present CHITRA, a web-based interactive tool designed to visualize synteny blocks, chromosomal rearrangements, and breakpoints in both linear and circular styles. CHITRA-enables real-time exploration of genome structural variations with an intuitive graphical interface, customizable visualization options, and high-resolution export capabilities for publication-ready figures. The tool supports chromosome- and scaffold-level assemblies and allows users to filter, highlight, and interactively examine syntenic relationships. AVAILABILITY AND IMPLEMENTATION: CHITRA is freely available at https://chitra.bioinformaticsonline.com/, with comprehensive documentation at https://chitra.bioinformaticsonline.com/docs. The source code is open-source and accessible on GitHub at https://github.com/pranjalpruthi/CHITRA.

Journal Article↗

PubMed2026

Malaria-GENOMAP: a web-based tool for exploring genomic variation of malaria parasites.

MOTIVATION: Malaria, caused by Plasmodium parasites, imposes a significant public health burden. While Plasmodium falciparum remains the primary target of elimination strategies due to its high mortality rate, lesser-known species such as P. malariae, P. vivax, and P. knowlesi continue to contribute to substantial human morbidity. Genomic approaches, including whole-genome sequencing, offer powerful tools for understanding the biology, transmission, and emerging drug resistance of these neglected Plasmodium species. However, there is an urgent need for informatic tools to summarize and visualize the high-dimensional and complex genomic data generated. RESULTS: We developed Malaria-GENOMAP, a user-friendly web-based tool, which integrates genomic variant data, such as allele frequencies, with geographical maps and chromosome-wide to gene views for in-depth exploration. The tool includes variation from P. knowlesi (n = 139), P. malariae (n = 158), P. ovale curtisi (n = 36), P. ovale wallikeri (n = 47), P. simium (n = 38), and P. vivax (n = 1359). It enables the investigation of population structure, geographic associations of mutations, and putative drug resistance markers, offering valuable insights for malaria control efforts. AVAILABILITY AND IMPLEMENTATION: Malaria-GENOMAP is available online at https://genomics.lshtm.ac.uk/malaria-genomaps.

Internet↗

PubMed2004

NetAffx Gene Ontology Mining Tool: a visual approach for microarray data analysis.

SUMMARY: The NetAffx Gene Ontology (GO) Mining Tool is a web-based, interactive tool that permits traversal of the GO graph in the context of microarray data. It accepts a list of Affymetrix probe sets and renders a GO graph as a heat map colored according to significance measurements. The rendered graph is interactive, with nodes linked to public web sites and to lists of the relevant probe sets. The GO Mining Tool provides visualization combining biological annotation with expression data, encompassing thousands of genes in one interactive view. AVAILABILITY: GO Mining Tool is freely available at http://www.affymetrix.com/analysis/query/go_analysis.affx

Abstracting and Indexing↗

PubMed2004

Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting.

UNLABELLED: A set of new algorithms and software tools for automatic protein identification using peptide mass fingerprinting is presented. The software is automatic, fast and modular to suit different laboratory needs, and it can be operated either via a Java user interface or called from within scripts. The software modules do peak extraction, peak filtering and protein database matching, and communicate via XML. Individual modules can therefore easily be replaced with other software if desired, and all intermediate results are available to the user. The algorithms are designed to operate without human intervention and contain several novel approaches. The performance and capabilities of the software is illustrated on spectra from different mass spectrometer manufacturers, and the factors influencing successful identification are discussed and quantified. MOTIVATION: Protein identification with mass spectrometric methods is a key step in modern proteomics studies. Some tools are available today for doing different steps in the analysis. Only a few commercial systems integrate all the steps in the analysis, often for only one vendor's hardware, and the details of these systems are not public. RESULTS: A complete system for doing protein identification with peptide mass fingerprints is presented, including everything from peak picking to matching the database protein. The details of the different algorithms are disclosed so that academic researchers can have full control of their tools. AVAILABILITY: The described software tools are available from the Halmstad University website www.hh.se/staff/bioinf/ SUPPLEMENTARY INFORMATION: Details of the algorithms are described in supporting information available from the Halmstad University website www.hh.se/staff/bioinf/

Algorithms↗

PubMed2005

An extensible automated protein annotation tool: standardizing input and output using validated XML.

MOTIVATION: There is a frequent need to apply a large range of local or remote prediction and annotation tools to one or more sequences. We have created a tool able to dispatch one or more sequences to assorted services by defining a consistent XML format for data and annotations. RESULTS: By analyzing annotation tools, we have determined that annotations can be described using one or more of the six forms of data: numeric or textual annotation of residues, domains (residue ranges) or whole sequences. With this in mind, XML DTDs have been designed to store the input and output of any server. Plug-in wrappers to a number of services have been written which are called from a master script. The resulting APATML is then formatted for display in HTML. Alternatively further tools may be written to perform post-analysis.

Amino Acid Sequence↗

PubMed2004

A distributed left hemisphere network active during planning of everyday tool use skills.

Determining the relationship between mechanisms involved in action planning and/or execution is critical to understanding the neural bases of skilled behaviors, including tool use. Here we report findings from two fMRI studies of healthy, right-handed adults in which an event-related design was used to distinguish regions involved in planning (i.e. identifying, retrieving and preparing actions associated with a familiar tools' uses) versus executing tool use gestures with the dominant right (experiment 1) and non-dominant left (experiment 2) hands. For either limb, planning tool use actions activates a distributed network in the left cerebral hemisphere consisting of: (i) posterior superior temporal sulcus, along with proximal regions of the middle and superior temporal gyri; (ii) inferior frontal and ventral premotor cortices; (iii) two distinct parietal areas, one located in the anterior supramarginal gyrus (SMG) and another in posterior SMG and angular gyrus; and (iv) dorsolateral prefrontal cortex (DLFPC). With the exception of left DLFPC, adjacent and partially overlapping sub-regions of left parietal, frontal and temporal cortex are also engaged during action execution. We suggest that this left lateralized network constitutes a neural substrate for the interaction of semantic and motoric representations upon which meaningful skills depend.

Adult↗

PubMed1999

ConStruct: a tool for thermodynamic controlled prediction of conserved secondary structure.

A tool for prediction of conserved secondary structure of a set of homologous single-stranded RNAs is presented. For each RNA of the set the structure distribution is calculated and stored in a base pair probability matrix. Gaps, resulting from a multiple sequence alignment of the RNA set, are introduced into the individual probability matrices. These 'aligned' probability matrices are summed up to give a consensus probability matrix emphasizing the conserved structural elements of the RNA set. Because the multiple sequence alignment is independent of any structural constraints, such an alignment may result in introduction of gaps into the homologous probability matrices that disrupt a common consensus structure. By use of its graphical user interface the presented tool allows the removal of such misalignments, which are easily recognized, from the individual probability matrices by optimizing the sequence alignment with respect to a structural alignment. From the consensus probability matrix a consensus structure is extracted, which is viewable in three different graphical representations. The functionality of the tool is demonstrated using a small set of U7 RNAs, which are involved in 3'-end processing of histone mRNA precursors. Supplementary Material lists further results obtained. Advantages and drawbacks of the tool are discussed in comparison to several other algorithms.

Algorithms↗