Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “software tools”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 1,333 records · Page 74Linked to original sources
PubMed2006

De novo structure-based design of bisurea hosts for tetrahedral oxoanion guests.

This paper presents a computational approach to the deliberate design of improved host architectures. De novo molecule building software, HostDesigner, is interfaced with molecular mechanics software, GMMX, providing a tool for generating and screening millions of potential structures. The efficacy of this computer-aided design methodology is illustrated with a search for bisurea podands that are structurally organized for complexation with tetrahedral oxoanions.

Journal Article↗
PubMed2003

[Analysis of EEG coherence in examination of an automation deficit in reading-spelling disorder--a pilot study].

OBJECTIVES: Do dyslexic children exhibit a general automatizational deficit as well as a phonological deficit? METHODS: In 16 children aged 9-11 years the reaction time, the number of mistakes and EEG (19 scalp electrodes) were measured in three experiments (verbal and nonverbal). The EEG data was baseline-corrected and after a fast fourier transformation, analyzed with the coherence tool of the Brainvision Software. RESULTS: The dyslexic group made more mistakes than the control group on all tasks but their reaction times were significantly longer only on the verbal tasks. There were no coherence differences on the nonverbal task. On the language-dependent tasks the dyslexics showed higher total-frontal and lower left-frontal coherences only in the theta-frequency range, while in the alpha and beta frequency ranges coherences did not differ. CONCLUSIONS: A language-dependent cognitive automatizational deficit in the dyslexic group is assumed that is depicted by the higher synchronization of total-frontal coherences (involvement of the central executive) and is based on the less established functional coupling of cortical subsystems for language processing.

Brain Mapping↗
PubMed2003

miLD and booLD programs for calculation and analysis of corrected linkage disequilibrium.

We describe software which calculates a set of linkage disequilibrium statistics, including multiallelic D' corrected by the bootstrap and permutation. The software also provides a tool for maximum likelihood and least squares estimation and testing of a set of hierarchical hypotheses formulated within the framework of the Malecot model of the decay of linkage disequilibrium with distance. Additionally, the bootstrap approach is used for estimation of the model parameter's confidence intervals and for hypothesis testing. The programs are available from http://www.geneticepi.com/Research/software/software.html

Algorithms↗
PubMed1999

Ergonomics and work organization: the relationship between tayloristic design and workers' health in banks and credit cards companies.

The discussion developed in this paper is based on the results of an ergonomic work analysis carried out with attendants at call centers. Some critical issues and difficulties, like working pace, inadequate tools and workstations, and software inadequacies were detected in working situations. Operator-customer interactions are presented, attempting to put in evidence working constraints, working conditions, and their connection with health problems. The main conclusion is that serving clients, especially when the job is to provide information, is not a simple task, as information is not always available in the computerized system and is completely fragmented. The scope of workers' actions is very restricted and complicated and recurrent requests are redirected to others. Workers (individually or as groups) have limited possibilities to make adjustments to be able to give more adequate and personalized treatment to clients and, at the same time, to work in a less stressful environment. In periods of increased workload and work intensification, the situation is very much favorable to the incidence of health disorders, such as work related musculoskeletal disorders (WMSD) and others. Some suggestions to improve the work situation are discussed.

Brazil↗
PubMed1995

MIST: a user-friendly metabolic simulator.

The Metabolic Interactive Simulation Tool, MIST, is a software package, running under Microsoft Windows 3.1, which can be used for dynamic simulations, stoichiometric calculations and control analysis of metabolic pathways. The pathways can be of any complexity and are defined by the user in a simple, interactive way. The user-defined enzymatic rate equations can be compiled either by an external or an internal compiler. Simulations of pathways compiled by an external compiler run significantly faster, but since these compilers are commercial software, they are not distributed together with MIST. The simulations are performed by numerical integration of a set of ordinary differential equations. The integration can be done by either an explicit fourth-order Runge-Kutta algorithm or a semi-implicit third-order Runge-Kutta algorithm, both with adjustable step size. The second algorithm can be used if the set of differential equations is stiff. Vector-based drawing facilities are included in the program, with which results can be presented in graphs. Results of simulations, including graphics, can be stored in files. MIST is a very user-friendly, flexible and yet powerful program, with the mathematical details regarding models, simulations and calculations hidden from the user. This makes it suitable for scientists and students with limited computer experience.

Algorithms↗
PubMed2003

New normalization methods for cDNA microarray data.

MOTIVATION: The focus of this paper is on two new normalization methods for cDNA microarrays. After the image analysis has been performed on a microarray and before differentially expressed genes can be detected, some form of normalization must be applied to the microarrays. Normalization removes biases towards one or other of the fluorescent dyes used to label each mRNA sample allowing for proper evaluation of differential gene expression. RESULTS: The two normalization methods that we present here build on previously described non-linear normalization techniques. We extend these techniques by firstly introducing a normalization method that deals with smooth spatial trends in intensity across microarrays, an important issue that must be dealt with. Secondly we deal with normalization of a new type of cDNA microarray experiment that is coming into prevalence, the small scale specialty or 'boutique' array, where large proportions of the genes on the microarrays are expected to be highly differentially expressed. AVAILABILITY: The normalization methods described in this paper are available via http://www.pi.csiro.au/gena/ in a software suite called tRMA: tools for R Microarray Analysis upon request of the authors. Images and data used in this paper are also available via the same link.

Algorithms↗
PubMed2004

Public web-based services from the European Bioinformatics Institute.

The mission of the European Bioinformatics Institute (EBI), an outstation of the European Molecular Biology Laboratory (EMBL) in Heidelberg, is to ensure that the growing body of information from molecular biology and genome research is placed in the public domain and is accessible freely to all parts of the scientific community in ways that promote scientific progress. To fulfil this mission, the EBI provides a wide variety of free, publicly available bioinformatics services. These can be divided into data submissions processing; access to query, analysis and retrieval systems and tools; ftp downloads of software and databases; training and education and user support. All of these services are available at the EBI website: http://www.ebi.ac.uk/services. This paper provides a detailed introduction to the interactive analysis systems that are available from the EBI and a brief introduction to other, related services.

Computational Biology↗
PubMed2006

Anterior segment measurements using digital photography: a simple technique.

PURPOSE: The purpose of this study is to describe a simple method of measuring anterior segment lesions from digital slit lamp images and confirm reliability of the technique. METHODS: Ten reference photos were taken of a PD ruler, refocusing on the ruler for each photo. Using Adobe Photoshop, the number of pixels per millimeter squared (area) and 1 mm (linear) were recorded for each photo. An Excel spreadsheet was set up to convert pixels to millimeters and millimeters squared. Interrater reliability was determined by two observers who independently calculated the area of 69 epithelial defects. A Bland and Altman plot was used to demonstrate the agreement between the two doctors. RESULTS: Interrater reliability was excellent as measured by an intraclass correlation coefficient (ICC 2,1) = 0.99. From the Bland and Altman plot it was determined that in 95% of cases, the area of the epithelial defect measured by provider 2 may be as much as 1.17 mm less than or 1.09 mm greater than that measured by provider 1. CONCLUSION: This simple method, which allows accurate measurements from digital images using common off-the-shelf software, is a valuable tool for clinical documentation as well as for research purposes.

Anterior Eye Segment↗
PubMed2006

Radio frequency ablation registration, segmentation, and fusion tool.

The radio frequency ablation segmentation tool (RFAST) is a software application developed using the National Institutes of Health's medical image processing analysis and visualization (MIPAV) API for the specific purpose of assisting physicians in the planning of radio frequency ablation (RFA) procedures. The RFAST application sequentially leads the physician through the steps necessary to register, fuse, segment, visualize, and plan the RFA treatment. Three-dimensional volume visualization of the CT dataset with segmented three dimensional (3-D) surface models enables the physician to interactively position the ablation probe to simulate burns and to semimanually simulate sphere packing in an attempt to optimize probe placement. This paper describes software systems contained in RFAST to address the needs of clinicians in planning, evaluating, and simulating RFA treatments of malignant hepatic tissue.

Algorithms↗
PubMed2005

Use of virtual, interactive, musculoskeletal system (VIMS) in modeling and analysis of shoulder throwing activity.

Our purpose in this study was to apply the virtual, interactive, musculoskeletal system (VIMS) software for modeling and biomechanical analysis of the glenohumeral joint during a baseball pitching activity. The skeletal model was from VIMS library and muscle fiber attachment sites were derived from the visible human dataset. The muscular moment arms and function changes are mainly due to the large humeral motion involved during baseball pitching. The graphic animation of the anatomic system using VIMS software is an effective tool to model and visualize the complex anatomical structure of the shoulder for biomechanical analysis.

Baseball↗
PubMed2004

Determining optimal two-beam axial orientations for heart sparing in left-sided breast cancer patients.

BACKGROUND AND PURPOSE: The optimal intensity fluence profile of a beam depends on the profiles of other beams but most optimizations assume fixed beam orientations, a priori. Breast cancer radiotherapy attempts to cover the target and to spare critical structures such as the heart and lungs. The study aims are (1) to determine and document the optimal two-beam orientation that best spares the heart for left-sided breast cancer patients and (2) to investigate the influence of the treatment technique (i.e., conformal versus intensity modulation) on the optimal objective cost function. MATERIAL AND METHODS: Ten left-sided breast cancer patients were planned using a conformal (3DCRT) and a simplified intensity modulated (sIMRT) technique using predefined segments and different two-beam orientations. Optimal segment weights were determined exhaustively for all axial two-beam combinations, in 5 degree increments, by minimizing a quadratic objective cost function. The resulting objective cost function was analyzed with respect to target geometry and treatment technique. RESULTS: The sIMRT plans are generally less sensitive to beam orientation compared to 3DCRT plans. Optimal two-beam orientations for 3DCRT and sIMRT plans exist and they correspond to a hinge angle of approximately 188 degrees and 160 degrees or 210 degrees (the latter is bimodal), respectively. CONCLUSIONS: The optimization software is a useful tool that can test many different beam combinations and estimate their associated objective cost values. Afterwards, the most promising beam orientations could be re-optimized under the TPS to fine-tune and verify the dose distributions. Optimal uniform two-beam orientations for the breast consist of opposing tangential medial and lateral beams. Optimal nonuniform two-beam orientations for left-sided breast cancers are bimodal, containing hinge angles around 160 degrees and 210 degrees. Nonuniform beam techniques are less sensitive to beam orientation compared to uniform beam techniques and result in significantly improved heart sparing but at a cost of slightly compromised planning target volume coverage.

Breast↗
PubMedDate not supplied

Volume rendering versus maximum intensity projection in CT angiography: what works best, when, and why.

The introduction and widespread availability of 16-section multi-detector row computed tomographic (CT) technology and, more recently, 64-section scanners, has greatly advanced the role of CT angiography in clinical practice. CT angiography has become a key component of state-of-the-art imaging, with applications ranging from oncology (eg, staging of pancreatic or renal cancer) to classic vascular imaging (eg, evaluation of aortic aneurysms and renal artery stenoses) as well as newer techniques such as coronary artery imaging and peripheral runoff studies. With an average of 400-1000 images in each volume data set, three-dimensional postprocessing is crucial to volume visualization. Radiologists now have workstations that provide capabilities for evaluation of these data sets by using a range of software programs and processing tools. Although different systems have unique capabilities and functionality, all provide the options of volume rendering and maximum intensity projection for image display and analysis. These two postprocessing techniques have different advantages and disadvantages when used in clinical practice, and it is important that radiologists understand when and how each technique should be used.

Algorithms↗
PubMed2004

A network-based system to improve care for schizophrenia: the Medical Informatics Network Tool (MINT).

The Medical Informatics Network Tool (MINT) is a software system that supports the management of care for chronic illness. It is designed to improve clinical information, facilitate teamwork, and allow management of health care quality. MINT includes a browser interface for entry and organization of data and preparation of real-time reports. It includes personal computer-based applications that interact with clinicians. MINT is being used in a project to improve the treatment of schizophrenia. At each patient visit, a nurse briefly assesses symptoms, side effects, and other key problems and enters this information into MINT. When the physician subsequently opens the patient's electronic medical record, a window appears with the assessment information, a messaging interface, and access to treatment guidelines. Clinicians and managers receive reports regarding the quality of patients' treatment. To date, MINT has been used with more than 165 patients and 29 psychiatrists and has supported practices that are consistent with improvements in the quality of care.

Decision Support Systems, Clinical↗
PubMed2005

A new three-dimensional method of assessing facial volumetric changes after orthognathic treatment.

OBJECTIVE: To validate a new method of facial volumetric assessment that is dependent on the use of stereophotogrammetric models and a software-based Facial Analysis Tool. DESIGN: The method was validated in vitro with three-dimensional (3D) models of a lifelike plastic female dummy head and in vivo with a male-subject head. METHODS: Thirty facial silicone explants were added in the nasal and perioral regions of each head, and their volumes were obtained by three different algorithms. These were compared with the actual values obtained by a "water displacement" method. RESULTS: The least mean error was found with the "tetrahedron formation" method followed by the "projection" method and the "back-plane construction" method. The error with the tetrahedron formation method was 0.071 cm(3) (95% confidence interval [CI]: -0.074 to 0.2161 cm3) with the in vitro models and 0.314 cm3 (95% CI: -0.080 to 0.708 cm3) with the in vivo models. The increased volumetric assessment error observed in vivo was attributed to the registration procedure and possible changes in facial expression. CONCLUSIONS: These results encourage the use of this method in the 3D assessment of orthognathic surgical outcome, provided a standardized facial expression is used for image acquisition.

Algorithms↗
PubMed2003

A partnership of universities and agri-business for an effective dairy herd management learning experience for undergraduates: the Dairy Challenge.

The Dairy Challenge contest allows undergraduate students to apply knowledge gained in the classroom in an evaluation of the management practices of commercial dairy farms. University faculty partnered with industry representatives to develop the competition. Participants in the Dairy Challenge do the following: 1) critically evaluate dairy herd management practices and make recommendations for improvements; 2) visit local dairy farms and gain knowledge of different farms' management practices; 3) meet and interact with potential employers from the dairy industry during the contest; 4) evaluate herd records and utilize knowledge of dairy herd management software and computer presentation tools; 5) test their speaking, presentation, and problem-solving skills; and 6) work as a team to build consensus and tag-team speaking formats. Teams of four undergraduate students critically evaluate a commercial dairy farm using herd records, a description of farm operations, and tour of the farm facilities. The farmer answers questions pertaining to management of the farm in a group interview with all teams and in a separate interview with each individual team. Teams give a 20-min presentation that is scored on the description and assessment of the management practices and recommendations for improvements in management and facilities. Additionally, scoring is based on apparent level of preparation, speaking, presentation skills, and responses to judges' questions. The judges are university specialists and dairy industry professionals. This capstone experience allows students to interact with dairy farmers and representatives from the dairy industry and expands their knowledge and skills gained during their academic career.

Agriculture↗
PubMed1990

Coordinating data management for multiple ongoing clinical trials and registries.

The Epidemiology Data Center at the University of Pittsburgh has developed a standard set of data management procedures, reports, and computing configurations for use on multicenter research projects. Based on budget restrictions and study design considerations, a project-specific data management system can be quickly constructed by utilizing appropriate components from the EDC tool kit: the PoP software system for the computerization of the database from paper forms to data entry screens; program shells for telecommunication and backup procedures; and procedural documents for providing the necessary training materials for centralized or decentralized processing environments. The EDC data flow specification provides quality control assurances from entry through statistical analysis.

Clinical Trials as Topic↗
PubMed1996

The teleos virtual environment toolkit for simulation-based surgical education.

In the past, surgical simulations have largely been created through the development of dedicated applications that require considerable programming and computer graphics skills. Advances in simulation-based surgical education have been limited by this dependence on computer graphics programming expertise. To lower barriers to the adoption of simulation-based training, we are developing tools based on Teleos, software technology that allows a wide variety of medical content developers to author surgical training simulations without programming.

Computer Graphics↗
PubMed1998

Patient education in the computer age.

The more educated the patient, the healthier the patient. That's the philosophy prompting a growing number of health care providers to take advantage of new patient education tools. Using patient education software and Internet resources helps caregivers ensure that the information delivered to a patient is appropriate and timely. Providers also are discovering that such systems yield significant clinical and financial benefits.

Computer Communication Networks↗