Software prediction
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BACKGROUNDS: The CORAL software has been developed as a tool to build up quantitative structure- activity relationships (QSAR) for various endpoints. OBJECTIVE: The task of the present work was to estimate and to compare QSAR models for biochemical activity of various therapeutic agents, which are built up by the CORAL software. METHOD: The Monte Carlo technique gives possibility to build up predictive model of an endpoint by means of selection of so-called correlation weights of various molecular features extracted from simplified molecular input-line entry system (SMILES). Descriptors calculated with these weights are basis for building up correlations "structure - endpoint". RESULTS: Optimal descriptors, which are aimed to predict values of endpoints with apparent influence upon metabolism are crytically compared in aspect of their robustness and heuristic potential. Arguments which are confirming the necessity of reformulation of basics of QSARs are listed: (i) each QSAR model is stochastic experiment. The result of this experiment is defined by distribution into the training set and validation set; (ii) predictive potential of a model should be checked up with a group of different splits; and (iii) only model stochastically stable for a group of splits can be estimated as a reliable tool for the prediction. Examples of the improvement of the models previously suggested are demonstrated. CONCLUSION: The current version of the CORAL software remains a convenient tool to build up predictive models. The Monte Carlo technique involved for the software confirms the principle "QSAR is a random event" is important paradigm for the QSPR/QSAR analyses.
- MeSH
- kvantitativní vztahy mezi strukturou a aktivitou * MeSH
- léčivé přípravky metabolismus MeSH
- lidé MeSH
- metoda Monte Carlo MeSH
- molekulární modely * MeSH
- software * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND AND OBJECTIVE: Precise estimation of neuronal activity from neuroimaging data is one of the central challenges of the application of noninvasive neuroimaging methods. One of the widely used methods for studying brain activity is functional magnetic resonance imaging, which is a neuroimaging procedure that measures brain activity based on the blood oxygenation level dependent effect. The blood oxygenation level dependent signal can be modeled as a linear convolution of a hemodynamic response function with an input signal corresponding to the neuronal activity. Estimating such input signals is a complicated problem. METHODS: We present a software tool for estimation of brain neuronal activity, which uses a combination of Wiener filtering with deconvolution methods, including the least absolute shrinkage and selection operator, the ordinary least squares method, and the Dantzig selector. The latter two are equipped with both established selection criteria (Akaike and Bayesian information criterion) as well as newly developed mixture criteria for selection of activations. RESULTS: The software tool was tested on two types of data: measurements during basic visual experiments and during complex naturalistic audiovisual stimulation (watching a movie segment). During testing the software showed reasonable results, with the mixture criteria performing well for temporally extended activations. CONCLUSIONS: The presented software tool can be used for estimation, visualization, and analysis of brain neuronal activity from functional magnetic resonance imaging blood oxygenation level dependent measurements. The implemented methods provide valid results not only in the sparse activity scenario studied previously but also for temporally extended activations.
- MeSH
- algoritmy MeSH
- automatizované zpracování dat MeSH
- Bayesova věta MeSH
- dospělí MeSH
- hemodynamika * MeSH
- kyslík krev MeSH
- lidé MeSH
- magnetická rezonanční tomografie * MeSH
- mapování mozku * MeSH
- metoda nejmenších čtverců MeSH
- mladý dospělý MeSH
- mozek diagnostické zobrazování fyziologie MeSH
- neurony fyziologie MeSH
- počítačová simulace MeSH
- počítačové zpracování obrazu MeSH
- počítačové zpracování signálu MeSH
- reprodukovatelnost výsledků MeSH
- software MeSH
- statistické modely MeSH
- zdraví dobrovolníci pro lékařské studie MeSH
- zobrazování trojrozměrné metody MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- mladý dospělý MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
Although the likelihood ratio is a well-known statistical technique, commercial off-the-shelf (COTS) software products for its calculation are not sufficiently validated to suit general requirements for the competence of testing and calibration laboratories (EN/ISO/IEC 17025:2005 norm) per se. The software in question can be considered critical as it directly weighs the forensic evidence allowing judges to decide on guilt or innocence or to identify person or kin (i.e.: in mass fatalities). For these reasons, accredited laboratories shall validate likelihood ratio software in accordance with the above norm. To validate software for calculating the likelihood ratio in parentage/kinship scenarios I assessed available vendors, chose two programs (Paternity Index and familias) for testing, and finally validated them using tests derived from elaboration of the available guidelines for the field of forensics, biomedicine, and software engineering. MS Excel calculation using known likelihood ratio formulas or peer-reviewed results of difficult paternity cases were used as a reference. Using seven testing cases, it was found that both programs satisfied the requirements for basic paternity cases. However, only a combination of two software programs fulfills the criteria needed for our purpose in the whole spectrum of functions under validation with the exceptions of providing algebraic formulas in cases of mutation and/or silent allele.
Optical Coherence Tomography (OCT) is an intravascular imaging modality enabling detailed evaluation of cardiac allograft vasculopathy (CAV) after heart transplantation (HTx). However, its clinical application remains hampered by time-consuming manual quantitative analysis. We aimed to validate a semi-automated quantitative OCT analysis software (Iowa Coronary Wall Analyzer, ICWA-OCT) to improve OCT-analysis in HTx patients. 23 patients underwent OCT evaluation of all three major coronary arteries at 3 months (3M) and 12 months (12M) after HTx. We analyzed OCT recordings using the semiautomatic software and compared results with measurements from a validated manual software. For semi-automated analysis, 31,228 frames from 114 vessels were available. The validation was based on a subset of 4287 matched frames. We applied mixed model statistics to accommodate the multilevel data structure with method as a fixed effect. Lumen (minimum, mean, maximum) and media (mean, maximum) metrics showed no significant differences. Mean and maximum intima area were underestimated by the semi-automated method (β-methodmean = - 0.289 mm2, p < 0.01; β-methodmax = - 0.695 mm2, p < 0.01). Bland-Altman analyses showed increasing semi-automatic underestimation of intima measurements with increasing intimal extent. Comparing 3M to 12M progression between methods, mean intimal area showed minor underestimation (β-methodmean = - 1.03 mm2, p = 0.04). Lumen and media metrics showed excellent agreement between the manual and semi-automated method. Intima metrics and progressions from 3M to 12M were slightly underestimated by the semi-automated OCT software with unknown clinical relevance. The semi-automated software has the future potential to provide robust and time-saving evaluation of CAV progression.
SUMMARY: We present the cpPredictor webserver that implements a novel template-based method for prediction of secondary structure of RNA. The method outperforms available prediction methods as it uses RNA structures of related molecules, either predicted or experimentally identified, as structural templates. The server aims at three major tasks: i) prediction of RNA secondary structures that are difficult to predict by available methods, ii) characterization of uncharacterized RNAs as compatible or incompatible with a chosen template structure and iii) an identification of the most relevant structure among different candidate structures of a single RNA ambiguously predicted by available methods. The web server is accompanied with a comprehensive documentation. AVAILABILITY AND IMPLEMENTATION: The web server is freely available at http://cppredictor.elixir-czech.cz/. The source code of the cpPredictor algorithm is freely available from the webserver under the Apache License, Version 2.0.
This paper presents an adaBoost approach for schizophrenia relapse prediction. The data for the adaBoost are extracted from patients answers to Early Warning Signs questionnaires sent regularly via mobile phone messages. The performance of the adaBoost algorithm is confronted with current ITAREPS system with sensitivity 0.65 and specificity 0.73. AdaBoost has the same sensitivity 0.65 but higher specificity 0.84 and is then ready to became the part of the ITAREPS care program.
- MeSH
- adherence pacienta MeSH
- algoritmy MeSH
- časové faktory MeSH
- chování MeSH
- diagnóza počítačová metody MeSH
- hospitalizace MeSH
- konzultace na dálku metody MeSH
- lidé MeSH
- posílání textových zpráv MeSH
- recidiva MeSH
- rozvoj plánování metody MeSH
- schizofrenie (psychologie) MeSH
- schizofrenie diagnóza prevence a kontrola MeSH
- software MeSH
- systémy pro podporu klinického rozhodování MeSH
- telemedicína metody MeSH
- znovupřijetí pacienta MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
MOTIVATION: G-quadruplex is a DNA or RNA form in which four guanine-rich regions are held together by base pairing between guanine nucleotides in coordination with potassium ions. G-quadruplexes are increasingly seen as a biologically important component of genomes. Their detection in vivo is problematic; however, sequencing and spectrometric techniques exist for their in vitro detection. We previously devised the pqsfinder algorithm for PQS identification, implemented it in C++ and published as an R/Bioconductor package. We looked for ways to optimize pqsfinder for faster and user-friendly sequence analysis. RESULTS: We identified two weak points where pqsfinder could be optimized. We modified the internals of the recursive algorithm to avoid matching and scoring many sub-optimal PQS conformations that are later discarded. To accommodate the needs of a broader range of users, we created a website for submission of sequence analysis jobs that does not require knowledge of R to use pqsfinder. AVAILABILITY AND IMPLEMENTATION: https://pqsfinder.fi.muni.cz, https://bioconductor.org/packages/pqsfinder. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
- MeSH
- algoritmy MeSH
- G-kvadruplexy * MeSH
- genom MeSH
- RNA MeSH
- software MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Here we introduce the Protein Cutter (http:// biochemie.upol.cz/software/proteincutter), a web application for the prediction of results of protein digestion by proteolytic enzymes, which is accessible over the Internet network. In the beginning, previous and current approaches for protein sequencing are summarized. This includes the use of dinitrofluorobenzene and substituted isothiocyanate reagents as well as mass-spectrometry-based strategies and translation of genomic sequences. The following text characterizes bioinformatics as a modern scientific discipline, which solves problems arising from the management and analysis of biological data. The most important nucleotide and amino acid sequence databases are described together with the databases of DNA and protein structures. The program Protein Cutter, which is described in detail with respect to its design and technology, allows predicting peptide sequences generated by proteolytic digestion of a protein (represented by a user-entered amino acid or coding nucleotide sequence). In addition to other comparable applications, Protein Cutter offers more complex information calculated from amino acid sequences (i.e. molecular mass, amino acid composition, isoelectric point, hydropathicity index etc.), it works with nucleotide sequences upon automatic translation, it is open and friendly for user-entered cutting rules and provides more options for the filtration and sorting of results.
- MeSH
- databáze proteinů * MeSH
- genomika MeSH
- hmotnostní spektrometrie * metody přístrojové vybavení využití MeSH
- matematické výpočty počítačové MeSH
- molekulární sekvence - údaje * MeSH
- peptidové mapování * MeSH
- polymerázová řetězová reakce metody využití MeSH
- proteasy * MeSH
- proteomika MeSH
- sekvence aminokyselin * MeSH
- sekvenční analýza proteinů * MeSH
- software * MeSH
- systémy řízení databází * MeSH
- výpočetní biologie MeSH
- Publikační typ
- práce podpořená grantem MeSH
Objective: A lack of acceptance has hindered the widespread adoption and implementation of clinical prediction rules (CPRs). The use of clinical decision support systems (CDSSs) has been advocated as one way of facilitating a broader dissemination and validation of CPRs. This requires computable models of clinical evidence based on open standards rather than closed proprietary content. Methods: The on-going TRANSFoRm project has developed ontological models of CPRs suitable for providing CPR based decision support.
- MeSH
- akutní nemoc MeSH
- algoritmy * MeSH
- apendicitida diagnóza MeSH
- diagnóza počítačová metody MeSH
- diferenciální diagnóza MeSH
- lidé MeSH
- medicína založená na důkazech MeSH
- metody pro podporu rozhodování * MeSH
- navrhování softwaru MeSH
- primární zdravotní péče MeSH
- reprodukovatelnost výsledků MeSH
- rozhodování MeSH
- systémy pro podporu klinického rozhodování * MeSH
- výzkumný projekt MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
