Software testing
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Nowadays, cardiovascular diseases represent the most common cause of death in western countries. Among various examination techniques, electrocardiography (ECG) is still a highly valuable tool used for the diagnosis of many cardiovascular disorders. In order to diagnose a person based on ECG, cardiologists can use automatic diagnostic algorithms. Research in this area is still necessary. In order to compare various algorithms correctly, it is necessary to test them on standard annotated databases, such as the Common Standards for Quantitative Electrocardiography (CSE) database. According to Scopus, the CSE database is the second most cited standard database. There were two main objectives in this work. First, new diagnoses were added to the CSE database, which extended its original annotations. Second, new recommendations for diagnostic software quality estimation were established. The ECG recordings were diagnosed by five new cardiologists independently, and in total, 59 different diagnoses were found. Such a large number of diagnoses is unique, even in terms of standard databases. Based on the cardiologists' diagnoses, a four-round consensus (4R consensus) was established. Such a 4R consensus means a correct final diagnosis, which should ideally be the output of any tested classification software. The accuracy of the cardiologists' diagnoses compared with the 4R consensus was the basis for the establishment of accuracy recommendations. The accuracy was determined in terms of sensitivity = 79.20-86.81%, positive predictive value = 79.10-87.11%, and the Jaccard coefficient = 72.21-81.14%, respectively. Within these ranges, the accuracy of the software is comparable with the accuracy of cardiologists. The accuracy quantification of the correct classification is unique. Diagnostic software developers can objectively evaluate the success of their algorithm and promote its further development. The annotations and recommendations proposed in this work will allow for faster development and testing of classification software. As a result, this might facilitate cardiologists' work and lead to faster diagnoses and earlier treatment.
- Klíčová slova
- Annotation of ECG record, CSE database, ECG, ECG classification, Recommendations, Software testing,
- MeSH
- databáze faktografické normy MeSH
- diagnóza počítačová normy MeSH
- elektrokardiografie normy MeSH
- kardiovaskulární nemoci diagnóza MeSH
- lidé MeSH
- reprodukovatelnost výsledků MeSH
- senzitivita a specificita MeSH
- směrnice pro lékařskou praxi jako téma * MeSH
- validace softwaru * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Česká republika MeSH
Super-resolution optical fluctuation imaging (SOFI) allows one to perform sub-diffraction fluorescence microscopy of living cells. By analyzing the acquired image sequence with an advanced correlation method, i.e. a high-order cross-cumulant analysis, super-resolution in all three spatial dimensions can be achieved. Here we introduce a software tool for a simple qualitative comparison of SOFI images under simulated conditions considering parameters of the microscope setup and essential properties of the biological sample. This tool incorporates SOFI and STORM algorithms, displays and describes the SOFI image processing steps in a tutorial-like fashion. Fast testing of various parameters simplifies the parameter optimization prior to experimental work. The performance of the simulation tool is demonstrated by comparing simulated results with experimentally acquired data.
- MeSH
- algoritmy MeSH
- fluorescenční mikroskopie * MeSH
- HeLa buňky MeSH
- lidé MeSH
- počítačové zpracování obrazu metody MeSH
- software * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
In the framework of forensic anthropology osteometric techniques are generally preferred over visual examinations due to a higher level of reproducibility and repeatability; qualities that are crucial within a legal context. The use of osteometric methods has been further reinforced by incorporating statistically-based algorithms and large reference samples in a variety of user-friendly software applications. However, the continued increase in admixture of human populations have made the use of osteometric methods for estimation of ancestry much more complex, which confounds one of major requirements of ancestry assessment - intra-population homogeneity. The present paper tests the accuracy of ancestry and sex assessment using four identification software tools, specifically FORDISC 2.0, FORDISC 3.1.293, COLIPR 1.5.2 and 3D-ID 1.0. Software accuracy was tested in a sample of 174 documented human crania of Brazilian origin composed of different ancestral groups (i.e., European Brazilians, Afro-Brazilians, and Japanese Brazilians and of admixed ancestry). The results show that regardless of the software algorithm employed and composition of the reference database, all methods were able to allocate approximately 50% of Brazilian specimens to an appropriate major reference group. Of the three ancestral groups, Afro-Brazilians were especially prone to misclassification. Japanese Brazilians, by contrast, were shown to be relatively easily recognizable as being of Asian descent but at the same time showed a strong affinity towards Hispanic crania, in particularly when the classification based on FDB was carried out in FORDISC. For crania of admixed origin all of the algorithms showed a considerable higher rate of inconsistency with a tendency for misclassification into Asian and American Hispanic groups. Sex assessments revealed an overall modest to poor reliability (60-71% of correctly classified specimens) using the tested software programs with unbalanced individual rates for males and females. The highest and atypically balanced rate of classification for sex assessment was provided by COLIPR software, which reached 78% of correctly assessed crania.
- Klíčová slova
- 3D-ID, Ancestry assessment, Brazilian crania, FORDISC, Sex assessment,
- MeSH
- lidé MeSH
- populační skupiny etnologie MeSH
- software normy MeSH
- soudní antropologie * metody MeSH
- určení pohlaví podle kostry metody MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- validační studie MeSH
- Geografické názvy
- Brazílie MeSH
The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.
- Klíčová slova
- CCP4, Collaborative Computational Project No. 4, crystallography software, macromolecular crystallography,
- MeSH
- krystalografie rentgenová MeSH
- makromolekulární látky MeSH
- proteiny * chemie MeSH
- software * MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- makromolekulární látky MeSH
- proteiny * 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.
A software system STESYS for interactive and flexible generation of stereological test systems is described. STESYS enables to implement many of the recent unbiased stereological methods applied to biomedical research and clinical diagnosis by using a simple personal computer. Advantages of the STESYS software are illustrated by several examples of stereological measurements for estimating the number, total and mean cross-sectional area, volume and surface area.
Quantitative structure-property/activity relationships (QSPRs/QSARs) are a tool (in silico) to rapidly predict various endpoints in general, and drug toxicity in particular. However, this dynamic evolution of experimental data (expansion of existing experimental data on drugs toxicity) leads to the problem of critical estimation of the data. The carcinogenicity, mutagenicity, liver effects and cardiac toxicity should be evaluated as the most important aspects of the drug toxicity. The toxicity is a multidimensional phenomenon. It is apparent that the main reasons for the increase in applications of in silico prediction of toxicity include the following: (i) the need to reduce animal testing; (ii) computational models provide reliable toxicity prediction; (iii) development of legislation that is related to use of new substances; (iv) filling data gaps; (v) reduction of cost and time; (vi) designing of new compounds; (vii) advancement of understanding of biology and chemistry. This mini-review provides analysis of existing databases and software which are necessary for use of robust computational assessments and robust prediction of potential drug toxicities by means of in silico methods.
- Klíčová slova
- Computational toxicology, Drug toxicity, In silico methods, In silico toxicology, QSAR,
- MeSH
- databáze faktografické * MeSH
- kvantitativní vztahy mezi strukturou a aktivitou * MeSH
- lidé MeSH
- nežádoucí účinky léčiv * MeSH
- počítačová simulace MeSH
- software MeSH
- testy toxicity MeSH
- výpočetní biologie * MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
We introduce CEval software (downloadable for free at echmet.natur.cuni.cz) that was developed for quicker and easier electrophoregram evaluation and further data processing in (affinity) capillary electrophoresis. This software allows for automatic peak detection and evaluation of common peak parameters, such as its migration time, area, width etc. Additionally, the software includes a nonlinear regression engine that performs peak fitting with the Haarhoff-van der Linde (HVL) function, including automated initial guess of the HVL function parameters. HVL is a fundamental peak-shape function in electrophoresis, based on which the correct effective mobility of the analyte represented by the peak is evaluated. Effective mobilities of an analyte at various concentrations of a selector can be further stored and plotted in an affinity CE mode. Consequently, the mobility of the free analyte, μA, mobility of the analyte-selector complex, μAS, and the apparent complexation constant, K('), are first guessed automatically from the linearized data plots and subsequently estimated by the means of nonlinear regression. An option that allows two complexation dependencies to be fitted at once is especially convenient for enantioseparations. Statistical processing of these data is also included, which allowed us to: i) express the 95% confidence intervals for the μA, μAS and K(') least-squares estimates, ii) do hypothesis testing on the estimated parameters for the first time. We demonstrate the benefits of the CEval software by inspecting complexation of tryptophan methyl ester with two cyclodextrins, neutral heptakis(2,6-di-O-methyl)-β-CD and charged heptakis(6-O-sulfo)-β-CD.
- Klíčová slova
- Affinity capillary electrophoresis, Complexation, Cyclodextrin, Electrophoretic mobility, Software, Statistical evaluation,
- MeSH
- chemické techniky analytické metody MeSH
- cyklodextriny analýza chemie MeSH
- elektroforéza kapilární * MeSH
- estery analýza chemie MeSH
- interpretace statistických dat MeSH
- software * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- cyklodextriny MeSH
- estery MeSH
In recent years the software coincidence counting system, designed for absolute activity measurement, has been developed in the Czech Metrology Institute. In this system a true coincidence count rate is calculated from the records of time and amplitude data of individual pulses and may be determined by two different methods. The first one uses a coincidence resolving time, in a manner similar to a classical coincidence measurement. The second method applies the pulse mixing method formulae, so that it does not use the resolving time and the correction for accidental coincidences. Both methods have been tested on the same data from a 4pibeta (PC)-gamma coincidence measurement of 60Co sources. The difference between the results obtained from both calculation methods applied on the data from the same measurement did not exceed 0.015%. The details of both methods and the results of their comparison are presented.
- MeSH
- algoritmy * MeSH
- beta částice MeSH
- počítačové zpracování signálu * MeSH
- radiometrie metody MeSH
- reprodukovatelnost výsledků MeSH
- senzitivita a specificita MeSH
- software * MeSH
- validace softwaru * MeSH
- záření gama * MeSH
- Publikační typ
- časopisecké články MeSH
- hodnotící studie MeSH
- srovnávací studie MeSH
- validační studie MeSH
Undiscovered gene-to-gene interaction (epistasis) is a possible explanation for the "missing heritability" of complex traits and diseases. On a genome-wide scale, screening for epistatic effects among all possible pairs of genetic markers faces two main complications. Firstly, the classical statistical methods for modeling epistasis are computationally very expensive, which makes them impractical on such large scale. Secondly, straightforward corrections for multiple testing using the classical methods tend to be too coarse and inefficient at discovering the epistatic effects in such a large scale application. In this chapter, we describe both the underlying framework and practical examples of two-stage statistical testing methods that alleviate both of the aforementioned complications.
- Klíčová slova
- Case-control design, Multiple testing, Screening and verification, Two-stage testing,
- MeSH
- fenotyp MeSH
- genetická epistáze * MeSH
- genetické asociační studie MeSH
- genetické testování metody MeSH
- genom lidský MeSH
- genotyp MeSH
- jednonukleotidový polymorfismus * MeSH
- kvantitativní znak dědičný * MeSH
- lidé MeSH
- lokus kvantitativního znaku MeSH
- modely genetické * MeSH
- software * MeSH
- typy dědičnosti MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
