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PubMedDate not supplied

Computer-aided identification of renal corpuscle elements in RGB and HLS color images.

UNLABELLED: The qualitative and quantitative changes in the structure of the renal corpuscle allow the assessment of the glomerular involvement degree, defining each type of glomerulonephritis. Recently, several works dedicated to glomerulonephritis focus on the quantitative investigation, achieved by digital (numerical) image processing, where the identification of the interest elements is a key stage. OBJECTIVES: The aim of the study was the elaboration of a technique for constructing reliable color models in the RGB and HLS spaces for each element of the structure of the renal corpuscle. MATERIAL AND METHODS: We analyzed images captured from trichrome stained fragments of renal biopsy. Each image contained a single renal corpuscle. The identification procedure used the software tools specialized in color image analysis provided by the Zeiss KS400 environment. RESULTS: There were defined specific chromatic domains in the RGB and HLS space for the identification of the following elements: the Bowman space and the glomerular capillaries (white colored regions), the nuclei (brown colored regions), the mesangium (green colored regions). DISCUSSIONS: In order to get a relevant picture of the role played by the decisions made in the definition of the chromatic domains, we performed two tests for the modification of the chromatic domain allocated to the mesangium in the RGB and HLS space, respectively. CONCLUSION: The procedures proposed for the identification of the RGB and HLS color models can successfully replace the manual delineation of the renal corpuscle elements. Such models represent an important step in our research visualizing the future development of computer programs for automated measurements of renal corpuscle elements.

Color↗
PubMed1991

Providing an integrated clinical data view in a hospital information system that manages multimedia data.

The VA's hospital information system, the Decentralized Hospital Computer Program (DHCP), is an integrated system based on a powerful set of software tools with shared data accessible from any of its application modules. It includes many functionally specific application subsystems such as laboratory, pharmacy, radiology, and dietetics. Physicians need applications that cross these application boundaries to provide useful and convenient patient data. One of these multi-specialty applications, the DHCP Imaging System, integrates multimedia data to provide clinicians with comprehensive patient-oriented information. User requirements for cross-disciplinary image access can be studied to define needs for similar text data access. Integration approaches must be evaluated both for their ability to deliver patient-oriented text data rapidly and their ability to integrate multimedia data objects. Several potential integration approaches are described as they relate to the DHCP Imaging System.

Computer Communication Networks↗
PubMed2003

Recent advances in the prediction of blood-brain partitioning from molecular structure.

The widely distributed software tools Cerius2 and ACD/log D Suite have been used to develop a new method for the prediction of the ratio of concentrations of a drug in the brain and blood (BB,quantified as log BB) from structure. The performances of all known blood-brain partitioning prediction methods are compared to give an up-to-date account on their accuracy, limitations, and usefulness. It is demonstrated that the new log BB prediction method is superior to other methods with regard to low-to-medium throughput log BB prediction, whereas the C2-ADME log BB two-dimensional (2D) method seems to offer the best compromise between speed and accuracy for ultra-high throughput processing of large compound databases for log BB prediction.

Blood-Brain Barrier↗
PubMed2004

VSQual: a visual system to assist DNA sequencing quality control.

A lack of pliant software tools that support small- to medium-scale DNA sequencing efforts is a major hindrance for recording and using laboratory workflow information to monitor the overall quality of data production. Here we describe VSQual, a set of Perl programs intended to provide simple and powerful tools to check several quality features of the sequencing data generated by automated DNA sequencing machines. The core program of VSQual is a flexible Perl-based pipeline, designed to be accessible and useful for both programmers and non-programmers. This pipeline directs the processing steps and can be easily customized for laboratory needs. Basically, the raw DNA sequencing trace files are processed by Phred and Cross_match, then the outputs are parsed, reformatted into Web-based graphical reports, and added to a Web site structure. The result is a set of real time sequencing reports easily accessible and understood by common laboratory people. These reports facilitate the monitoring of DNA sequencing as well as the management of laboratory workflow, significantly reducing operational costs and ensuring high quality and scientifically reliable results.

Database Management Systems↗
PubMed2004

Handling multiple testing while interpreting microarrays with the Gene Ontology Database.

BACKGROUND: The development of software tools that analyze microarray data in the context of genetic knowledgebases is being pursued by multiple research groups using different methods. A common problem for many of these tools is how to correct for multiple statistical testing since simple corrections are overly conservative and more sophisticated corrections are currently impractical. A careful study of the nature of the distribution one would expect by chance, such as by a simulation study, may be able to guide the development of an appropriate correction that is not overly time consuming computationally. RESULTS: We present the results from a preliminary study of the distribution one would expect for analyzing sets of genes extracted from Drosophila, S. cerevisiae, Wormbase, and Gramene databases using the Gene Ontology Database. CONCLUSIONS: We found that the estimated distribution is not regular and is not predictable outside of a particular set of genes. Permutation-based simulations may be necessary to determine the confidence in results of such analyses.

Animals↗
PubMed2006

PHY.FI: fast and easy online creation and manipulation of phylogeny color figures.

BACKGROUND: The need to depict a phylogeny, or some other kind of abstract tree, is very frequently experienced by researchers from a broad range of biological and computational disciplines. Thousands of papers and talks include phylogeny figures, and often during everyday work, one would like to quickly get a graphical display of, e.g., the phylogenetic relationship between a set of sequences as calculated by an alignment program such as ClustalW or the phylogenetic package Phylip. A wealth of software tools capable of tree drawing exists; most are comprehensive packages that also perform various types of analysis, and hence they are available only for download and installing. Some online tools exist, too. RESULTS: This paper presents an online tool, PHY.FI, which encompasses all the qualities of existing online programs and adds functionality to hopefully eliminate the need for post-processing the phylogeny figure in some other general-purpose graphics program. PHY.FI is versatile, easy-to-use and fast, and supports comprehensive graphical control, several download image formats, and the possibility of dynamically collapsing groups of nodes into named subtrees (e.g. "Primates"). The user can create a color figure from any phylogeny, or other kind of tree, represented in the widely used parenthesized Newick format. CONCLUSION: PHY.FI is fast and easy to use, yet still offers full color control, tree manipulation, and several image formats. It does not require any downloading and installing, and thus any internet user regardless of computer skills, and computer platform, can benefit from it. PHY.FI is free for all and is available from this web address: http://cgi-www.daimi.au.dk/cgi-chili/phyfi/go.

Algorithms↗
PubMed2006

The many metrics of cardiac chronotropy: a pragmatic primer and a brief comparison of metrics.

This paper focuses on pragmatic issues in obtaining measures of cardiac vagal control, and overviews a set of freely available software tools for obtaining several widely used metrics that putatively reflect sympathetic and/or parasympathetic contributions to cardiac chronotropy. After an overview of those metrics, and a discussion of potential confounds and extraneous influences, an empirical examination of the relationships amongst these metrics is provided. This study examined 10 metrics in 96 unselected college students under conditions of resting baseline and serial paced arithmetic. Intercorrelations between metrics were very high. Factor analyses were conducted on the metrics reflecting variability in cardiac rate, once at baseline and again during mental arithmetic. Factor structure was highly stable across tasks, and included a factor that had high loadings of all variables except Toichi's "cardiac sympathetic index" (CSI), and a second factor that was defined predominantly by the CSI. Although generally highly correlated, the various metrics responded differently under challenge.

Arrhythmia, Sinus↗
PubMed2024

metaExpertPro: A Computational Workflow for Metaproteomics Spectral Library Construction and Data-Independent Acquisition Mass Spectrometry Data Analysis.

Analysis of large-scale data-independent acquisition mass spectrometry metaproteomics data remains a computational challenge. Here, we present a computational pipeline called metaExpertPro for metaproteomics data analysis. This pipeline encompasses spectral library generation using data-dependent acquisition MS, protein identification and quantification using data-independent acquisition mass spectrometry, functional and taxonomic annotation, as well as quantitative matrix generation for both microbiota and hosts. By integrating FragPipe and DIA-NN, metaExpertPro offers compatibility with both Orbitrap and timsTOF MS instruments. To evaluate the depth and accuracy of identification and quantification, we conducted extensive assessments using human fecal samples and benchmark tests. Performance tests conducted on human fecal samples indicated that metaExpertPro quantified an average of 45,000 peptides in a 60-min diaPASEF injection. Notably, metaExpertPro outperformed three existing software tools by characterizing a higher number of peptides and proteins. Importantly, metaExpertPro maintained a low factual false discovery rate of approximately 5% for protein groups across four benchmark tests. Applying a filter of five peptides per genus, metaExpertPro achieved relatively high accuracy (F-score = 0.67-0.90) in genus diversity and showed a high correlation (rSpearman = 0.73-0.82) between the measured and true genus relative abundance in benchmark tests. Additionally, the quantitative results at the protein, taxonomy, and function levels exhibited high reproducibility and consistency across the commonly adopted public human gut microbial protein databases IGC and UHGP. In a metaproteomic analysis of dyslipidemia patients, metaExpertPro revealed characteristic alterations in microbial functions and potential interactions between the microbiota and the host.

Proteomics↗
PubMed2004

Modeling performance and alertness: the QinetiQ approach.

The basis of the QinetiQ alertness model used at the heart of the System for Aircrew Fatigue Evaluation (SAFE) free-standing software tool is described. A number of extensions to the basic model that are applicable to the civil aviation environment are outlined, based on the analysis of eight studies involving sleep diaries gathered from pilots undertaking a range of duty schedules. The relationship between subjective alertness and performance of laboratory tasks is described and it is concluded that different tasks are affected differentially by fatigue. In general, there is a larger impact on the incidence of errors than on response time. The implementation of the full model in the Integrated Performance Modeling Environment is described and the application of both the alertness and performance models to two scenarios provided by the workshop organizers is outlined. It is concluded that further work is needed in three areas: cumulative fatigue, the impact of sleep architecture, and the prediction of performance for complex tasks in systems.

Aerospace Medicine↗
PubMed2005

Improved classification of mass spectrometry database search results using newer machine learning approaches.

Manual analysis of mass spectrometry data is a current bottleneck in high throughput proteomics. In particular, the need to manually validate the results of mass spectrometry database searching algorithms can be prohibitively time-consuming. Development of software tools that attempt to quantify the confidence in the assignment of a protein or peptide identity to a mass spectrum is an area of active interest. We sought to extend work in this area by investigating the potential of recent machine learning algorithms to improve the accuracy of these approaches and as a flexible framework for accommodating new data features. Specifically we demonstrated the ability of boosting and random forest approaches to improve the discrimination of true hits from false positive identifications in the results of mass spectrometry database search engines compared with thresholding and other machine learning approaches. We accommodated additional attributes obtainable from database search results, including a factor addressing proton mobility. Performance was evaluated using publically available electrospray data and a new collection of MALDI data generated from purified human reference proteins.

Amino Acid Sequence↗
PubMed2003

Viewing and annotating sequence data with Artemis.

Artemis is a widely used software tool for annotating and viewing sequence data. No database is required to use Artemis. Instead, individual sequence data files can be analysed with little or no formatting, making it particularly suited to the study of small genomes and chromosomes, and straightforward for a novice user to get started. Since its release in 1999, Artemis has been used to annotate a diverse collection of prokaryotic and eukaryotic genomes, ranging from Streptomyces coelicolor to, more recently, a large proportion of the Plasmodium falciparum genome. Artemis allows annotated genomes to be easily browsed and makes it simple to add useful biological information to raw sequence data. This paper gives an overview of some of the features of Artemis and includes how it facilitates manual gene prediction and can provide an overview of entire chromosomes or small compact genomes--useful for uncovering unusual features such as pathogenicity islands.

Animals↗
PubMed2003

Processing sequence annotation data using the Lua programming language.

The data processing language in a graphical software tool that manages sequence annotation data from genome databases should provide flexible functions for the tasks in molecular biology research. Among currently available languages we adopted the Lua programming language. It fulfills our requirements to perform computational tasks for sequence map layouts, i.e. the handling of data containers, symbolic reference to data, and a simple programming syntax. Upon importing a foreign file, the original data are first decomposed in the Lua language while maintaining the original data schema. The converted data are parsed by the Lua interpreter and the contents are stored in our data warehouse. Then, portions of annotations are selected and arranged into our catalog format to be depicted on the sequence map. Our sequence visualization program was successfully implemented, embedding the Lua language for processing of annotation data and layout script. The program is available at http://staff.aist.go.jp/yutaka.ueno/guppy/.

Computational Biology↗
PubMed2005

DNA microarray data imputation and significance analysis of differential expression.

MOTIVATION: Significance analysis of differential expression in DNA microarray data is an important task. Much of the current research is focused on developing improved tests and software tools. The task is difficult not only owing to the high dimensionality of the data (number of genes), but also because of the often non-negligible presence of missing values. There is thus a great need to reliably impute these missing values prior to the statistical analyses. Many imputation methods have been developed for DNA microarray data, but their impact on statistical analyses has not been well studied. In this work we examine how missing values and their imputation affect significance analysis of differential expression. RESULTS: We develop a new imputation method (LinCmb) that is superior to the widely used methods in terms of normalized root mean squared error. Its estimates are the convex combinations of the estimates of existing methods. We find that LinCmb adapts to the structure of the data: If the data are heterogeneous or if there are few missing values, LinCmb puts more weight on local imputation methods; if the data are homogeneous or if there are many missing values, LinCmb puts more weight on global imputation methods. Thus, LinCmb is a useful tool to understand the merits of different imputation methods. We also demonstrate that missing values affect significance analysis. Two datasets, different amounts of missing values, different imputation methods, the standard t-test and the regularized t-test and ANOVA are employed in the simulations. We conclude that good imputation alleviates the impact of missing values and should be an integral part of microarray data analysis. The most competitive methods are LinCmb, GMC and BPCA. Popular imputation schemes such as SVD, row mean, and KNN all exhibit high variance and poor performance. The regularized t-test is less affected by missing values than the standard t-test. AVAILABILITY: Matlab code is available on request from the authors.

Algorithms↗
PubMed2006

WHAP: haplotype-based association analysis.

UNLABELLED: We describe a software tool to perform haplotype-based association analysis, for quantitative and qualitative traits, in population and family samples, using single nucleotide polymorphism or multiallelic marker data. A range of tests is offered: omnibus and haplotype-specific tests; prospective and retrospective likelihoods; covariates and moderators; sliding window analyses; permutation P-values. We focus on the ability to flexibly impose constraints on haplotype effects, which allows for a range of conditional haplotype-based likelihood ratio tests: for example, whether an allele has an effect independent of its haplotypic background, or whether a single variant can explain the overall association at a locus. We illustrate using these tests to dissect a multi-locus association. AVAILABILITY: WHAP is a C/C++ program, freely available from the author's website: http://pngu.mgh.harvard.edu/purcell/whap/

Algorithms↗
PubMed2003

Angular dependence of the luminance and contrast in medical monochrome liquid crystal displays.

Active-matrix liquid crystal displays (AMLCDs) are light-modulating devices that generate images by differentially transmitting a nearly uniform luminous field provided by a backlight. While emissive displays exhibit a quasi-Lambertian emission with almost constant contrast at off-normal viewing, the anisotropy of the electro-optic effect that controls light transmission in AMLCDs causes a pixel luminance that varies, sometimes strongly, with viewing angle. These variations are not identical for all gray levels and can eventually cause grayscale inversions. In this paper, we measured the luminance emission of a monochrome medical AMLCD, a medical cathode-ray tube monitor, and a color desktop AMLCD, using a collimated photopic probe positioned on a manual rotation arm, and a research radiometer with automatic readout. The probe measures luminance with a small acceptance angle and provides optical shielding from emissions at other viewing directions that contaminate the readings. We obtained luminance response curves versus angle in the vertical, horizontal and at 45 degrees diagonal directions. The display systems were calibrated to reflect the DICOM Part 3.14 standard grayscale display function (GDF) when measured using the manufacturer's probe and software tools. We analyzed the measurements at different viewing directions with respect to their departure from the GDF by computing the normalized contrast (deltaL/L) as a function of the DICOM just-noticeable difference index. Although cathode-ray tubes are known to be quasi-Lambertian emitters, the luminance at normal viewing is higher than the luminance observed at large angles. This decrease in luminance is however proportionally similar for all gray levels, resulting in a relatively flat contrast response for all angles. In addition to being more pronounced, the angular variation in AMLCDs does not follow the same profile at different intensities with the subsequent variation in the achieved display contrast. The changes due to off-normal viewing are substantial at large angles in the horizontal and vertical directions, and much worse in the diagonal viewing directions.

Anisotropy↗
PubMed2005

Manipulating multiple sequence alignments via MaM and WebMaM.

MaM is a software tool that processes and manipulates multiple alignments of genomic sequence. MaM computes the exact location of common repeat elements, exons and unique regions within aligned genomics sequences using a variety of user identified programs, databases and/or tables. The program can extract subalignments, corresponding to these various regions of DNA to be analyzed independently or in conjunction with other elements of genomic DNA. Graphical displays further allow an assessment of sequence variation throughout these different regions of the aligned sequence, providing separate displays for their repeat, non-repeat and coding portions of genomic DNA. The program should facilitate the phylogenetic analysis and processing of different portions of genomic sequence as part of large-scale sequencing efforts. MaM source code is freely available for non-commercial use at http://compbio.cs.sfu.ca/MAM.htm; and the web interface WebMaM is hosted at http://atgc.lirmm.fr/mam.

Exons↗
PubMed2002

Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria.

Metabolite balancing has turned out to be a powerful computational tool in metabolic engineering. However, the linear equation systems occurring in this analysis are often underdetermined. If it is difficult or impossible to find the missing constraints, it is nevertheless feasible in some cases to determine the values of a subset of the unknown rates. Here, a procedure for finding out which reaction rates can be uniquely calculated in underdetermined metabolic networks and computing these rates is given. The method is based on the null space to the stoichiometry matrix corresponding to the reactions with unknown rates. It is shown that this method is considerably easier to handle than an algorithm given previously (Van der Heijden et al., 1994a). Furthermore, a useful elementary representation of the null space is presented which is closely related with the elementary flux modes. This unique representation is central to a more general approach to observability/calculability analysis. In particular, it allows one to find, in an easy way, those sets of measurable rates that enable a calculation of a certain unknown rate. Besides, rates which are never calculable by metabolite balancing may be easily detected by this method. The applicability of these methods is illustrated by a model of the central metabolism in purple nonsulfur bacteria. The photoheterotrophic growth of these representatives of anoxygenic photosynthetic bacteria is stoichiometrically analyzed. Interesting metabolic constraints caused by the necessary balancing of NADPH can be detected in a highly underdetermined system. This is, to our knowledge, the first application of stoichiometric analysis to the metabolic network in this bacteria group using metabolite balancing techniques. A new software tool, the FluxAnalyzer, is introduced. It allows quantitative and structural analysis of metabolic networks in a graphical user interface.

Algorithms↗
PubMed2003

Comparison of measurements made on digital and plaster models.

Measuring plaster models by hand is the traditional method of assessing malocclusion. Recent technologic advances now allow the models to be digitized, measured with software tools, stored electronically, and retrieved with a computer. OrthoCAD (Cadent, Fairview, NJ) performs this service. The purpose of this study was to evaluate the reliability of the OrthoCAD system. Two independent examiners measured tooth size, overbite, and overjet on both digital and plaster models. The results were compared, and interexaminer reliability was assessed. The study sample consisted of 76 randomly selected pretreatment patients. The results showed a statistically significant difference between the 2 groups for tooth size and overbite, with the digital measurements smaller than the manual measurements. However, the magnitude of these differences ranged from 0.16 mm to 0.49 mm and can be considered clinically not relevant. No difference was found between the 2 groups in the measurement of overjet. Interexaminer reliability was consistent for both the plaster and the digital models.

Analysis of Variance↗