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PubMed2003

Quantitative image analysis: software systems in drug development trials.

Multi-dimensional image analysis is being used increasingly to arrive at surrogate end-points for drug development trials. Various imaging modalities such as computed tomography (CT), magnetic resonance imaging (MRI), positron emission tomography (PET) and ultrasound are used to analyze treatments for diseases such as cancer, multiple sclerosis, osteoarthritis, and Alzheimer's disease. However, extracting information from images can be tedious and is prone to high user variability. The medical image analysis community is moving towards advanced software systems specifically designed for drug development trials. These systems can automatically identify the anatomy of interest in medical images (segmentation methods), can compare the anatomy over time or between patients (registration methods) and allow the quantitative extraction of anatomical features and the integration of the data and results into a database management system, automatically tracking the changes made to the data (audit trail generation). In this article, we present a case study using a prototype system that is used for quantifying multiple sclerosis lesions from multivariate MRI.

Clinical Trials as Topic↗

PubMed1998

A two focal plane method for digital quantification of nuclear immunoreactivity in large brain areas using NIH-image software.

In principle, digital acquisition of cell-count data from serially-sectioned immunocytochemical material is a straightforward enterprise. First, a serial brain section is magnified by use of a microscope interfaced to a computer. Then, using appropriate hardware and software, a digital image is captured, and cellular profiles of interest are segmented from background objects according to mean grayscale intensity and pixel area. Ideally, the cells of interest would be uniformly distinguishable from other objects or areas of the image, with respect to grayscale intensity and size. However, due to non-uniformity in background staining of neuropil, immunocytochemical material often departs markedly from this ideal situation. As a consequence, determining grayscale intensity and cell size cutoff values which separate cells of interest from background becomes laborious and arbitrary. This problem can be diminished by increasing the magnification of the digitized image, which increases the figure-ground resolution of the image. However, high-magnification images make tissue navigation difficult and require that multiple images be captured. This paper describes a two focal plane procedure for obtaining cell counts from nuclear-stained immunocytochemistry material. This procedure allows the capturing and cell counting of relatively low-magnification images with high digital figure-ground resolution.

Animals↗

PubMed1997

Quantitative evaluation of clinical software, exemplified by decision support systems.

To ensure the correctness of publicity material ('truth in labelling') and to inform their licensing decisions, agencies certifying or regulating any clinical computer system will need information about the system's structure, performance and likely impact on users and the environment in which they work. This information must be reliable and complete, so it needs to be collected in a structured, rigorous evaluation programme. Clinical decision support systems are generally more complex and their effects less easy to predict than most other clinical software, so pose the greatest challenge to evaluators. They are therefore the focus of this paper.

Bias↗

PubMed2004

Biosimulation software is changing research.

Biosimulation software is being used in pharmaceutical drug development to mimic diseases. Virtual clinical trials of new developing pharmaceutical drugs can be conducted on computers running disease simulations. Using virtual patients instead of clinical research patients can save both time and money for pharmaceutical companies in their search to discover new drugs and bring them to market. In the future, this type of research will be commonplace.

Biomedical Research↗

PubMed2005

A comprehensive software suite for the analysis of cDNAs.

We have developed a comprehensive software suite for bioinformatics research of cDNAs; it is aimed at rapid characterization of the features of genes and the proteins they code. Methods implemented include the detection of translation initiation and termination signals, statistical analysis of codon usage, comparative study of amino acid composition, comparative modeling of the structures of product proteins, prediction of alternative splice forms, and metabolic pathway reconstruction.

Alternative Splicing↗

PubMed2006

Optimal settings of fingerprint-type analysing computer software for the analysis of enterohaemorrhagic Escherichia coli pulsed-field gel electrophoresis patterns.

Settings of fingerprint-type analysing computer software were optimized for analysis of enterohaemorrhagic Escherichia coli (EHEC) pulsed-field gel electrophoresis (PFGE) patterns. Under the lowest values of parameters, maximum value of similarities calculated using the Dice coefficient were obtained between PFGE patterns from one EHEC strain on the same gel when reference lanes for calibration of distortions during electrophoresis were set to every fourth lane. PFGE patterns of 15 EHEC strains on different gels were investigated. Similarity values calculated using the Pearson product-moment correlation coefficient (Pearson correlation) were significantly higher than those using the Dice coefficient with optimal values of parameters determined by the program (P < 0.01). When PFGE patterns of 45 EHEC strains were analysed by the computer program, EHEC strains from one mass outbreak and three intra-family outbreaks were each clustered and the similarity values within the clusters were > 90% using Pearson correlation.

Bacterial Typing Techniques↗

PubMed2006

Pro-CrossLink. Software tool for protein cross-linking and mass spectrometry.

To facilitate structural analysis of proteins and protein-protein interactions, we developed Pro-CrossLink, a suite of software tools consisting of three programs (Figure 1), DetectShift, IdentifyXLink, and AssignXLink. DetectShift was developed to detect ions of cross-linked peptide pairs in a mixture of 18O-labeled peptides obtained from protein proteolytic digests. The selected candidate ions of cross-linked peptide pairs subsequently undergo tandem mass spectrometric (MS/MS) analysis for sequence determination. Based on the masses of candidate ions as well as y- and b-type ions in the tandem mass spectra, IdentifyXLink assigns the candidate ions to cross-linked peptide pairs. For an identified cross-linked peptide pair, AssignXLink generates an extensive fragment ion list, including a-, b-, c-type, x-, y-, z-type, internal, and immonium ions with associated common losses of H2O, NH3, CO, and CO2, and facilitates a precise location of the cross-linked residues. Pro-CrossLink is automated, highly configurable by the user, and applicable to many studies that map low-resolution protein structures and molecular interfaces in protein complexes.

Amino Acid Sequence↗

PubMed2006

Software tools for analysis of mass spectrometric lipidome data.

New software tools for quantitative analysis of mass spectrometric lipidome data have been developed. The LIMSA tool finds and integrates peaks in a mass spectrum, matches the peaks with a user-supplied list of expected lipids, corrects for overlap in their isotopic patterns, and quantifies the identified lipid species according to internal standards. Three different algorithms for isotopic correction (deconvolution) were implemented and compared. LIMSA has a convenient user interface and can be applied on any type of MS spectrum. Typically, analysis of one spectrum takes only a few seconds. The SECD tool, designed for analysis of LC-MS data sets, provides an intuitive and informative display of MS chromatograms as two-dimensional "maps" for visual inspection of the data and allows the user to extract mass spectra, to be further analyzed with LIMSA, from arbitrary regions of these maps. More reliable analysis of complex lipidome data with improved signal-to-noise ratio is obtained when compared to standard time-range averaged spectra. The functionality of these tools is demonstrated by analysis of standard mixtures as well as complex biological samples. The tools described here make accurate, high-throughput analysis of extensive sample sets feasible and are made available to the scientific community free of charge.

Computational Biology↗

PubMedDate not supplied

A software tool to assist business-process decision-making in the biopharmaceutical industry.

Conventionally, software tools for the design of bioprocesses have provided only limited business-related information for decision-making. There is an industrial need to investigate manufacturing options and to gauge the impact of various decisions from economic as well as process perspectives. This paper describes the development and use of a tool to provide an assessment of whole flowsheets by capturing both process and business aspects. The tool is demonstrated by considering the issues concerned when making decisions between two potential flowsheets for a common product. A case study approach is used to compare the process and business benefits of a conventional process route employing packed chromatography beds and an alternative that uses expanded bed adsorption (EBA). The tool allows direct evaluation of the benefits of capital cost reduction and increased yield offered by EBA against penalties of using potentially more expensive EBA matrix with lower lifetimes. Furthermore, the tool provides the ability to gauge the process robustness of each flowsheet option.

Adsorption↗

PubMedDate not supplied

Structure-fate relationships of organic chemicals derived from the software packages E4CHEM and WHASSE.

A risk assessment of chemicals is to be performed on the basis of the model EUSES, developed by the Commission of the European Union. The model package E4CHEM (Exposure Estimation for Potentially Ecotoxic Environmental Chemicals), developed in 1984-1992, is presented and applied in this paper as a model which allows a model-supported evaluation of chemicals. E4CHEM consequently does not have the wide applicability and technical comfort of the more recently developed model EUSES. The simulation models of E4CHEM characterize the chemical behavior in the environment by many aspects. Hence, there is a need to condense all of these aspects to get a clear impression of what will be the fate of the chemicals. Starting with the already published concept of exposure maps, we will discuss how partial orders may be helpful in establishing generalized structure-fate relationships. The software WHASSE is applied.

Chemistry, Organic↗

PubMedDate not supplied

P-Mod: an algorithm and software to map modifications to peptide sequences using tandem MS data.

The discovery of unanticipated protein modifications is one of the most challenging problems in proteomics. Whereas widely used algorithms such as Sequest and Mascot enable mapping of modifications when the mass and amino acid specificity are known, unexpected modifications cannot be identified with these tools. We have developed an algorithm and software called P-Mod, which enables discovery and sequence mapping of modifications to target proteins known to be represented in the analysis or identified by Sequest. P-Mod matches MS/MS spectra to peptide sequences in a search list. For spectra of modified peptides, P-Mod calculates mass differences between search peptide sequences and MS/MS precursors and localizes the mass shift to a sequence position in the peptide. Because modifications are detected as mass shifts, P-Mod does not require the user to guess at masses or sequence locations of modifications. P-Mod uses extreme value statistics to assign p value estimates to sequence-to-spectrum matches. The reported p values are scaled to account for the number of comparisons, so that error rates do not increase with the expanded search lists that result from incorporating potential peptide modifications. Combination of P-Mod searches from multiple LC-MS/MS analyses and multiple samples revealed previously unreported BSA modifications, including a novel decarboxymethylation or D-->G substitution at position 579 of the protein. P-Mod can serve a unique role in the identification of protein modifications both from exogenous and endogenous sources and may be useful for identifying modified protein forms as biomarkers for toxicity and disease processes.

Algorithms↗

PubMedDate not supplied

STEM: a software tool for large-scale proteomic data analyses.

We describe the software, STEM (STrategic Extractor for Mascot's results), which efficiently processes large-scale mass spectrometry-based proteomics data. V (View)-mode evaluates the Mascot peptide identification dataset, removes unreliable candidates and redundant assignments, and integrates the results with key information in the experiment. C (Comparison)-mode compares peptide coverage among multiple datasets and displays proteins commonly/specifically found therein, and processes data for quantitative studies that utilize conventional isotope tags or tags having a smaller mass difference. STEM significantly improves throughput of proteomics study.

Algorithms↗

PubMed2006

Comparison of software tools to improve the detection of carcinogen induced changes in the rat liver proteome by analyzing SELDI-TOF-MS spectra.

A common animal model of chemical hepatocarcinogenesis was used to demonstrate the potential identification of carcinogenicity related protein signatures/biomarkers. Therefore, an animal study in which rats were treated with the known liver carcinogen N-nitrosomorpholine (NNM) or the corresponding vehicle was evaluated. Histopathological investigation as well as SELDI-TOF-MS analysis was performed. SELDI-TOF-MS is an affinity-based mass spectrometry method in which subsets of proteins from biological samples are selectively adsorbed to a chemically modified surface. The proteins are subsequently analyzed with respect to their mass-charge ratios (m/z) by a time of flight (TOF) mass spectrometry (MS) approach. As data preprocessing of SELDI-TOF-MS spectra is essential, baseline correction, normalization, peak detection, and alignment of raw spectra were performed using either the Ciphergen ProteinChip Software 3.1 or functions implemented in the library PROcess of the BioConductor Project. Baseline correction and normalization algorithms of both tools lead to comparable results, whereas results after peak detection and alignment steps differed. Variability between technical and biological replicates was investigated. A linear mixed model with factors experimental group and time point was applied for each protein peak, taking into account the different correlation structure of technical and biological replicates. Alternatively, only median intensity values of technical replicates were used. Results of both models were similar and correlated well with those of the histopathological evaluation of the study. In conclusion, statistical analyses lead to comparable results, whereas parameter settings for preprocessing proved to be crucial.

Animals↗

PubMed2006

GAPP: a fully automated software for the confident identification of human peptides from tandem mass spectra.

This paper introduces the genome annotating proteomic pipeline (GAPP), a totally automated publicly available software pipeline for the identification of peptides and proteins from human proteomic tandem mass spectrometry data. The pipeline takes as its input a series of MS/MS peak lists from a given experimental sample and produces a series of database entries corresponding to the peptides observed within the sample, along with related confidence scores. The pipeline is capable of finding any peptides expected, including those that cross intron-exon boundaries, and those due to single nucleotide polymorphisms (SNPs), alternate splicing, and post-translational modifications (PTMs). GAPP can therefore be used to re-annotate genomes, and this is supported through the inclusion of a Distributed Annotation System (DAS) server, which allows the peptides identified by the pipeline to be displayed in their genomic context within the Ensembl genome browser. GAPP is freely available via the web, at www. gapp.info.

Alternative Splicing↗

PubMed2001

Software development for medical instrumentation.

Computer-assisted medical instrumentation has recently become more common. For accuracy and precision, the computer and interfacing circuit with the associated digital signal processing algorithm can be used for the evaluation of biological signal. The measurement system based on this structure has a very high degree of efficiency and flexibility because different algorithms can be used. In addition, the system can employ some newly developed software packages. This paper will submit a procedure for computer-assisted medical instrumentation, and also will show a specific application on blood flow.

Blood Circulation↗

PubMed2001

Identification and classification of key variables and their role in environmental impact assessment: methodology and software package INTRA.

There is, as yet, no proven methodology to enable, objectively, the identification of key parameters out of a large number one normally encounters during any EIA. As EIA is a costly and time-consuming exercise, it is necessary to separate the man from the boys--so to speak--in order to optimize costs and efforts. In this paper a methodology for distinguishing the more important parameters from the less important ones, developed by us, is described. The methodology aims at identifying and shortlisting the key parameters which ought to be studied in a given EIA situation, thereby helping in reducing time, effort, and cost of EIA. With this methodology a system structure is developed which gives hierarchical pattern of inter-parameter interaction, and reveals several distinguishing features of each parameter. A software package INTRA (INTer-parameter Relationship Analysis) based on this methodology, has been developed. The paper also describes a case study in which INTRA has been used to study the environmental impacts of urbanization of a typical third world town (Roorkee).

Developing Countries↗

PubMed2002

Stochastic trees and the StoTree modeling environment: models and software for medical decision analysis.

In this paper we present a review of stochastic trees, a convenient modeling approach for medical treatment decision analyses. Stochastic trees are a generalization of decision trees that incorporate useful features from continuous-time Markov chains. We also discuss StoTree, a freely available software tool for the formulation and solution of stochastic trees, implemented in the Excel spreadsheet environment.

Decision Support Systems, Clinical↗

PubMed2002

A software tool for the prediction of Xaa-Pro peptide bond conformations in proteins based on 13C chemical shift statistics.

The chemical shift difference (delta[13C(beta)]-delta[13C(gamma)]) is a reference-independent indicator of the Xaa-Pro peptide bond conformation. Based on a statistical analysis of the 13C chemical shifts of 1,033 prolines from 304 proteins deposited in the BioMagRes database, a software tool was created to predict the probabilities for cis or trans conformations of Xaa-Pro peptide bonds. Using this approach, the conformation at a given Xaa-Pro bond can be identified in a simple NOE-independent way immediately after obtaining its NMR resonance assignments. This will allow subsequent structure calculations to be initiated using the correct polypeptide chain conformation.

Amino Acids↗