Open source system for analyzing, validating, and storing protein identification data

This paper describes an open-source system for analyzing, storing, and validating proteomics information derived from tandem mass spectrometry. It is based on a combination of data analysis servers, a user interface, and a relational database. The database was designed to store the minimum amount of information necessary to search and retrieve data obtained from the publicly available data analysis servers. Collectively, this system was referred to as the Global Proteome Machine (GPM). The components of the system have been made available as open source development projects. A publicly available system has been established, comprised of a group of data analysis servers and one main database server.     

MRD: a microsatellite repeats database for prokaryotic and eukaryotic genomes

MRD is a database system to access the microsatellite repeats information of genomes such as archea, eubacteria, and other eukaryotic genomes whose sequence information is available in public domains. MRD stores information about simple tandemly repeated k-mer sequences where k= 1 to 6, i.e. monomer to hexamer. The web interface allows the users to search for the repeat of their interest and to know about the association of the repeat with genes and genomic regions in the specific organism. The data contains the abundance and distribution of microsatellites in the coding and non-coding regions of the genome. The exact location of repeats with respect to genomic regions of interest (such as UTR, exon, intron or intergenic regions) whichever is applicable to organism is highlighted. MRD is available on the World Wide Web at and/or . The database is designed as an open-ended system to accommodate the microsatellite repeats information of other genomes whose complete sequences will be available in future through public domain.     

玉米 线辣椒套作系统中土壤养分与根际土壤微生物、酶活性的关系

采用玉米单作、线辣椒单作、玉米-线辣椒套作3种栽培模式,并在玉米-线辣椒套作的种间根部设3种不同隔离处理（膜隔、网隔和无隔）,研究了玉米-线辣椒套作系统中土壤生物因子与土壤养分的关系．结果表明：玉米-线辣椒套作具有明显优势;与两作物单作和玉米-线辣椒套作种间根区膜隔处理相比,玉米-线辣椒根区无隔和网隔处理复合群体中两作物根际土壤酶活性、微生物数量、土壤养分均显著提高;除有效镁与真菌种群数量、过氧化氢酶活性呈负相关外,其余速效养分与各生物因子均呈显著或极显著正相关．通径分析表明,该系统中促进有机质累积的主要生物因素是脲酶、过氧化氢酶、细菌和蛋白酶,蔗糖酶是影响碱解氮的最主要因子,脲酶是影响有效磷的最主要因子,细菌是影响有效钾的最主要因子,碱性磷酸酶、真菌只是选择性地对有机质的累积和氮、磷、钾有效养分的形成起作用,放线菌对土壤养分的直接作用系数为负,对土壤养分形成的作用较小．     

Defining standard of care in the developing world: the intersection of international research ethics and health systems analysis

In recent years there has been intense debate regarding the level of medical care provided to 'standard care' control groups in clinical trials in developing countries, particularly when the research sponsors come from wealthier countries. The debate revolves around the issue of how to define a standard of medical care in a country in which many people are not receiving the best methods of medical care available in other settings. In this paper, we argue that additional dimensions of the standard of care have been hitherto neglected, namely, the structure and efficiency of the national health system. The health system affects locally available medical care in two important ways: first, the system may be structured to provide different levels of care at different sites with referral mechanisms to direct patients to the appropriate level of care. Second, inefficiencies in this system may influence what care is available in a particular locale. As a result of these two factors locally available care cannot be equated with a national 'standard'. A reasonable approach is to define the national standard of care as the level of care that ought to be delivered under conditions of appropriate and efficient referral in a national system. This standard is the minimum level of care that ought to be provided to a control group. There may be additional moral arguments for higher levels of care in some circumstances. This health system analysis may be helpful to researchers and ethics committees in designing and reviewing research involving standard care control groups in developing country research.     

Global identifiability of the parameters of nonlinear systems with specified inputs: a comparison of methods

The two methods available for analyzing the global structural identifiability of the parameters of a nonlinear system with a specified input function, the Taylor series approach and the similarity transformation approach, are compared and contrasted through application to three examples. It is shown that, as for linear systems, it is very difficult to predict which of the available methods will result in the least effort for a particular example. The role of modern symbolic manipulation packages in the analysis is assessed. The third example proves intractable using the similarity transformation approach as originally formulated, but the analysis is completed using a reformulation that exploits the polynominal form of the system equations in the example.     

A public domain image-analysis program for the single-cell gel-electrophoresis (comet) assay

The single-cell gel electrophoresis (or comet) assay has gained widespread acceptance as a cheap and simple genotoxicity test, but it requires a computer-assisted image-analysis system. As commercial programs are expensive and inflexible, we decided to develop an image-analysis system based on public domain programs and make it publicly available for the scientific community. Our system is based on the scientific image-processing program NIH Image, and was written in its Pascal-like macro language. User interaction was kept as simple as possible, to enable the measurement of a large number of cells with a few keystrokes. Therefore, the time for image analysis is very low, even on slow computers. The comet macro can be obtained from http://mailbox.univie.ac.at/christoph.helma++ +/comet/, NIH Image is available at http://rsb.info.nih.gov/nih-image/. Both programs are free of charge.     

Using ERDS to Infer Copy-Number Variants in High-Coverage Genomes

Although there are many methods available for inferring copy-number variants (CNVs) from next-generation sequence data, there remains a need for a system that is computationally efficient but that retains good sensitivity and specificity across all types of CNVs. Here, we introduce a new method, estimation by read depth with single-nucleotide variants (ERDS), and use various approaches to compare its performance to other methods. We found that for common CNVs and high-coverage genomes, ERDS performs as well as the best method currently available (Genome STRiP), whereas for rare CNVs and high-coverage genomes, ERDS performs better than any available method. Importantly, ERDS accommodates both unique and highly amplified regions of the genome and does so without requiring separate alignments for calling CNVs and other variants. These comparisons show that for genomes sequenced at high coverage, ERDS provides a computationally convenient method that calls CNVs as well as or better than any currently available method.     

Complex NAPL Site Characterization Using Fluorescence Part 2: Analysis of Soil Matrix Effects on the Excitation/Emission Matrix

Commercially available cone penetrometer (CPT)fluorescence based sensor platforms have been used to detect non-aqueous phase liquids (NAPLs), such as petroleum oils and lubricants, in situf or more than a decade. These approaches have also been used to detect dense non-aqueous phase liquid (DNAPL) source zones by detecting commingled oilsfuels, and naturally occurring organic materials entrained by DNAPLs and carried to depths below the water table. Several neat NAPLs and mixtureswere added to various soil types and analyzedfor specific fluorescence characteristics to determine the optimal excitation source for site characterization efforts. Using excitationlemission matrices (EEMs), we demonstrate that an optimized excitation wavelength can be determinedfor specific fiuowphores within the NAPL mixtures, and that available systems can be ranked based on the specific contaminant and site soil types. An optimal excitation wavelength yields the maximum fluorescence within an EEM spectrum. We ranked commercially available cone penetrometer fluorescence detection systems according to the potential for ease of detection based on maximum fluorescence response. When soils were added tocomplexNAPLmixtures,analytefluorescence emissionwasattenuatedinpreferential portions of the EEM, leading to differences in the optimal excitation source wavelength. Furthermore, impure silica-containing minerals impact the emission signal, potentially leading to incorrect conclusionsf or several commercially available systems. Our find ings suggest that afrequency-agile (e.g., tunable excitation source) probe system would be superior to any other system commercially available, provided the system would be relatively easy to operate and would have rapid in-situ EEM generating capabilitiesfo r optimization in the field.     

Mutagenicity testing with transgenic mice. Part II: Comparison with the mouse spot test

The mouse spot test, an in vivo mutation assay, has been used to assess a number of chemicals. It is at present the only in vivo mammalian test system capable of detecting somatic gene mutations according to OECD guidelines (OECD guideline 484). It is however rather insensitive, animal consuming and expensive type of test. More recently several assays using transgenic animals have been developed. From data in the literature, the present study compares the results of in vivo testing of over twenty chemicals using the mouse spot test and compares them with results from the two transgenic mouse models with the best data base available, the lacI model (commercially available as the Big Blue(R) mouse), and the lacZ model (commercially available as the Mutatrade mark Mouse). There was agreement in the results from the majority of substances. No differences were found in the predictability of the transgenic animal assays and the mouse spot test for carcinogenicity. However, from the limited data available, it seems that the transgenic mouse assay has several advantages over the mouse spot test and may be a suitable test system replacing the mouse spot test for detection of gene but not chromosome mutations in vivo.     

Mitochondrial calpain system: An overview

Calpain system is generally known to be comprised of three molecules: two Ca²⁺-dependent proteases: μ- and m-calpains, and their endogenous inhibitor, calpastatin. While calpains have previously been considered as the cytoplasmic enzymes, research in the recent past demonstrated that μ-calpain, m-calpain and calpain 10 are present in mitochondria, which play important roles in a variety of pathophysiological conditions including necrotic and apoptotic cell death phenomena. Although a number of original research articles on mitochondrial calpain system are available, yet to the best of our knowledge, a precise review article on mitochondrial calpain system has, however, not been available. This review outlines the key features of the mitochondrial calpain system, and its roles in several cellular and biochemical events under normal and some pathophysiological conditions.     

Control of the HIV infection and drug dosage

An increasing number of sophisticated control algorithms become available in the current literature to optimize the HIV therapy. Unfortunately, the pharmacokinetics and pharmacodynamics of antiretroviral drugs are ignored and these algorithms remain purely theoretic. This issue is investigated explicitly in this paper. An elementary pharmacodynamics model is combined with a non linear feedback control computed from standard engineering methods. It is shown that it results in the design of a realistic dosage regimen which drives the immunological system close to the healthy equilibrium state. Although the problem is dealt as a single input system, it is argued that the procedure can be extended to a multitherapy design or to any available control law.     

A general computational model of mitochondrial metabolism in a whole organelle scale

SUMMARY: A computational tool for mitochondrial systems biology has been developed as a simulation model of E-Cell2, a publicly available simulation system. The general model consists of 58 enzymatic reactions and 117 metabolites, representing the respiratory chain, the TCA cycle, the fatty acid beta-oxidation and the inner-membrane transport system. It is based on previously published enzyme kinetics studies in the literature; we have successfully integrated and packaged them into a single large model. The model can be easily extended and modified so that mitochondrial biologists/physiologists can integrate their own models and evaluate them in the context of the whole organelle metabolism. AVAILABILITY: The mitochondrial model is bundled up with E-Cell2 simulation system, which can be downloaded from http://www.e-cell.org. CD-ROMs are also available and are distributed at major conferences. SUPPLEMENTARY INFORMATION: All the kinetic data are available via http://www.e-cell.org     

华北平原山药主产区土壤肥力和养分平衡现状及环境风险评价

以华北平原山药主产区为研究区域,通过实地调研、跟踪监测的方法,对山药田肥力现状和施肥现状进行分析,并利用农田养分输入输出模型解析山药田土壤养分平衡状况,同时对山药种植体系的环境风险进行综合评价。结果表明: 1)山药田土壤有机质、全氮含量等级为极低水平,有效磷和有效锌含量为偏低水平,硝态氮、有效铜含量为中等水平,缓效钾、交换性钙、交换性镁、有效硫含量均达极高水平,速效钾、有效铁、有效锰含量则为高水平;2)山药全生育期氮(N)、磷(P₂O₅)、钾(K₂O)养分投入量分别为575～943、341～981、655～1219 kg·hm^-2,其中化肥氮(N)、磷(P₂O₅)、钾(K₂O)投入占比分别高达83.0%、88.6%、91.3%,重无机轻有机以及养分投入过量和失衡问题突出;3)山药种植体系土壤氮、磷、钾盈余量分别达271.14、466.34、739.97 kg·hm^-2,盈余率分别达48.7%、258.1%、324.5%,氮、磷、钾盈余量均超出环境安全阈值,分别属于中度风险、严重风险和严重风险等级。山药生产中化肥的投入对环境造成的风险总体上达到了重度风险等级。     

Ensembl 2002: accommodating comparative genomics

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of human, mouse and other genome sequences, available as either an interactive web site or as flat files. Ensembl also integrates manually annotated gene structures from external sources where available. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. These range from sequence analysis to data storage and visualisation and installations exist around the world in both companies and at academic sites. With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation.     

Surveillance strategies for renal cell carcinoma patients following nephrectomy

Renal cell carcinoma (RCC) is the most lethal of urologic malignancies, accounting for an estimated 36,000 new cases of carcinoma and 12,000 deaths in 2005. Nephrectomy is the usual treatment; however, after nephrectomy, RCC recurs in 20% to 40% of patients with clinically localized disease. A consensus surveillance protocol does not exist for follow-up of RCC after nephrectomy. In this article, available protocols are reviewed with a goal of developing an evidence-based system including the prognostic factors for recurrent disease, chronology and sites of recurrence, available treatment options if recurrent disease is found, and modalities of diagnostic testing available to urologists. New surveillance recommendations are presented based on prognostic factors as well as the University of California, Los Angeles Integrated Staging System for RCC.     

BioCaster: detecting public health rumors with a Web-based text mining system

SUMMARY: BioCaster is an ontology-based text mining system for detecting and tracking the distribution of infectious disease outbreaks from linguistic signals on the Web. The system continuously analyzes documents reported from over 1700 RSS feeds, classifies them for topical relevance and plots them onto a Google map using geocoded information. The background knowledge for bridging the gap between Layman's terms and formal-coding systems is contained in the freely available BioCaster ontology which includes information in eight languages focused on the epidemiological role of pathogens as well as geographical locations with their latitudes/longitudes. The system consists of four main stages: topic classification, named entity recognition (NER), disease/location detection and event recognition. Higher order event analysis is used to detect more precisely specified warning signals that can then be notified to registered users via email alerts. Evaluation of the system for topic recognition and entity identification is conducted on a gold standard corpus of annotated news articles. AVAILABILITY: The BioCaster map and ontology are freely available via a web portal at http://www.biocaster.org.     

An information-search system for micro-organism collection

A search-information system has been developed which allows to keep and provide the needed information concerning collections of any microorganisms. The system contains up to 20 000 strains which can be characterized by 4000 properties. The system allows to find all strains corresponding to the given set of characters and also provides the information available for the strain required. The survey of the set of 1000 strains takes as much as 10 sec; the time of search grows linearly with the increase of the strain number. The system is realized on the electronic computer EC1010.