μ-CS: An extension of the TM4 platform to manage Affymetrix binary data

<p>Abstract</p> <p>Background</p> <p>A main goal in understanding cell mechanisms is to explain the relationship among genes and related molecular processes through the combined use of technological platforms and bioinformatics analysis. High throughput platforms, such as microarrays, enable the investigation of the whole genome in a single experiment. There exist different kind of microarray platforms, that produce different types of binary data (images and raw data). Moreover, also considering a single vendor, different chips are available. The analysis of microarray data requires an initial preprocessing phase (i.e. normalization and summarization) of raw data that makes them suitable for use on existing platforms, such as the TIGR M4 Suite. Nevertheless, the annotations of data with additional information such as gene function, is needed to perform more powerful analysis. Raw data preprocessing and annotation is often performed in a manual and error prone way. Moreover, many available preprocessing tools do not support annotation. Thus novel, platform independent, and possibly open source tools enabling the semi-automatic preprocessing and annotation of microarray data are needed.</p> <p>Results</p> <p>The paper presents <it>μ</it>-CS (Microarray Cel file Summarizer), a cross-platform tool for the automatic normalization, summarization and annotation of Affymetrix binary data. <it>μ</it>-CS is based on a client-server architecture. The <it>μ</it>-CS client is provided both as a plug-in of the TIGR M4 platform and as a Java standalone tool and enables users to read, preprocess and analyse binary microarray data, avoiding the manual invocation of external tools (e.g. the Affymetrix Power Tools), the manual loading of preprocessing libraries, and the management of intermediate files. The <it>μ</it>-CS server automatically updates the references to the summarization and annotation libraries that are provided to the <it>μ</it>-CS client before the preprocessing. The <it>μ</it>-CS server is based on the web services technology and can be easily extended to support more microarray vendors (e.g. Illumina).</p> <p>Conclusions</p> <p>Thus <it>μ</it>-CS users can directly manage binary data without worrying about locating and invoking the proper preprocessing tools and chip-specific libraries. Moreover, users of the <it>μ</it>-CS plugin for TM4 can manage Affymetrix binary files without using external tools, such as APT (Affymetrix Power Tools) and related libraries. Consequently, <it>μ</it>-CS offers four main advantages: (i) it avoids to waste time for searching the correct libraries, (ii) it reduces possible errors in the preprocessing and further analysis phases, e.g. due to the incorrect choice of parameters or the use of old libraries, (iii) it implements the annotation of preprocessed data, and finally, (iv) it may enhance the quality of further analysis since it provides the most updated annotation libraries. The <it>μ</it>-CS client is freely available as a plugin of the TM4 platform as well as a standalone application at the project web site (<url>http://bioingegneria.unicz.it/M-CS</url>).</p

Cliophysics: Socio-political Reliability Theory, Polity Duration and African Political (In)stabilities

Quantification of historical sociological processes have recently gained attention among theoreticians in the effort of providing a solid theoretical understanding of the behaviors and regularities present in sociopolitical dynamics. Here we present a reliability theory of polity processes with emphases on individual political dynamics of African countries. We found that the structural properties of polity failure rates successfully capture the risk of political vulnerability and instabilities in which 87.50%, 75%, 71.43%, and 0% of the countries with monotonically increasing, unimodal, U-shaped and monotonically decreasing polity failure rates, respectively, have high level of state fragility indices. The quasi-U-shape relationship between average polity duration and regime types corroborates historical precedents and explains the stability of the autocracies and democracies.Comment: 4 pages, 3 figures, 1 tabl

Inhaled nitric oxide in premature infants: effect on tracheal aspirate and plasma nitric oxide metabolites

ObjectiveInhaled nitric oxide (iNO) is a potential new therapy for prevention of bronchopulmonary dysplasia and brain injury in premature infants. This study examined dose-related effects of iNO on NO metabolites as evidence of NO delivery.Study designA subset of 102 premature infants in the NO CLD trial, receiving 24 days of iNO (20 p.p.m. decreasing to 2 p.p.m.) or placebo, were analyzed. Tracheal aspirate (TA) and plasma samples collected at enrollment and at intervals during study gas were analyzed for NO metabolites.ResultiNO treatment increased NO metabolites in TA at 20 and 10 p.p.m. (1.7- to 2.3-fold vs control) and in plasma at 20, 10, and 5 p.p.m. (1.6- to 2.3-fold). In post hoc analysis, treated infants with lower metabolite levels at entry had an improved clinical outcome.ConclusioniNO causes dose-related increases in NO metabolites in the circulation as well as lung fluid, as evidenced by TA analysis, showing NO delivery to these compartments

Isolated core training improves sprint performance in national-level junior swimmers

Purpose: The aim of our study was to quantify the effects of a 12-week isolated core training programme on 50-m front crawl swim time and measures of core musculature functionally relevant to swimming. Methods: Twenty national-level junior swimmers (ten male and ten female, 16 ± 1 y, 171 ± 5 cm, 63 ± 4 kg) participated in the study. Group allocation (intervention [n=10], control [n=10]) was based on two pre-existing swim training groups who were part of the same swimming club but trained in different groups. The intervention group completed the core training, incorporating exercises targeting the lumbo-pelvic complex and upper region extending to the scapula, three times per week for 12 weeks. While the training was performed in addition to the normal pool-based swimming programme, the control group maintained their usual pool-based swimming programme. We made probabilistic magnitude-based inferences about the effect of the core training on 50-m swim time and functionally relevant measures of core function. Results: Compared to the control group, the core training intervention group had a possibly large beneficial effect on 50-m swim time (-2.0%; 90% confidence interval -3.8 to -0.2%). Moreover it showed smallmoderate improvements on a timed prone-bridge test (9.8%; 3.9 to 16.0%) and asymmetric straight-arm pull-down test (21.9%; 12.5 to 32.1%), there were moderate-large increases in peak EMG activity of core musculature during isolated tests of maximal voluntary contraction. Conclusion: This is the first study to demonstrate a clear beneficial effect of isolated core training on 50-m front crawl swim performance

Systematic Planning of Genome-Scale Experiments in Poorly Studied Species

Genome-scale datasets have been used extensively in model organisms to screen for specific candidates or to predict functions for uncharacterized genes. However, despite the availability of extensive knowledge in model organisms, the planning of genome-scale experiments in poorly studied species is still based on the intuition of experts or heuristic trials. We propose that computational and systematic approaches can be applied to drive the experiment planning process in poorly studied species based on available data and knowledge in closely related model organisms. In this paper, we suggest a computational strategy for recommending genome-scale experiments based on their capability to interrogate diverse biological processes to enable protein function assignment. To this end, we use the data-rich functional genomics compendium of the model organism to quantify the accuracy of each dataset in predicting each specific biological process and the overlap in such coverage between different datasets. Our approach uses an optimized combination of these quantifications to recommend an ordered list of experiments for accurately annotating most proteins in the poorly studied related organisms to most biological processes, as well as a set of experiments that target each specific biological process. The effectiveness of this experiment- planning system is demonstrated for two related yeast species: the model organism Saccharomyces cerevisiae and the comparatively poorly studied Saccharomyces bayanus. Our system recommended a set of S. bayanus experiments based on an S. cerevisiae microarray data compendium. In silico evaluations estimate that less than 10% of the experiments could achieve similar functional coverage to the whole microarray compendium. This estimation was confirmed by performing the recommended experiments in S. bayanus, therefore significantly reducing the labor devoted to characterize the poorly studied genome. This experiment-planning framework could readily be adapted to the design of other types of large-scale experiments as well as other groups of organisms

A Unified Model of the GABA(A) Receptor Comprising Agonist and Benzodiazepine Binding Sites

We present a full-length α(1)β(2)γ(2) GABA receptor model optimized for agonists and benzodiazepine (BZD) allosteric modulators. We propose binding hypotheses for the agonists GABA, muscimol and THIP and for the allosteric modulator diazepam (DZP). The receptor model is primarily based on the glutamate-gated chloride channel (GluCl) from C. elegans and includes additional structural information from the prokaryotic ligand-gated ion channel ELIC in a few regions. Available mutational data of the binding sites are well explained by the model and the proposed ligand binding poses. We suggest a GABA binding mode similar to the binding mode of glutamate in the GluCl X-ray structure. Key interactions are predicted with residues α(1)R66, β(2)T202, α(1)T129, β(2)E155, β(2)Y205 and the backbone of β(2)S156. Muscimol is predicted to bind similarly, however, with minor differences rationalized with quantum mechanical energy calculations. Muscimol key interactions are predicted to be α(1)R66, β(2)T202, α(1)T129, β(2)E155, β(2)Y205 and β(2)F200. Furthermore, we argue that a water molecule could mediate further interactions between muscimol and the backbone of β(2)S156 and β(2)Y157. DZP is predicted to bind with interactions comparable to those of the agonists in the orthosteric site. The carbonyl group of DZP is predicted to interact with two threonines α(1)T206 and γ(2)T142, similar to the acidic moiety of GABA. The chlorine atom of DZP is placed near the important α(1)H101 and the N-methyl group near α(1)Y159, α(1)T206, and α(1)Y209. We present a binding mode of DZP in which the pending phenyl moiety of DZP is buried in the binding pocket and thus shielded from solvent exposure. Our full length GABA(A) receptor is made available as Model S1

Experiences With and Attitudes Toward Death and Dying Among Homeless Persons

BACKGROUND: Homeless persons face many barriers to health care, have few resources, and experience high death rates. They live lives of disenfranchisement and neglect. Few studies have explored their experiences and attitudes toward death and dying. Unfortunately, studies done in other populations may not apply to homeless persons. Exploring these experiences and attitudes may provide insight into life, health care, and end-of-life (EOL) concerns of this population. OBJECTIVE: To explore the experiences and attitudes toward death and dying among homeless persons. DESIGN: Qualitative study utilizing focus groups. PARTICIPANTS: Fifty-three homeless persons recruited from homeless service agencies. MEASUREMENTS: In-depth interviews, which were audiotaped and transcribed. RESULTS: We present seven themes, some of which are previously unreported. Homeless persons described many significant experiences with death and dying, and many participants suffered losses while very young. These encounters influenced participants’ attitudes toward risks and risky behavior: e.g., for some, these experiences provided justification for high-risk behaviors and influenced their behaviors while living on the streets. For others, they may be associated with their homelessness. Finally, these experiences informed their attitudes toward death and dying as well as EOL care; homeless persons believe that care will be poor at the EOL. CONCLUSIONS: Findings from this study have implications for addressing social services, health promotion, prevention, and EOL care for homeless persons, as well as for others who are poor and disenfranchised

Clinical impact of a targeted next-generation sequencing gene panel for autoinflammation and vasculitis.

BACKGROUND: Monogenic autoinflammatory diseases (AID) are a rapidly expanding group of genetically diverse but phenotypically overlapping systemic inflammatory disorders associated with dysregulated innate immunity. They cause significant morbidity, mortality and economic burden. Here, we aimed to develop and evaluate the clinical impact of a NGS targeted gene panel, the "Vasculitis and Inflammation Panel" (VIP) for AID and vasculitis. METHODS: The Agilent SureDesign tool was used to design 2 versions of VIP; VIP1 targeting 113 genes, and a later version, VIP2, targeting 166 genes. Captured and indexed libraries (QXT Target Enrichment System) prepared for 72 patients were sequenced as a multiplex of 16 samples on an Illumina MiSeq sequencer in 150bp paired-end mode. The cohort comprised 22 positive control DNA samples from patients with previously validated mutations in a variety of the genes; and 50 prospective samples from patients with suspected AID in whom previous Sanger based genetic screening had been non-diagnostic. RESULTS: VIP was sensitive and specific at detecting all the different types of known mutations in 22 positive controls, including gene deletion, small INDELS, and somatic mosaicism with allele fraction as low as 3%. Six/50 patients (12%) with unclassified AID had at least one class 5 (clearly pathogenic) variant; and 11/50 (22%) had at least one likely pathogenic variant (class 4). Overall, testing with VIP resulted in a firm or strongly suspected molecular diagnosis in 16/50 patients (32%). CONCLUSIONS: The high diagnostic yield and accuracy of this comprehensive targeted gene panel validate the use of broad NGS-based testing for patients with suspected AID