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Search Results: 1 - 10 of 44953 matches for " Michael McClelland "
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WebArray: an online platform for microarray data analysis
Xiaoqin Xia, Michael McClelland, Yipeng Wang
BMC Bioinformatics , 2005, DOI: 10.1186/1471-2105-6-306
Abstract: The currently implemented functions were based on limma and affy package from Bioconductor, the spacings LOESS histogram (SPLOSH) method, PCA-assisted normalization method and genome mapping method. WebArray incorporates these packages and provides a user-friendly interface for accessing a wide range of key functions of limma and others, such as spot quality weight, background correction, graphical plotting, normalization, linear modeling, empirical bayes statistical analysis, false discovery rate (FDR) estimation, chromosomal mapping for genome comparison.WebArray offers a convenient platform for bench biologists to access several cutting-edge microarray data analysis tools. The website is freely available at http://bioinformatics.skcc.org/webarray/ webcite. It runs on a Linux server with Apache and MySQL.Microarray techniques are being used more and more widely, and many models and algorithms have been developed for microarray data analysis. However, in many cases, people need to have a sufficient knowledge of mathematics, statistics and computer skills in order to utilize these methods. A perfect example is Bioconductor [1]. As a leading open source project on genomic data analysis, Bioconductor gathered a wide range of packages available for the analysis of microarray data. However, command line interface programming skills are essential for using Bioconductor and R computer language, which could be an impediment to many biologists. To bridge the gap between biologist's real world problems and the best microarray data analysis methods, we developed WebArray to assist biologists with using tools for microarray data analysis, including some packages from Bioconductor and others.limma (Linear Models for Microarray Analysis) is one of the most commonly used packages in Bioconductor, which has incorporated the most cutting-edge statistical analysis methods, providing normalization and statistical analysis for cDNA microarray. The key function of the limma package is
Selection of Salmonella enterica Serovar Typhi Genes Involved during Interaction with Human Macrophages by Screening of a Transposon Mutant Library
Sébastien C. Sabbagh, Christine Lepage, Michael McClelland, France Daigle
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0036643
Abstract: The human-adapted Salmonella enterica serovar Typhi (S. Typhi) causes a systemic infection known as typhoid fever. This disease relies on the ability of the bacterium to survive within macrophages. In order to identify genes involved during interaction with macrophages, a pool of approximately 105 transposon mutants of S. Typhi was subjected to three serial passages of 24 hours through human macrophages. Mutants recovered from infected macrophages (output) were compared to the initial pool (input) and those significantly underrepresented resulted in the identification of 130 genes encoding for cell membrane components, fimbriae, flagella, regulatory processes, pathogenesis, and many genes of unknown function. Defined deletions in 28 genes or gene clusters were created and mutants were evaluated in competitive and individual infection assays for uptake and intracellular survival during interaction with human macrophages. Overall, 26 mutants had defects in the competitive assay and 14 mutants had defects in the individual assay. Twelve mutants had defects in both assays, including acrA, exbDB, flhCD, fliC, gppA, mlc, pgtE, typA, waaQGP, SPI-4, STY1867-68, and STY2346. The complementation of several mutants by expression of plasmid-borne wild-type genes or gene clusters reversed defects, confirming that the phenotypic impairments within macrophages were gene-specific. In this study, 35 novel phenotypes of either uptake or intracellular survival in macrophages were associated with Salmonella genes. Moreover, these results reveal several genes encoding molecular mechanisms not previously known to be involved in systemic infection by human-adapted typhoidal Salmonella that will need to be elucidated.
TabSQL: a MySQL tool to facilitate mapping user data to public databases
Xiao-Qin Xia, Michael McClelland, Yipeng Wang
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-342
Abstract: We developed TabSQL, a MySQL-based application tool, for viewing, filtering and querying data files with large numbers of rows. TabSQL provides functions for downloading and installing table files from public databases including the Gene Ontology database (GO), the Ensembl databases, and genome databases from the UCSC genome bioinformatics site. Any other database that provides tab-delimited flat files can also be imported. The downloaded gene annotation tables can be queried together with users' data in TabSQL using either a graphic interface or command line.TabSQL allows queries across the user's data and public databases without programming. It is a convenient tool for biologists to annotate and enrich their data.In high-throughput genomics and proteomics studies, raw data and the results of analyses are usually organized in a table-like format (e.g., [1-3]), with rows representing genes or probes, while columns denote experimental features and annotations, such as sample identifiers, gene annotations, fold changes in signal, or the p values of statistical analyses. It is common for biologists to want to add additional annotations. There are public databases that can be useful sources of such annotations. The Gene Ontology (GO) project http://www.geneontology.org webcite develops and maintains a controlled vocabulary of gene and gene product attributes, and provides detailed and unified gene and gene products annotation files [4,5]; the Ensembl project http://www.ensembl.org webcite offers genome databases for a variety of organisms [6]; the UCSC genome bioinformatics site http://genome.ucsc.edu/ webcite has also been widely used by researchers from all over the world [7].Microsoft Access http://office.microsoft.com/access webcite is a commonly used desktop database management system that biologists use to view, map and query large data files. However, Access does not provide any tools to directly link to public databases in genome research. Thus, we designed Tab
What Women Want in a Man: The Role of Age, Social Class, Ethnicity, and Height  [PDF]
Adrian Furnham, Alastair McClelland
Psychology (PSYCH) , 2015, DOI: 10.4236/psych.2015.63028
Abstract: This study aimed to use a budget allocation model to examine mate preference. 303 female respondents with a mean age of 21.75 years were asked about their preferences for someone to take on a blind date. They were presented with descriptions of 16 hypothetical men which they were asked to rate for personal choice and suitability. The hypothetical men differed on age (18 - 20 years vs. 30 - 33 years), social class (I/II vs. III/IV), ethnicity (Caucasian vs. Asian) and height (short/average from 5’6” to 5’8” and tall 6’1” to 6’3”). Overall females preferred younger, taller males from their own racial group and with a higher social class. Women showed a strong preference for men their own age, ethnicity and especially height.
What Men Want in a Woman: Personality Is More Important than Academic Record or Athleticism  [PDF]
Adrian Furnham, Alastair McClelland
Psychology (PSYCH) , 2015, DOI: 10.4236/psych.2015.68092
Abstract: Two hundred and fifty eight male respondents with a mean age of 24.5 years were presented with sixteen hypothetical females which they were asked to rate for suitability as long term partners. The hypothetical females differed with respect to: academic record ability (high/average); athleticism (high/low) and two personality variables; Extraversion (introvert/extravert) and Neuroticism (stable/neurotic). Overall males preferred intelligent, athletic, extraverted, stable females as potential long term partners. Effect sizes showed that being Extravert was seen as being the most important characteristic and being athletic as the least important. However, there were also a number of significant two- and three-way interactions between the characteristics of the potential dates. Limitations of the study are noted.
THE MOCHE BOTANICAL FROG (La rana botánica mochica)
Donna McClelland
Arqueología Iberoamericana , 2011,
Abstract: Plants and animals with features which identify them as supernaturals characterize the art of the Precolumbian Moche culture of northern Peru. Among these animals is a frog with feline attributes and a consistent association with manioc tubers, stalks, and plants, the Botanical Frog. The Botanical Frog appears to have been patterned on Leptodactylus pentadactylus. It is shown copulating with felines. Fine line painted vessels and ones with low relief decoration show the Botanical Frog performing as part of a ritual involving other animals and cultivated crops, suggesting that the Botanical Frog was associated with agriculture. ESPA OL: El arte de la cultura mochica de la costa norte del Perú presenta plantas y animales mostrando rasgos sobrenaturales. Uno de los animales es una rana con elementos felinos y asociada con tubérculos, ramas y plantas de yuca. La Rana Botánica probablemente tiene su origen en Leptodactylus pentadactylus, una rana carnívora de la selva amazónica. La Rana Botánica copula con felinos y, en vasijas pintadas con líneas finas o con escenarios representados en bajorrelieve, toma parte en ceremonias involucrando a otros animales y cosechas domésticas. Parece ser que la Rana Botánica era un ser sobrenatural asociado con la agricultura.
Specific Responses of Salmonella enterica to Tomato Varieties and Fruit Ripeness Identified by In Vivo Expression Technology
Jason T. Noel,Nabil Arrach,Ali Alagely,Michael McClelland,Max Teplitski
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0012406
Abstract: Recent outbreaks of vegetable-associated gastroenteritis suggest that enteric pathogens colonize, multiply and persist in plants for extended periods of time, eventually infecting people. Genetic and physiological pathways, by which enterics colonize plants, are still poorly understood.
An Accurate Prostate Cancer Prognosticator Using a Seven-Gene Signature Plus Gleason Score and Taking Cell Type Heterogeneity into Account
Xin Chen, Shizhong Xu, Michael McClelland, Farah Rahmatpanah, Anne Sawyers, Zhenyu Jia, Dan Mercola
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0045178
Abstract: One of the major challenges in the development of prostate cancer prognostic biomarkers is the cellular heterogeneity in tissue samples. We developed an objective Cluster-Correlation (CC) analysis to identify gene expression changes in various cell types that are associated with progression. In the Cluster step, samples were clustered (unsupervised) based on the expression values of each gene through a mixture model combined with a multiple linear regression model in which cell-type percent data were used for decomposition. In the Correlation step, a Chi-square test was used to select potential prognostic genes. With CC analysis, we identified 324 significantly expressed genes (68 tumor and 256 stroma cell expressed genes) which were strongly associated with the observed biochemical relapse status. Significance Analysis of Microarray (SAM) was then utilized to develop a seven-gene classifier. The Classifier has been validated using two independent Data Sets. The overall prediction accuracy and sensitivity is 71% and 76%, respectively. The inclusion of the Gleason sum to the seven-gene classifier raised the prediction accuracy and sensitivity to 83% and 76% respectively based on independent testing. These results indicated that our prognostic model that includes cell type adjustments and using Gleason score and the seven-gene signature has some utility for predicting outcomes for prostate cancer for individual patients at the time of prognosis. The strategy could have applications for improving marker performance in other cancers and other diseases.
Coordinated Regulation of Virulence during Systemic Infection of Salmonella enterica Serovar Typhimurium
Hyunjin Yoon,Jason E. McDermott,Steffen Porwollik,Michael McClelland,Fred Heffron
PLOS Pathogens , 2009, DOI: 10.1371/journal.ppat.1000306
Abstract: To cause a systemic infection, Salmonella must respond to many environmental cues during mouse infection and express specific subsets of genes in a temporal and spatial manner, but the regulatory pathways are poorly established. To unravel how micro-environmental signals are processed and integrated into coordinated action, we constructed in-frame non-polar deletions of 83 regulators inferred to play a role in Salmonella enteriditis Typhimurium (STM) virulence and tested them in three virulence assays (intraperitoneal [i.p.], and intragastric [i.g.] infection in BALB/c mice, and persistence in 129X1/SvJ mice). Overall, 35 regulators were identified whose absence attenuated virulence in at least one assay, and of those, 14 regulators were required for systemic mouse infection, the most stringent virulence assay. As a first step towards understanding the interplay between a pathogen and its host from a systems biology standpoint, we focused on these 14 genes. Transcriptional profiles were obtained for deletions of each of these 14 regulators grown under four different environmental conditions. These results, as well as publicly available transcriptional profiles, were analyzed using both network inference and cluster analysis algorithms. The analysis predicts a regulatory network in which all 14 regulators control the same set of genes necessary for Salmonella to cause systemic infection. We tested the regulatory model by expressing a subset of the regulators in trans and monitoring transcription of 7 known virulence factors located within Salmonella pathogenicity island 2 (SPI-2). These experiments validated the regulatory model and showed that the response regulator SsrB and the MarR type regulator, SlyA, are the terminal regulators in a cascade that integrates multiple signals. Furthermore, experiments to demonstrate epistatic relationships showed that SsrB can replace SlyA and, in some cases, SlyA can replace SsrB for expression of SPI-2 encoded virulence factors.
Virulence of 32 Salmonella Strains in Mice
Matthew C. Swearingen, Steffen Porwollik, Prerak T. Desai, Michael McClelland, Brian M. M. Ahmer
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0036043
Abstract: Virulence and persistence in the BALB/c mouse gut was tested for 32 strains of Salmonella enterica for which genome sequencing is complete or underway, including 17 serovars within subspecies I (enterica), and two representatives of each of the other five subspecies. Only serovar Paratyphi C strain BAA1715 and serovar Typhimurium strain 14028 were fully virulent in mice. Three divergent atypical Enteritidis strains were not virulent in BALB/c, but two efficiently persisted. Most of the other strains in all six subspecies persisted in the mouse intestinal tract for several weeks in multiple repeat experiments although the frequency and level of persistence varied considerably. Strains with heavily degraded genomes persisted very poorly, if at all. None of the strains tested provided immunity to Typhimurium infection. These data greatly expand on the known significant strain-to-strain variation in mouse virulence and highlight the need for comparative genomic and phenotypic studies.
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