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Search Results: 1 - 10 of 174 matches for " Errol Strain "
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Analysis of High-Throughput Flow Cytometry Data Using plateCore
Errol Strain,Florian Hahne,Ryan R. Brinkman,Perry Haaland
Advances in Bioinformatics , 2009, DOI: 10.1155/2009/356141
Abstract: Flow cytometry (FCM) software packages from R/Bioconductor, such as flowCore and flowViz, serve as an open platform for development of new analysis tools and methods. We created plateCore, a new package that extends the functionality in these core packages to enable automated negative control-based gating and make the processing and analysis of plate-based data sets from high-throughput FCM screening experiments easier. plateCore was used to analyze data from a BD FACS CAP screening experiment where five Peripheral Blood Mononucleocyte Cell (PBMC) samples were assayed for 189 different human cell surface markers. This same data set was also manually analyzed by a cytometry expert using the FlowJo data analysis software package (TreeStar, USA). We show that the expression values for markers characterized using the automated approach in plateCore are in good agreement with those from FlowJo, and that using plateCore allows for more reproducible analyses of FCM screening data.
flowCore: a Bioconductor package for high throughput flow cytometry
Florian Hahne, Nolwenn LeMeur, Ryan R Brinkman, Byron Ellis, Perry Haaland, Deepayan Sarkar, Josef Spidlen, Errol Strain, Robert Gentleman
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-106
Abstract: We developed a set of flexible open source computational tools in the R package flowCore to facilitate the analysis of these complex data. A key component of which is having suitable data structures that support the application of similar operations to a collection of samples or a clinical cohort. In addition, our software constitutes a shared and extensible research platform that enables collaboration between bioinformaticians, computer scientists, statisticians, biologists and clinicians. This platform will foster the development of novel analytic methods for flow cytometry.The software has been applied in the analysis of various data sets and its data structures have proven to be highly efficient in capturing and organizing the analytic work flow. Finally, a number of additional Bioconductor packages successfully build on the infrastructure provided by flowCore, open new avenues for flow data analysis.Automation technologies developed during the last several years have enabled the use of flow cytometry (FCM) to generate large, complex data sets in both basic and clinical research applications [1]. A serious bottleneck in the interpretation of existing studies and the application of high throughput FCM to even larger, more complex problems is that data management and data analysis methods have not advanced sufficiently far from the methods developed for applications of FCM to small-scale, tube-based studies [2]. In particular, the data often need to be organized into groups of samples based on combinations of additional covariates and similar operations need to be applied to these groups in a transparent and reproducible manner. Furthermore, the growing depth of knowledge in the field of immunology, for instance the characterization of distinct human T-cell sub-population [3], clearly argues for more systematic approaches.Some of the consequences of the lag of efficient software solutions are difficulties in maintaining the integrity and documentation of large dat
Phylogenetics and Differentiation of Salmonella Newport Lineages by Whole Genome Sequencing
Guojie Cao, Jianghong Meng, Errol Strain, Robert Stones, James Pettengill, Shaohua Zhao, Patrick McDermott, Eric Brown, Marc Allard
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0055687
Abstract: Salmonella Newport has ranked in the top three Salmonella serotypes associated with foodborne outbreaks from 1995 to 2011 in the United States. In the current study, we selected 26 S. Newport strains isolated from diverse sources and geographic locations and then conducted 454 shotgun pyrosequencing procedures to obtain 16–24 × coverage of high quality draft genomes for each strain. Comparative genomic analysis of 28 S. Newport strains (including 2 reference genomes) and 15 outgroup genomes identified more than 140,000 informative SNPs. A resulting phylogenetic tree consisted of four sublineages and indicated that S. Newport had a clear geographic structure. Strains from Asia were divergent from those from the Americas. Our findings demonstrated that analysis using whole genome sequencing data resulted in a more accurate picture of phylogeny compared to that using single genes or small sets of genes. We selected loci around the mutS gene of S. Newport to differentiate distinct lineages, including those between invH and mutS genes at the 3′ end of Salmonella Pathogenicity Island 1 (SPI-1), ste fimbrial operon, and Clustered, Regularly Interspaced, Short Palindromic Repeats (CRISPR) associated-proteins (cas). These genes in the outgroup genomes held high similarity with either S. Newport Lineage II or III at the same loci. S. Newport Lineages II and III have different evolutionary histories in this region and our data demonstrated genetic flow and homologous recombination events around mutS. The findings suggested that S. Newport Lineages II and III diverged early in the serotype evolution and have evolved largely independently. Moreover, we identified genes that could delineate sublineages within the phylogenetic tree and that could be used as potential biomarkers for trace-back investigations during outbreaks. Thus, whole genome sequencing data enabled us to better understand the genetic background of pathogenicity and evolutionary history of S. Newport and also provided additional markers for epidemiological response.
High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach
Marc W Allard, Yan Luo, Errol Strain, Cong Li, Christine E Keys, Insook Son, Robert Stones, Steven M Musser, Eric W Brown
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-32
Abstract: Intraserovar lineages of S. Montevideo differ by thousands of SNPs, that are only slightly less than the number of SNPs observed between S. Montevideo and other distinct serovars. Much less variability was discovered within an individual S. Montevideo clade implicated in a recent foodborne outbreak as well as among individual NGS replicates. These findings were similar to previous reports documenting homopolymeric and deletion error rates with the Roche 454 GS Titanium technology. In no case, however, did variability associated with sequencing methods or sample preparations create inconsistencies with our current phylogenetic results or the subsequent molecular epidemiological evidence gleaned from these data.Implementation of a validated pipeline for NGS data acquisition and analysis provides highly reproducible results that are stable and predictable for molecular epidemiological applications. When draft genomes are collected at 15×-20× coverage and passed through a quality filter as part of a data analysis pipeline, including sub-passaged replicates defined by a few SNPs, they can be accurately placed in a phylogenetic context. This reproducibility applies to all levels within and between serovars of Salmonella suggesting that investigators using these methods can have confidence in their conclusions.Foodborne pathogens cause an estimated 9.4 million human illnesses in the U.S. each year, resulting in nearly 60,000 hospitalizations and over 1,300 deaths [1-4]. Salmonella enterica remains one of the most devastating of these foodborne pathogens with 11% of all food related deaths being attributed from exposure to this bacterium [4]. The genus Salmonella comprises two species, S. enterica and S. bongori, both of which have been found in the food supply. Six subspecies of S. enterica have been described (I-IIIa, IIIb, IV, and VI) that can be found in a variety of mammalian and non-mammalian hosts including humans, cattle, birds, turtles, and snakes. Most non-typhoid
Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere
Andrea R. Ottesen, Antonio Gonzalez, Rebecca Bell, Caroline Arce, Steven Rideout, Marc Allard, Peter Evans, Errol Strain, Steven Musser, Rob Knight, Eric Brown, James B. Pettengill
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0073079
Abstract: The ability to detect a specific organism from a complex environment is vitally important to many fields of public health, including food safety. For example, tomatoes have been implicated numerous times as vehicles of foodborne outbreaks due to strains of Salmonella but few studies have ever recovered Salmonella from a tomato phyllosphere environment. Precision of culturing techniques that target agents associated with outbreaks depend on numerous factors. One important factor to better understand is which species co-enrich during enrichment procedures and how microbial dynamics may impede or enhance detection of target pathogens. We used a shotgun sequence approach to describe taxa associated with samples pre-enrichment and throughout the enrichment steps of the Bacteriological Analytical Manual's (BAM) protocol for detection of Salmonella from environmental tomato samples. Recent work has shown that during efforts to enrich Salmonella (Proteobacteria) from tomato field samples, Firmicute genera are also co-enriched and at least one co-enriching Firmicute genus (Paenibacillus sp.) can inhibit and even kills strains of Salmonella. Here we provide a baseline description of microflora that co-culture during detection efforts and the utility of a bioinformatic approach to detect specific taxa from metagenomic sequence data. We observed that uncultured samples clustered together with distinct taxonomic profiles relative to the three cultured treatments (Universal Pre-enrichment broth (UPB), Tetrathionate (TT), and Rappaport-Vassiliadis (RV)). There was little consistency among samples exposed to the same culturing medias, suggesting significant microbial differences in starting matrices or stochasticity associated with enrichment processes. Interestingly, Paenibacillus sp. (Salmonella inhibitor) was significantly enriched from uncultured to cultured (UPB) samples. Also of interest was the sequence based identification of a number of sequences as Salmonella despite indication by all media, that samples were culture negative for Salmonella. Our results substantiate the nascent utility of metagenomic methods to improve both biological and bioinformatic pathogen detection methods.
The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica
James B. Pettengill,Ruth E. Timme,Rodolphe Barrangou,Magaly Toro,Marc W. Allard,Errol Strain,Steven M. Musser,Eric W. Brown
PeerJ , 2015, DOI: 10.7717/peerj.340
Abstract: Evolutionary studies of clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated (cas) genes can provide insights into host-pathogen co-evolutionary dynamics and the frequency at which different genomic events (e.g., horizontal vs. vertical transmission) occur. Within this study, we used whole genome sequence (WGS) data to determine the evolutionary history and genetic diversity of CRISPR loci and cas genes among a diverse set of 427 Salmonella enterica ssp. enterica isolates representing 64 different serovars. We also evaluated the performance of CRISPR loci for typing when compared to whole genome and multilocus sequence typing (MLST) approaches. We found that there was high diversity in array length within both CRISPR1 (median = 22; min = 3; max = 79) and CRISPR2 (median = 27; min = 2; max = 221). There was also much diversity within serovars (e.g., arrays differed by as many as 50 repeat-spacer units among Salmonella ser. Senftenberg isolates). Interestingly, we found that there are two general cas gene profiles that do not track phylogenetic relationships, which suggests that non-vertical transmission events have occurred frequently throughout the evolutionary history of the sampled isolates. There is also considerable variation among the ranges of pairwise distances estimated within each cas gene, which may be indicative of the strength of natural selection acting on those genes. We developed a novel clustering approach based on CRISPR spacer content, but found that typing based on CRISPRs was less accurate than the MLST-based alternative; typing based on WGS data was the most accurate. Notwithstanding cost and accessibility, we anticipate that draft genome sequencing, due to its greater discriminatory power, will eventually become routine for traceback investigations.
Amplitudes and Cross Sections at the LHC
Gotsman, Errol
High Energy Physics - Phenomenology , 2013,
Abstract: We describe the elements of the GLM model that successfully describes soft hadronic interactions at energies from ISR to LHC. This model is based on a single Pomeron with a large intercept $\Delta_{\pom}$ = 0.23 and slope $\alpha_{\pom}'$ = 0, and so provides a natural matching with perturbative QCD. We analyze the elastic, single diffractive and double diffractive amplitudes, and compare the behaviour of the GLM amplitudes to those of other parameterizations. We summarize the main features and results of competing models for soft interactions at LHC energies.
Survival Probability at the LHC
Gotsman, Errol
High Energy Physics - Phenomenology , 2008, DOI: 10.1063/1.3122177
Abstract: Using a model based on two elements: the Good-Walker mechanism for low mass diffraction and multi-pomeron interactions for high mass diffraction, we obtain an excellent description of all aspects of soft scattering at high energy. The parameters of the model are determined by a fit to experimental data, giving the slope of pomeron to be $\alpha'_{IP} \approx 0.01 GeV^{-2}$. We calculate the survival probability of diffractive Higgs production, and obtained a value for this observable, which is smaller than 1% for the LHC energy range.
Fair Trade and the Role of Small Farmers and ARBs on Food Sovereignty in the Philippines
Errol Ramos
Kasarinlan : Philippine Journal of Third World Studies , 2011,
Abstract: In light of global economic uncertainties, food shortages in many parts of the world, and climate change that greatly affects global agricultural production, how can small farmers and agrarian reform beneficiaries (ARBs), a large majority of which own one or less than one hectare of land, be truly the champions of food sovereignty and ultimately become the frontrunners of the new agricultural revolution in the Philippines? The answer would lie somehow on how small farmers and ARBs will be motivated to produce and how the government and the private sector will contribute effectively in arresting the decline of agricultural productivity. This paper explores how small farmers and ARBs must take the lead in agricultural development for the country to achieve food sovereignty and win in globalization.
“Take the Trip” Down Under: The Significance of Stone (1974)
Vieth, Errol
International Journal of Motorcycle Studies , 2008,
Abstract:
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