Ecological Niche Modelling of the Bacillus anthracis A1.a sub-lineage in Kazakhstan

<p>Abstract</p> <p>Background</p> <p><it>Bacillus anthracis</it>, the causative agent of anthrax, is a globally distributed zoonotic pathogen that continues to be a veterinary and human health problem in Central Asia. We used a database of anthrax outbreak locations in Kazakhstan and a subset of genotyped isolates to model the geographic distribution and ecological associations of <it>B. anthracis </it>in Kazakhstan. The aims of the study were to test the influence of soil variables on a previous ecological niche based prediction of <it>B. anthracis </it>in Kazakhstan and to determine if a single sub-lineage of <it>B. anthracis </it>occupies a unique ecological niche.</p> <p>Results</p> <p>The addition of soil variables to the previously developed ecological niche model did not appreciably alter the limits of the predicted geographic or ecological distribution of <it>B. anthracis </it>in Kazakhstan. The A1.a experiment predicted the sub-lineage to be present over a larger geographic area than did the outbreak based experiment containing multiple lineages. Within the geographic area predicted to be suitable for <it>B. anthracis </it>by all ten best subset models, the A1.a sub-lineage was associated with a wider range of ecological tolerances than the outbreak-soil experiment. Analysis of rule types showed that logit rules predominate in the outbreak-soil experiment and range rules in the A1.a sub-lineage experiment. Random sub-setting of locality points suggests that models of <it>B. anthracis </it>distribution may be sensitive to sample size.</p> <p>Conclusions</p> <p>Our analysis supports careful consideration of the taxonomic resolution of data used to create ecological niche models. Further investigations into the environmental affinities of individual lineages and sub-lineages of <it>B. anthracis </it>will be useful in understanding the ecology of the disease at large and small scales. With model based predictions serving as approximations of disease risk, these efforts will improve the efficacy of public health interventions for anthrax prevention and control.</p

The Grizzly, February 10, 2011

Bonners Give Insight on Organization • Kappa Alpha Psi Fraternity to Participate in Spring Intake • Future UC President Dr. Bobby Fong Receives National Award • Ursinus College Plays Host to W. R. Crigler • GRE Makeover and Helpful Hints to Ace the Test • Calvin Levels Performs One Man Show in the Blackbox • New Program Brings Students and Professors Closer • Internship Profile: Matt Angle • Opinion: UC Town Hall Meeting Proved a Bit Disappointing; Letter to a Writer; A Multicultural Ursinus Campus on the Way; Upheaval in the Middle East: Why Students Should Care • Murren Adds Name to History Books During Seasonhttps://digitalcommons.ursinus.edu/grizzlynews/1829/thumbnail.jp

The Grizzly, January 27, 2011

Bonner Leaders Host Hunger Banquet • UC Alumnus Discusses Alternative Careers in Science • Students Find Internships While Studying Abroad • Berman Museum Opens Two New Exhibitions • MLK Celebrations • Student Experiences Australian Flood • Students Travel to Spain for New Experiences • Internship Profile: Ananda Holton • Diversity Through Monologues • Opinion: Scheduling Classes is Too Difficult; Tragedy in Arizona: The Work of a Madman; Snapshots of London From my Time Studying Abroad • Swimming Training Trip to Florida Proves Rewardinghttps://digitalcommons.ursinus.edu/grizzlynews/1827/thumbnail.jp

Predicting the Spectrum of UGC 2885, Rubin’s Galaxy with Machine Learning

Wu & Peek predict SDSS-quality spectra based on Pan-STARRS broadband grizy images using machine learning (ML). In this article, we test their prediction for a unique object, UGC 2885 ( Rubin\u27s galaxy ), the largest and most massive, isolated disk galaxy in the local universe (D \u3c 100 Mpc). After obtaining the ML predicted spectrum, we compare it to all existing spectroscopic information that is comparable to an SDSS spectrum of the central region: two archival spectra, one extracted from the VIRUS-P observations of this galaxy, and a new, targeted MMT/Binospec observation. Agreement is qualitatively good, though the ML prediction prefers line ratios slightly more toward those of an active galactic nucleus (AGN), compared to archival and VIRUS-P observed values. The MMT/Binospec nuclear spectrum unequivocally shows strong emission lines except Hβ, the ratios of which are consistent with AGN activity. The ML approach to galaxy spectra may be a viable way to identify AGN supplementing NIR colors. How such a massive disk galaxy (M* = 1011 M⊙), which uncharacteristically shows no sign of interaction or mergers, manages to fuel its central AGN remains to be investigated

The Grizzly, November 12, 2009

Picasso at the Lapin Agile Draws in Audiences • Ursinus Awarded Teagle Grant • H1N1: How Ursinus is Battling the Swine Flu • Health Stats on the Ursinus Campus • Guest Speaker Addresses Urban (Dis)order • Four Students Hope to Pursue their Dreams with Watson Fellowship • Philly\u27s Practically Single Proves Pop-Punk Prevails; Set to Play Ursinus Friday • Veterans: The Brave Who Allow Us to be Free • Ghost Hunter Gives Presentation on Campus • Opinion: Hamid Karzai: Further Complicating Issues in Afghanistan; Ursinus\u27 Need for an Intro to Writing Class • Field Hockey Hoists C.C. Trophy for Sixth Consecutive Yearhttps://digitalcommons.ursinus.edu/grizzlynews/1799/thumbnail.jp

The Grizzly, October 15, 2009

Dr. Jekyll and Mr. Hyde Draws in Large Audiences • MRSA Awareness Month • UC Student Hit by Car on Main Street, Makes $50 • Omega Chi Sponsors Blood Drive • E-Mail Outsourcing and its Effects on the Ursinus Community • Study Abroad Programs Create Great Opportunities for Students •$10,000 Grant Brings Danny Buraczeski\u27s Swing Concerto to Dance Students • Senior Halloween Party Planners Leave Under 21-Year-Olds Out • Opinions: Obama\u27s Nobel Prize: Criticism Warranted?; Assisted Living: Call it Assisted Dying for Many • Women\u27s Rugby Gets Down and Dirty for 2009 Season • Record Falls After the Bears\u27 Big Defeat Over Gettysburghttps://digitalcommons.ursinus.edu/grizzlynews/1795/thumbnail.jp

The Grizzly, September 24, 2009

CIE Celebrates 10 Year Anniversary, Makes Changes • Introducing Ursinus\u27 New Graduate Assistant • Tenth Annual Fringe Festival Kicks Off This Week • Visiting Professor Taije Silverman Shares Poetry • Is American Idol Rigged? An Investigatory Review • How Far Will You Go to Stretch Your Dollar in This Economy? • Restaurant Review: Molly Maguire\u27s Irish Restaurant and Pub • Opinions: Freshmen Parking on Campus; Glenn Beck and Rush Limbaugh • Ursinus Women\u27s Gymnastics Spends Weekend Volunteering • Coach Thomas Announces Baseball Captains for 2010 Seasonhttps://digitalcommons.ursinus.edu/grizzlynews/1792/thumbnail.jp

Bacillus anthracis Diversity and Geographic Potential across Nigeria, Cameroon and Chad: Further Support of a Novel West African Lineage.

Zoonoses, diseases affecting both humans and animals, can exert tremendous pressures on human and veterinary health systems, particularly in resource limited countries. Anthrax is one such zoonosis of concern and is a disease requiring greater public health attention in Nigeria. Here we describe the genetic diversity of Bacillus anthracis in Nigeria and compare it to Chad, Cameroon and a broader global dataset based on the multiple locus variable number tandem repeat (MLVA-25) genetic typing system. Nigerian B. anthracis isolates had identical MLVA genotypes and could only be resolved by measuring highly mutable single nucleotide repeats (SNRs). The Nigerian MLVA genotype was identical or highly genetically similar to those in the neighboring countries, confirming the strains belong to this unique West African lineage. Interestingly, sequence data from a Nigerian isolate shares the anthrose deficient genotypes previously described for strains in this region, which may be associated with vaccine evasion. Strains in this study were isolated over six decades, indicating a high level of temporal strain stability regionally. Ecological niche models were used to predict the geographic distribution of the pathogen for all three countries. We describe a west-east habitat corridor through northern Nigeria extending into Chad and Cameroon. Ecological niche models and genetic results show B. anthracis to be ecologically established in Nigeria. These findings expand our understanding of the global B. anthracis population structure and can guide regional anthrax surveillance and control planning

Introductory programming: a systematic literature review

As computing becomes a mainstream discipline embedded in the school curriculum and acts as an enabler for an increasing range of academic disciplines in higher education, the literature on introductory programming is growing. Although there have been several reviews that focus on specific aspects of introductory programming, there has been no broad overview of the literature exploring recent trends across the breadth of introductory programming. This paper is the report of an ITiCSE working group that conducted a systematic review in order to gain an overview of the introductory programming literature. Partitioning the literature into papers addressing the student, teaching, the curriculum, and assessment, we explore trends, highlight advances in knowledge over the past 15 years, and indicate possible directions for future research

Prediction of Lung Cancer Histological Types by RT-qPCR Gene Expression in FFPE Specimens

Lung cancer histologic diagnosis is clinically relevant because there are histology-specific treatment indications and contraindications. Histologic diagnosis can be challenging owing to tumor characteristics, and it has been shown to have less-than-ideal agreement among pathologists reviewing the same specimens. Microarray profiling studies using frozen specimens have shown that histologies exhibit different gene expression trends; however, frozen specimens are not amenable to routine clinical application. Herein, we developed a gene expression–based predictor of lung cancer histology for FFPE specimens, which are routinely available in clinical settings. Genes predictive of lung cancer histologies were derived from published cohorts that had been profiled by microarrays. Expression of these genes was measured by quantitative RT-PCR (RT-qPCR) in a cohort of patients with FFPE lung cancer. A histology expression predictor (HEP) was developed using RT-qPCR expression data for adenocarcinoma, carcinoid, small cell carcinoma, and squamous cell carcinoma. In cross-validation, the HEP exhibited mean accuracy of 84% and κ = 0.77. In separate independent validation sets, the HEP was compared with pathologist diagnoses on the same tumor block specimens, and the HEP yielded similar accuracy and precision as the pathologists. The HEP also exhibited good performance in specimens with low tumor cellularity. Therefore, RT-qPCR gene expression from FFPE specimens can be effectively used to predict lung cancer histology