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Search Results: 1 - 10 of 215416 matches for " Robert D Arbeit "
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High-Resolution Melting System to Perform Multilocus Sequence Typing of Campylobacter jejuni
Simon Lévesque,Sophie Michaud,Robert D. Arbeit,Eric H. Frost
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0016167
Abstract: Multi-locus sequence typing (MLST) has emerged as the state-of-the-art method for resolving bacterial population genetics but it is expensive and time consuming. We evaluated the potential of high resolution melting (HRM) to identify known MLST alleles of Campylobacter jejuni at reduced cost and time. Each MLST locus was amplified in two or three sub fragments, which were analyzed by HRM. The approach was investigated using 47 C. jejuni isolates, previously characterized by classical MLST, representing isolates from diverse environmental, animal and clinical sources and including the six most prevalent sequence types (ST) and the most frequent alleles. HRM was then applied to a validation set of 84 additional C. jejuni isolates from chickens; 92% of the alleles were resolved in 35 hours of laboratory time and the cost of reagents per isolate was $20 compared with $100 for sequence-based typing. HRM has the potential to complement sequence-based methods for resolving SNPs and to facilitate a wide range of genotyping studies.
Reliable identification of mycobacterial species by PCR-restriction enzyme analysis (PRA)-hsp65 in a reference laboratory and elaboration of a sequence-based extended algorithm of PRA-hsp65 patterns
Erica Chimara, Lucilaine Ferrazoli, Suely Ueky, Maria Martins, Alan Durham, Robert D Arbeit, Sylvia Le?o
BMC Microbiology , 2008, DOI: 10.1186/1471-2180-8-48
Abstract: A total of 434 NTM isolates were obtained from 5019 cultures submitted to the Institute Adolpho Lutz, Sao Paulo Brazil, between January 2000 and January 2001. Species identification was performed for all isolates using conventional phenotypic methods and PRA-hsp65. For isolates for which these methods gave discordant results, definitive species identification was obtained by sequencing a 441 bp fragment of hsp65. Phenotypic evaluation and PRA-hsp65 were concordant for 321 (74%) isolates. These assignments were presumed to be correct. For the remaining 113 discordant isolates, definitive identification was based on sequencing a 441 bp fragment of hsp65. PRA-hsp65 identified 30 isolates with hsp65 alleles representing 13 previously unreported PRA-hsp65 patterns. Overall, species identification by PRA-hsp65 was significantly more accurate than by phenotype methods (392 (90.3%) vs. 338 (77.9%), respectively; p < .0001, Fisher's test). Among the 333 isolates representing the most common pathogenic species, PRA-hsp65 provided an incorrect result for only 1.2%.PRA-hsp65 is a rapid and highly reliable method and deserves consideration by any clinical microbiology laboratory charged with performing species identification of NTM.The genus Mycobacterium comprises organisms that are heterogeneous in terms of metabolism, growth, environmental niche, epidemiology, pathogenicity, geographic distribution and disease association [1]. While there are notable pathogens such as Mycobacterium tuberculosis, Mycobacterium bovis and Mycobacterium leprae, most are environmental organisms typically acting as opportunistic pathogens. These species, often collectively called nontuberculous mycobacteria (NTM), have been associated with a variety of problems including pulmonary, lymph node, skin, soft tissue, skeletal, and disseminated infections as well as nosocomial outbreaks related to inadequate disinfection/sterilization of medical devices [2]. In recent years, infections due to the subset
Campylobacteriosis in Urban versus Rural Areas: A Case-Case Study Integrated with Molecular Typing to Validate Risk Factors and to Attribute Sources of Infection
Simon Lévesque, Eric Fournier, Nathalie Carrier, Eric Frost, Robert D. Arbeit, Sophie Michaud
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0083731
Abstract: Campylobacter infection is a leading cause of bacterial gastroenteritis worldwide, and most clinical cases appear as isolated, sporadic infections for which the source is rarely apparent. From July 2005 to December 2007 we conducted a prospective case-case study of sporadic, domestically-acquired Campylobacter enteritis in rural versus urban areas and a prevalence study of Campylobacter in animal and environmental sources in the Eastern Townships, Quebec. Isolates were typed using Multilocus Sequence Typing (MLST) to reinforce the case-case findings and to assign a source probability estimate for each human isolate. The risk of human campylobacteriosis was 1.89-fold higher in rural than urban areas. Unconditional multivariate logistic regression analysis identified two independent risk factors associated with human Campylobacter infections acquired in rural area: occupational exposure to animals (OR = 10.6, 95% CI: 1.2–91, p = 0.032), and household water coming from a private well (OR = 8.3, 95% CI: 3.4–20.4, p<0.0001). A total of 851 C. jejuni isolates (178 human, 257 chicken, 87 bovine, 266 water, 63 wild bird) were typed using MLST. Among human isolates, the incidence rates of clonal complexes (CC) CC-21, CC-45, and CC-61 were higher in rural than urban areas. MLST-based source attribution analysis indicated that 64.5% of human C. jejuni isolates were attributable to chicken, followed by cattle (25.8%), water (7.4%), and wild birds (2.3%). Chicken was the attributable source for the majority of cases, independent of residential area, sex and age. The increased incidence in rural compared to urban areas was associated with occupational exposure to animals, particularly cattle among those aged 15–34 years, and with consumption of private well water. Both bovine and water exposure appeared to contribute to the seasonal variation in campylobacteriosis. These results provide a basis for developing public education and preventive programs targeting the risk factors identified.
Polyantigenic Interferon-γ Responses Are Associated with Protection from TB among HIV-Infected Adults with Childhood BCG Immunization
Timothy Lahey, Brian K. Mitchell, Robert D. Arbeit, Siddharth Sheth, Mecky Matee, C. Robert Horsburgh, Todd MacKenzie, Lillian Mtei, Muhammad Bakari, Jenni M. Vuola, Kisali Pallangyo, C. Fordham von Reyn
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0022074
Abstract: Background Surrogate immunologic markers for natural and vaccine-mediated protection against tuberculosis (TB) have not been identified. Methods HIV-infected adults with childhood BCG immunization entering the placebo arm of the DarDar TB vaccine trial in Dar es Salaam, Tanzania, were assessed for interferon gamma (IFN-γ) responses to three mycobacterial antigen preparations – secreted Mycobacterium tuberculosis antigens 85 (Ag85), early secretory antigenic target 6 (ESAT-6) and polyantigenic whole cell lysate (WCL). We investigated the association between the number of detectable IFN-γ responses at baseline and the subsequent risk of HIV-associated TB. Results During a median follow-up of 3.3 years, 92 (9.4%) of 979 placebo recipients developed TB. The incidence of TB was 14% in subjects with no detectable baseline IFN-γ responses vs. 8% in subjects with response to polyantigenic WCL (P = 0.028). Concomitant responses to secreted antigens were associated with further reduction in the incidence of HIV-associated TB. Overall the percentage of subjects with 0, 1, 2 and 3 baseline IFN-γ responses to mycobacterial preparations who developed HIV-associated TB was 14%, 8%, 7% and 4%, respectively (P = 0.004). In a multivariate Cox regression model, the hazard of developing HIV-associated TB was 46% lower with each increment in the number of detectable baseline IFN-γ responses (P<0.001). Conclusions Among HIV-infected adults who received BCG in childhood and live in a TB-endemic country, polyantigenic IFN-γ responses are associated with decreased risk of subsequent HIV-associated TB. Trial Registration ClinicalTrials.gov NCT0052195
Basis for treatment of tuberculosis among HIV-infected patients in Tanzania: the role of chest x-ray and sputum culture
Muhammad Bakari, Robert D Arbeit, Lillian Mtei, Johnson Lyimo, Richard Waddell, Mecky Matee, Bernard F Cole, Susan Tvaroha, C Robert Horsburgh, Hanna Soini, Kisali Pallangyo, C Fordham von Reyn
BMC Infectious Diseases , 2008, DOI: 10.1186/1471-2334-8-32
Abstract: Ambulatory HIV-positive subjects with CD4 counts ≥ 200/mm3 entering a Phase III TB vaccine study in Tanzania were screened for TB with a physical examination, standard interview, CD4 count, chest x-ray (CXR), blood culture for TB, and three sputum samples for acid fast bacillus (AFB) smear and culture.Among 1176 subjects 136 (12%) were treated for presumptive TB. These patients were more frequently male than those without treatment (34% vs. 25%, respectively; p = 0.049) and had lower median CD4 counts (319/μL vs. 425/μL, respectively; p < .0001). Among the 136 patients treated for TB, 38 (28%) had microbiologic confirmation, including 13 (10%) who had a normal CXR and no symptoms. There were 58 (43%) treated patients in whom the only positive finding was an abnormal CXR. Blood cultures were negative in all patients.Many ambulatory HIV-infected patients with CD4 counts ≥ 200/mm3 are treated for presumptive TB. Our data suggest that optimal detection requires comprehensive evaluation, including CXR and sputum culture on both symptomatic and asymptomatic subjects.Tuberculosis (TB) is the major cause of death from AIDS in most areas of the developing world [1,2]. The high mortality of HIV-associated TB reflects multiple factors, including lack of access to care, delayed or missed diagnosis of TB and acceleration of HIV infection [2-5]. Active TB is considered an indication for anti-retroviral therapy (ART) in HIV-infected persons with CD4 counts <350, but treatment of co-infection may be complicated by drug interactions and by immune reconstitution syndrome [6,7]. For these reasons screening for active TB is recommended for patients with HIV living in TB-endemic regions. However, only limited data are available on the relative sensitivity of different methods of screening for active TB among HIV-infected patients with CD4 counts ≥ 200. The World Health Organization (WHO) recommends screening for TB prior to ART based on symptoms followed by sputum acid fast bacillus (AF
Suppression of Molecular Inflammatory Pathways by Toll-Like Receptor 7, 8, and 9 Antagonists in a Model of IL-23-Induced Skin Inflammation
Mayte Suárez-Fari?as, Robert Arbeit, Weiwen Jiang, Francesca S. Ortenzio, Tim Sullivan, James G. Krueger
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0084634
Abstract: Psoriasis is a complex inflammatory disease resulting from the activation of T helper (Th) 1 and Th17 cells. Recent evidence suggests that abnormal activation of Toll-like receptors (TLRs) 7, 8 and 9 contributes to the initiation and maintenance of psoriasis. We have evaluated the effects of TLR antagonists on the gene expression profile in an IL-23-induced skin inflammation model in mice. Psoriasis-like skin lesions were induced in C57BL/6 mice by intradermal injection of IL-23 in the dorsum. Two TLR antagonists were compared: IMO-3100, an antagonist of TLRs 7 and 9, and IMO-8400, an antagonist of TLRs 7, 8 and 9, both of which previously have been shown to reduce epidermal hyperplasia in this model. Skin gene expression profiles of IL-23-induced inflammation were compared with or without TLR antagonist treatment. IL-23 injection resulted in alteration of 5100 gene probes (fold change ≥ 2, FDR < 0.05) including IL-17 pathways that are up-regulated in psoriasis vulgaris. Targeting TLRs 7, 8 and 9 with IMO-8400 resulted in modulation of more than 2300 mRNAs while targeting TLRs 7 and 9 with IMO-3100 resulted in modulation of more than 1900 mRNAs. Both agents strongly decreased IL-17A expression (>12-fold reduction), normalized IL-17 induced genes such as beta-defensin and CXCL1, and normalized aberrant expression of keratin 16 (indicating epidermal hyperplasia). These results suggest that IL-23-driven inflammation in mouse skin may be dependent on signaling mediated by TLRs 7, 8, and 9 and that these receptors represent novel therapeutic targets in psoriasis vulgaris and other diseases with similar pathophysiology.
YeaNay: An Open Source Tool to Rate the Votes of Members of the United States House of Representatives and Senate  [PDF]
Eric Venlet, D. Robert Adams
Open Journal of Political Science (OJPS) , 2015, DOI: 10.4236/ojps.2015.54029
Abstract: Government transparency is typically regarded as the most viable way to strengthen its accountability to the public (Shkabatur, 2012). Even on the international stage, the right to access government information is regarded as fundamental to democracy (Bertot, Jaeger, & Grimes, 2011). In order to improve transparency, the US government made data, like bills and votes, available online (Brito, 2008b). One popular way to organize the data available to the public is through the creation of voter guides. The method an organization used for developing a voter guide was analyzed for this project. In response to the method, a web application (YeaNay) was developed to take the largely manual process and make a highly automated solution. YeaNay utilizes HTML, CSS, and JavaScript to build the user interface and ColdFusion and PL/SQL to query the data necessary for the development of a voter guide. The data are queried either from the database or from Congress API v3 (provided by the Sunlight Foundation). One user, with minimal training, is able to use YeaNay to find and score legislation within minutes for use in a voter guide. YeaNay focuses the firehose of congressional information that is now available and presents it in a manageable and usable environment.
Zion File System Simulator  [PDF]
Frederic Paladin, D. Robert Adams
Journal of Computer and Communications (JCC) , 2016, DOI: 10.4236/jcc.2016.44002
Abstract: File systems are fundamental for computers and devices with data storage units. They allow operating systems to understand and organize streams of bytes and obtain readable files from them. There are numerous file systems available in the industry, all with their own unique features. Understanding how these file systems work is essential for computer science students, but their complex nature can be difficult and challenging to grasp, especially for students at the beginning of their career. The Zion File System Simulator was designed with this in mind. Zion is a teaching and experimenting tool, in the form of a small application, built to help students understand how the I/O manager of an operating system interacts with the drive through the file system. Users can see and analyze the structure of a simple, flat file system provided with Zion, or simulate the most common structures such as FAT or NTFS. Students can also create their own implementations and run them through the simulator to analyze the different behaviors. Zion runs on Windows, and the application is provided with dynamic-link libraries that include the interfaces of a file system and a volume manager. These interfaces allow programmers to build their own file system or volume manager in Visual Studio using any .NET language (3.0 or above). Zion gives the users the power to adjust simulated architectural parameters such as volume and block size, or performance factors such as seek and transfer time. Zion runs workloads of I/O operations such as “create,” “delete,” “read,” and “write,” and analyzes the resulting metrics including I/O operations, read/write time, and disk fragmentation. Zion is a learning tool. It is not designed for measuring accurate performance of file systems and volume managers. The robustness of the application, together with its expandability, makes Zion a potential laboratory tool for computer science classes, helping students learn how file systems work and interact with an operating system.
Varying Tolerance to Glyphosate in a Population of Palmer Amaranth with Low EPSPS Gene Copy Number  [PDF]
Neal D. Teaster, Robert E. Hoagland
American Journal of Plant Sciences (AJPS) , 2013, DOI: 10.4236/ajps.2013.412297
Abstract:

A Palmer amaranth population (seeds collected in the year 2000; Washington Co., MS) suspected to be susceptible to glyphosate was examined as a population and as individual plants and found to exhibit varying tolerance or resistance to glyphosate. Whole plant spraying of glyphosate (0.84 kg·ha?1) to the population revealed that approximately 40% of this population were resistant to glyphosate and an LD50 of 0.75 kg·ha?1 was determined. Spray application of glyphosate indicated that some plants displayed varying degrees of resistance 14 days after treatment. Initial tests using leaf disc bioassays on 10 individual plants selected randomly from the population, allowed characterization of glyphosate resistance using both visual ratings of injury and quantitative measurement via chlorophyll content analysis. After initial bioassays and spray application, five plants with a range of tolerance to glyphosate were selected for cloning so that further studies could be accomplished on these individuals. Q-PCR analysis of these clones showed that resistance was not due to elevated EPSPS gene copy number. Shikimate levels were lower in the resistant and higher in the susceptible clones which correlated with varying degrees of resistance demonstrated in bioassays and spray application of glyphosate of these clones. Results demonstrate that individuals in a population can vary widely with respect to herbicide resistance and suggest that uptake, translocation, sequestration, metabolism or altered target site may contribute to the resistance in some individuals of this population.

An Assessment Capability for LNG Leaks in Complex Environments  [PDF]
Sydney D. Ryan, Robert C. Ripley
Journal of Geoscience and Environment Protection (GEP) , 2018, DOI: 10.4236/gep.2018.66005
Abstract: Pollutants may be introduced into urban or marine settings by various means and could result in an adverse impact to public safety and the environment. Therefore, it is important for emergency management personnel to understand the potential risks and physical extents of a leaked substance, whether it is toxic, flammable or explosive. Traditional tools for predicting the atmospheric dispersion of leaked substances are quick and simple to use, but may not adequately consider the effects of the built environment that includes complex urban and terrain geometries. Alternatively, CFD methods have been increasing in application; although, their superior accuracy is met with commensurate manual effort. The All Hazards Planner is a fast, accurate gas dispersion modelling tool for city and port environments, which employs a full-physics CFD approach but automates the intensive manual effort. In this work, a credible LNG leak from a 12-mm-diameter hole is modelled for two hypothetical case studies: adjacent to an LNG tanker and between a cruise ship and pier during bunkering. The LNG vapour flammability extents are compared to an empirical model in the absence of geometry effects and are contrasted with geometry effects to highlight the importance of the real environment. The free-field extents are invariant, whereas the inclusion of geometry is shown to reduce the flammability extents by spreading at the ground-level and forcing the plume upwards.
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