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R W W Brouwer, M C G N van den Hout, C E M Kockx, E Brosens, B Eussen, A de Klein, F Sleutels, W F J van IJcken
Motivation: PCR-based DNA enrichment followed by massively parallel sequencing is a straightforward and cost effective method to sequence genes up to high depth. The full potential of amplicon based sequencing assays is currently not achieved as analysis methods do not take into account the source amplicons of the detected variants. Tracking the source amplicons has the potential to identify systematic biases, enhance variant calling and improve the designs of future assays. Results: We present Nimbus, a software suite for the analysis of amplicon based sequencing data...
March 10, 2018: Bioinformatics
Dragos G Zaharescu, Antonio Palanca-Soler, Peter S Hooda, Catalin Tanase, Carmen I Burghelea, Richard N Lester
Alpine regions are under increased attention worldwide for their critical role in early biogeochemical cycles, their high sensitivity to environmental change, and as repositories of natural resources of high quality. Their riparian ecosystems, at the interface between aquatic and terrestrial environments, play important geochemical functions in the watershed and are biodiversity hotspots, despite a harsh climate and topographic setting. With climate change rapidly affecting the alpine biome, we still lack a comprehensive understanding of the extent of interactions between riparian surface, lake and catchment environments...
December 1, 2017: Science of the Total Environment
K Hidalgo, K Mouline, W Mamai, N Foucreau, K R Dabiré, A Bouchereau, F Simard, D Renault
In dry savannahs of West-Africa, the malarial mosquitoes of the Anopheles gambiae sensu stricto complex annually survive the harsh desiccating conditions of the dry season. However, the physiological and biochemical mechanisms underlying how these mosquitoes survive such desiccating conditions are still undefined, and controversial. In this context, we provide the first work examining both proteomic and metabolomic changes in the two molecular forms of A. gambiae s.s (M and S forms) experimentally exposed to the rainy and dry season conditions as they experience in the field...
December 2015: Data in Brief
Roberto Rosales-Reyes, María Dolores Alcántar-Curiel, Ma Dolores Jarillo-Quijada, Catalina Gayosso-Vázquez, María Del Rayo Morfin-Otero, Eduardo Rodríguez-Noriega, José Ignacio Santos-Preciado
BACKGROUND: Acinetobacter baumannii has emerged as a major cause of hospital-associated infections with increased morbidity and mortality among those affected. METHODS: A total of 85 isolates of a highly prevalent multidrug-resistant clone, identified during the period 2007-2011, were analyzed for biofilm formation on a polystyrene surface. The minimal inhibitory concentration was determined by the Sensititre System, the agar disk diffusion method and then read by means of the BIOMIC system and serial dilutions on Müller-Hinton agar...
2016: Chemotherapy
Susumu Tomiya
Mammalian body mass strongly correlates with life history and population properties at the scale of mouse to elephant. Large body size is thus often associated with elevated extinction risk. I examined the North American fossil record (28-1 million years ago) of 276 terrestrial genera to uncover the relationship between body size and extinction probability above the species level. Phylogenetic comparative analysis revealed no correlation between sampling-adjusted durations and body masses ranging 7 orders of magnitude, an observation that was corroborated by survival analysis...
December 2013: American Naturalist
Katharine M Benedict, Sheryl P Gow, Sylvia Checkley, Calvin W Booker, Tim A McAllister, Paul S Morley
BACKGROUND: The purpose of this study was to objectively compare methodological approaches that might be utilized in designing an antimicrobial resistance (AMR) surveillance program in beef feedlot cattle. Specifically, four separate comparisons were made to investigate their potential impact on estimates for prevalence of AMR. These included investigating potential differences between 2 different susceptibility testing methods (broth microdilution and disc diffusion), between 2 different target bacteria (non-type-specific E...
2013: BMC Veterinary Research
Ana R Gómez Cano, Juan L Cantalapiedra, Aurora Mesa, Ana Moreno Bofarull, Manuel Hernández Fernández
BACKGROUND: Several macroevolutionary hypotheses propose a synchrony between climatic changes and variations in the structure of faunal communities. Some of them focus on the importance of the species ecological specialization because of its effects on evolutionary processes and the resultant patterns. Particularly, Vrba's turnover pulse hypothesis and resource-use hypothesis revolve around the importance of biome inhabitation. In order to test these hypotheses, we used the Biomic Specialization Index, which is based on the number of biomes occupied by each species, and evaluated the changes in the relative importance of generalist and specialist rodents in more than forty fossil sites from the Iberian Plio-Pleistocene...
2013: BMC Evolutionary Biology
Robert C Fader, Emily Weaver, Rhonda Fossett, Michele Toyras, John Vanderlaan, David Gibbs, Andrew Wang, Nikolaus Thierjung
This study compared the Biomic automated well reader results to the MicroScan WalkAway results for reading MicroScan antimicrobial susceptibility and identification panels at four different sites. Routine fresh clinical isolates and quality control (QC) organisms were tested at each study site. A total of 46,176 MicroScan panel drug-organism combinations were read. The Biomic category agreement for 3,117 Gram-negative bacteria was 98.4%, with 1.4% minor and 0.2% major discrepancies. The Biomic category agreement for 5,233 Gram-positive bacteria was 98...
May 2013: Journal of Clinical Microbiology
Richard Kellermayer
The gut microbiota, the intestinal mucosa and the host immune system are among the large biological networks involved in the development of inflammatory bowel disease (IBD), which includes Crohn disease (CD) and ulcerative colitis (UC). Host genetics and environmental factors can significantly modulate the interactive relationships among these biological systems and influence predilection toward IBD. High monozygotic twin discordance rates and the rapid rise in the prevalence of IBD indicate that environmental influences may be as important or even more important in their pathogenesis than genetic susceptibility...
December 2012: Canadian Journal of Gastroenterology, Journal Canadien de Gastroenterologie
Juan L Cantalapiedra, Manuel Hernández Fernández, Jorge Morales
The resource-use hypothesis proposed by E.S. Vrba predicts that specialist species have higher speciation and extinction rates than generalists because they are more susceptible to environmental changes and vicariance. In this work, we test some of the predictions derived from this hypothesis on the 197 extant and recently extinct species of Ruminantia (Cetartiodactyla, Mammalia) using the biomic specialization index (BSI) of each species, which is based on its distribution within different biomes. We ran 10000 Monte Carlo simulations of our data in order to get a null distribution of BSI values against which to contrast the observed data...
2011: PloS One
Stefan H E Kaufmann
Tuberculosis is one of the most deadly infectious diseases. The situation is worsening because of co-infection with HIV and increased occurrence of drug resistance. Although the BCG vaccine has been in use for 90 years, protection is insufficient; new vaccine candidates are therefore needed. 12 potential vaccines have gone into clinical trials. Ten are aimed at prevention of tuberculosis and, of these, seven are subunit vaccines either as adjuvanted or viral-vectored antigens. These vaccines would be boosters of BCG-prime vaccination...
August 2011: Lancet Infectious Diseases
Ana Carolina Azevedo, Fernando César Bizerra, Daniel Arquimedes da Matta, Leila Paula de Almeida, Robert Rosas, Arnaldo Lopes Colombo
We evaluated all Candida spp. isolates obtained from patients admitted to two tertiary care hospitals between 1999 and 2003 in the city of São Paulo, Brazil. The in vitro activities of fluconazole (FCZ) and voriconazole were determined by the agar disk diffusion test using the Clinical and Laboratory Standards Institute M44-A guidelines. The inhibition zone diameters were read and interpreted automatically by the BIOMIC(®) image-analysis plate reader system. We tested a total of 4,625 strains, including 2,393 strains of C...
June 2011: Mycopathologia
Mi Kyung Lee, Dongeun Yong, Myungsook Kim, Mi Na Kim, Kyungwon Lee
BACKGROUND: We utilized results from the ARTEMIS DISK Global Antifungal Surveillance Program to evaluate the species distribution and fluconazole and voriconazole susceptibilities of yeast isolates from clinical specimens in South Korea from 2001 to 2007. METHODS: Data were collected on 5,665 yeast isolates from all body sites at three locations. All investigators tested clinical yeast isolates using the CLSI M44-A disk diffusion method. Test plates were automatically read and results were recorded using the BIOMIC image analysis plate reader system (Giles Scientific, USA)...
August 2010: Korean Journal of Laboratory Medicine
Shreemanta K Parida, Stefan H E Kaufmann
No new vaccine has been licensed for tuberculosis (TB) for more than three-quarters of a century, and no new drug has been licensed for half a century. One major drawback has been the attrition caused by the lack of a reliable biological indicator (biomarker) to predict toxicity and efficacy early in the development pipeline. This review portrays the landscape of biomarker discovery for TB in the context of drug and vaccine development using emerging global biomics platforms. The time is ripe to move from single markers for correlates of protection to a biosignature comprising a well-defined set of robust indicators in TB that can accelerate rapid screening and early selection of potential drug and vaccine candidates...
February 2010: Drug Discovery Today
Fatma Budak, Patrice Nordmann, Delphine Girlich, Deniz Gür
The rate of in vitro resistance to various antimicrobials in 179 consecutive isolates of Salmonella spp., which included serogroups D (109), B (52), C1 (10) and C2 (8) isolated from children, was investigated. Production of extended-spectrum beta-lactamase (ESBL) was studied in ampicillin-resistant isolates. Antimicrobial susceptibilities were determined by disk diffusion tests and by BIOMIC video reader system. Overall resistance rates to ampicillin and amoxicillin/clavulanate were 26.3% and 10.6%, respectively...
January 2009: Turkish Journal of Pediatrics
W A DiMichele, I P Montañez, C J Poulsen, N J Tabor
The late Paleozoic earth experienced alternation between glacial and non-glacial climates at multiple temporal scales, accompanied by atmospheric CO2 fluctuations and global warming intervals, often attended by significant vegetational changes in equatorial latitudes of Pangaea. We assess the nature of climate-vegetation interaction during two time intervals: middle-late Pennsylvanian transition and Pennsylvanian-Permian transition, each marked by tropical warming and drying. In case study 1, there is a catastrophic intra-biomic reorganization of dominance and diversity in wetland, evergreen vegetation growing under humid climates...
March 2009: Geobiology
Ellen Jo Baron, Holly D'Souza, Andrew Qi Wang, David L Gibbs
The Biomic V3 microbiology system identifies bacteria by reading the color of colonies selected by the user. For CHROMagar orientation, Biomic results agreed with conventional methods for 94% of the strains assayed. For CHROMagar MRSA, Biomic correctly identified 100% of the strains tested and did not misidentify two methicillin-susceptible Staphylococcus aureus strains growing on the plates.
October 2008: Journal of Clinical Microbiology
Ana Moreno Bofarull, Antón Arias Royo, Manuel Hernández Fernández, Edgardo Ortiz-Jaureguizar, Jorge Morales
BACKGROUND: This paper tests Vrba's resource-use hypothesis, which predicts that generalist species have lower specialization and extinction rates than specialists, using the 879 species of South American mammals. We tested several predictions about this hypothesis using the biomic specialization index (BSI) for each species, which is based on its geographical range within different climate-zones. The four predictions tested are: (1) there is a high frequency of species restricted to a single biome, which henceforth are referred to as stenobiomic species, (2) certain clades are more stenobiomic than others, (3) there is a higher proportion of biomic specialists in biomes that underwent through major expansion-contraction alternation due to the glacial-interglacial cycles, (4) certain combinations of inhabited biomes occur more frequently among species than do others...
2008: BMC Evolutionary Biology
M A Pfaller, D J Diekema, D L Gibbs, V A Newell, J F Meis, I M Gould, W Fu, A L Colombo, E Rodriguez-Noriega et al.
Fluconazole in vitro susceptibility test results for 205,329 yeasts were collected from 134 study sites in 40 countries from June 1997 through December 2005. Data were collected for 147,776 yeast isolates tested with voriconazole from 2001 through 2005. All investigators tested clinical yeast isolates by the CLSI M44-A disk diffusion method. Test plates were automatically read and results recorded with a BIOMIC image analysis system. Species, drug, zone diameter, susceptibility category, and quality control results were collected quarterly...
June 2007: Journal of Clinical Microbiology
Ilona Dóczi, Gy Mestyán, Erzsébet Puskás, Radka Nikolova, I Barcs, Elisabeth Nagy
The ARTEMIS Global Antifungal Susceptibility Program provides the collection of epidemiological data and the results of the fluconazole and voriconazole susceptibility testing of yeast isolates. Participating in this study, a total of 7318 clinical yeast isolates were tested from different geographical areas in Hungary in the period 2001 to 2003. The species isolated most frequently was C. albicans (68.8%), followed by C. glabrata (11.8%), C. tropicalis (5.7%) and C. krusei (4.6%). Isolates of C. albicans, C...
June 2006: Acta Microbiologica et Immunologica Hungarica
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