bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Epidemiological Analysis of Escherichia coli Sequence Type ST131 (O25:H4) and
bla
CTX-M-15
among Extended-Spectrum-β-Lactamase-Producing E. coli from the United States, 2000 to 2009
Authors: Johnson James R. , Urban Carl , Weissman Scott J. , Jorgensen James H. , Lewis James S. , Hansen Glen , Edelstein Paul H. , Robicsek Ari , Cleary Timothy , Adachi Javier , Paterson David , Quinn John , Hanson Nancy D. , Johnston Brian D. , Clabots Connie , Kuskowski Michael A. ,   the AMERECUS Investigators
Published: February 2012

ABSTRACT

Escherichia coli
sequence type ST131 (from phylogenetic group B2), often carrying the extended-spectrum-β-lactamase (ESBL) gene
bla
CTX-M-15
, is an emerging globally disseminated pathogen that has received comparatively little attention in the United States. Accordingly, a convenience sample of 351 ESBL-producing
E. coli
isolates from 15 U.S. centers (collected in 2000 to 2009) underwent PCR-based phylotyping and detection of ST131 and
bla
CTX-M-15
. A total of 200 isolates, comprising 4 groups of 50 isolates each that were (i)
bla
CTX-M-15
negative non-ST131, (ii)
bla
CTX-M-15
positive non-ST131, (iii)
bla
CTX-M-15
negative ST131, or (iv)
bla
CTX-M-15
positive ST131, also underwent virulence genotyping, antimicrobial susceptibility testing, and pulsed-field gel electrophoresis (PFGE). Overall, 201 (57%) isolates exhibited
bla
CTX-M-15
, whereas 165 (47%) were ST131. ST131 accounted for 56% of
bla
CTX-M-15
-positive- versus 35% of
bla
CTX-M-15
-negative isolates (
P
< 0.001). Whereas ST131 accounted for 94% of the 175 total group B2 isolates, non-ST131 isolates were phylogenetically distributed by
bla
CTX-M-15
status, with groups A (
bla
CTX-M-15
-positive isolates) and D (
bla
CTX-M-15
-negative isolates) predominating. Both
bla
CTX-M-15
and ST131 occurred at all participating centers, were recovered from children and adults, increased significantly in prevalence post-2003, and were associated with molecularly inferred virulence. Compared with non-ST131 isolates, ST131 isolates had higher virulence scores, distinctive virulence profiles, and more-homogeneous PFGE profiles.
bla
CTX-M-15
was associated with extensive antimicrobial resistance and ST131 with fluoroquinolone resistance. Thus,
E. coli
ST131 and
bla
CTX-M-15
are emergent, widely distributed, and predominant among ESBL-positive
E. coli
strains in the United States, among children and adults alike. Enhanced virulence and antimicrobial resistance have likely promoted the epidemiological success of these emerging public health threats.
Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Bacteriophage SPN3UB
Authors: Lee Ju-Hoon , Shin Hakdong , Ryu Sangryeol 
Published: February 2012

ABSTRACT

Salmonella
is one of the major pathogenic bacteria that cause food poisoning. To elucidate the host infection mechanism of
Salmonella enterica
serovar Typhimurium-targeting phages, the bacteriophage SPN3UB was isolated from a chicken fecal sample. This phage belongs morphologically to the
Siphoviridae
family and infects the host via the O antigen of lipopolysaccharide (LPS). To further understand its infection mechanism, we completely sequenced and analyzed the genome. Here, we announce its complete genome sequence and report major findings from the genomic analysis results.
How they won Rugby World Cup through height, mass and collective experience
Authors: Sedeaud Adrien , Marc Andy , Schipman Julien , Tafflet Muriel , Hager Jean-Philippe , Toussaint Jean-François 
Published: February 2012

ObjectivesTo investigate the evolution of anthropometric characteristics in World Cup rugby players and identify elements associated with performance.DesignAge, weight and height were collected for 2692 World Cup rugby players as well as rankings in each World Cup, and collective experience of winners, finalists, semifinalists and quarter finalists in comparison to the rest of the competitors. Anthropometric parameters were compared according to age and position (back and forwards).ResultsFrom 1987 to 2007, forwards and backs have become heavier by 6.63 and 6.68 kg and taller by 0.61 and 1.09 cm, respectively. The collective experience of the forwards' pack is a value increasing with the final ranking attained, as well as the weight of forwards and the height of backs.ConclusionsFor all Rugby World Cups, the highest performing teams have the tallest backs and heaviest forwards with the highest percentage of collective experience.
Pten Loss and RAS/MAPK Activation Cooperate to Promote EMT and Metastasis Initiated from Prostate Cancer Stem/Progenitor Cells
Authors: Mulholland David J. , Kobayashi Naoko , Ruscetti Marcus , Zhi Allen , Tran Linh M. , Huang Jiaoti , Gleave Martin , Wu Hong 
Published: February 2012

Abstract
PTEN loss or PI3K/AKT signaling pathway activation correlates with human prostate cancer progression and metastasis. However, in preclinical murine models, deletion of Pten alone fails to mimic the significant metastatic burden that frequently accompanies the end stage of human disease. To identify additional pathway alterations that cooperate with PTEN loss in prostate cancer progression, we surveyed human prostate cancer tissue microarrays and found that the RAS/MAPK pathway is significantly elevated in both primary and metastatic lesions. In an attempt to model this event, we crossed conditional activatable K-rasG12D/WT mice with the prostate conditional Pten deletion model. Although RAS activation alone cannot initiate prostate cancer development, it significantly accelerated progression caused by PTEN loss, accompanied by epithelial-to-mesenchymal transition (EMT) and macrometastasis with 100% penetrance. A novel stem/progenitor subpopulation with mesenchymal characteristics was isolated from the compound mutant prostates, which was highly metastatic upon orthotopic transplantation. Importantly, inhibition of RAS/MAPK signaling by PD325901, a mitogen–activated protein (MAP)–extracellular signal–regulated (ER) kinase (MEK) inhibitor, significantly reduced the metastatic progression initiated from transplanted stem/progenitor cells. Collectively, our findings indicate that activation of RAS/MAPK signaling serves as a potentiating second hit to alteration of the PTEN/PI3K/AKT axis, and cotargeting both the pathways is highly effective in preventing the development of metastatic prostate cancers. Cancer Res; 72(7); 1878–89. ©2012 AACR.
Proximal Fluid Proteome Profiling of Mouse Colon Tumors Reveals Biomarkers for Early Diagnosis of Human Colorectal Cancer
Authors: Fijneman Remond J.A. , de Wit Meike , Pourghiasian Maral , Piersma Sander R. , Pham Thang V. , Warmoes Marc O. , Lavaei Mehrdad , Piso Chloe , Smit Fiona , Delis-van Diemen Pien M. , van Turenhout Sietze T. , Terhaar sive Droste Jochim S. , Mulder Chris J.J. , Blankenstein Marinus A. , Robanus-Maandag Els C. , Smits Ron , Fodde Riccardo , van Hinsbergh Victor W.M. , Meijer Gerrit A. , Jimenez Connie R. 
Published: February 2012

AbstractPurpose: Early detection of colorectal cancer (CRC) and its precursor lesions is an effective approach to reduce CRC mortality rates. This study aimed to identify novel protein biomarkers for the early diagnosis of CRC.Experimental Design: Proximal fluids are a rich source of candidate biomarkers as they contain high concentrations of tissue-derived proteins. The FabplCre;Apc15lox/+ mouse model represents early-stage development of human sporadic CRC. Proximal fluids were collected from normal colon and colon tumors and subjected to in-depth proteome profiling by tandem mass spectrometry. Carcinoembryonic antigen (CEA) and CHI3L1 human serum protein levels were determined by ELISA.Results: Of the 2,172 proteins identified, quantitative comparison revealed 192 proteins that were significantly (P &lt; 0.05) and abundantly (&gt;5-fold) more excreted by tumors than by controls. Further selection for biomarkers with highest specificity and sensitivity yielded 52 candidates, including S100A9, MCM4, and four other proteins that have been proposed as candidate biomarkers for human CRC screening or surveillance, supporting the validity of our approach. For CHI3L1, we verified that protein levels were significantly increased in sera from patients with adenomas and advanced adenomas compared with control individuals, in contrast to the CRC biomarker CEA.Conclusion: These data show that proximal fluid proteome profiling with a mouse tumor model is a powerful approach to identify candidate biomarkers for early diagnosis of human cancer, exemplified by increased CHI3L1 protein levels in sera from patients with CRC precursor lesions. Clin Cancer Res; 18(9); 2613–24. ©2012 AACR.
A Panel of Four miRNAs Accurately Differentiates Malignant from Benign Indeterminate Thyroid Lesions on Fine Needle Aspiration
Authors: Keutgen Xavier M. , Filicori Filippo , Crowley Michael J. , Wang Yongchun , Scognamiglio Theresa , Hoda Rana , Buitrago Daniel , Cooper David , Zeiger Martha A. , Zarnegar Rasa , Elemento Olivier , Fahey Thomas J. 
Published: February 2012

Abstract
Purpose: Indeterminate thyroid lesions on fine needle aspiration (FNA) harbor malignancy in about 25% of cases. Hemi- or total thyroidectomy has, therefore, been routinely advocated for definitive diagnosis. In this study, we analyzed miRNA expression in indeterminate FNA samples and determined its prognostic effects on final pathologic diagnosis.
Experimental Design: A predictive model was derived using 29 ex vivo indeterminate thyroid lesions on FNA to differentiate malignant from benign tumors at a tertiary referral center and validated on an independent set of 72 prospectively collected in vivo FNA samples. Expression levels of miR-222, miR-328, miR-197, miR-21, miR-181a, and miR-146b were determined using reverse transcriptase PCR. A statistical model was developed using the support vector machine (SVM) approach.
Results: A SVM model with four miRNAs (miR-222, miR-328, miR-197, and miR-21) was initially estimated to have 86% predictive accuracy using cross-validation. When applied to the 72 independent in vivo validation samples, performance was actually better than predicted with a sensitivity of 100% and specificity of 86%, for a predictive accuracy of 90% in differentiating malignant from benign indeterminate lesions. When Hurthle cell lesions were excluded, overall accuracy improved to 97% with 100% sensitivity and 95% specificity.
Conclusions: This study shows that that the expression of miR-222, miR-328, miR-197, and miR-21 combined in a predictive model is accurate at differentiating malignant from benign indeterminate thyroid lesions on FNA. These findings suggest that FNA miRNA analysis could be a useful adjunct in the management algorithm of patients with thyroid nodules. Clin Cancer Res; 18(7); 2032–8. ©2012 AACR.
Responses of Shallow Cumulus Convection to Large-Scale Temperature and Moisture Perturbations: A Comparison of Large-Eddy Simulations and a Convective Parameterization Based on Stochastically Entraining Parcels
Authors: Nie Ji , Kuang Zhiming 
Published: February 2012

Abstract
Responses of shallow cumuli to large-scale temperature/moisture perturbations are examined through diagnostics of large-eddy simulations (LESs) of the undisturbed Barbados Oceanographic and Meteorological Experiment (BOMEX) case and a stochastic parcel model. The perturbations are added instantaneously and allowed to evolve freely afterward. The parcel model reproduces most of the changes in the LES-simulated cloudy updraft statistics in response to the perturbations. Analyses of parcel histories show that a positive temperature perturbation forms a buoyancy barrier, which preferentially eliminates parcels that start with lower equivalent potential temperature or have experienced heavy entrainment. Besides the amount of entrainment, the height at which parcels entrain is also important in determining their fate. Parcels entraining at higher altitudes are more likely to overcome the buoyancy barrier than those entraining at lower altitudes. Stochastic entrainment is key for the parcel model to reproduce the LES results. Responses to environmental moisture perturbations are quite small compared to those to temperature perturbations because changing environmental moisture is ineffective in modifying buoyancy in the BOMEX shallow cumulus case.
The second part of the paper further explores the feasibility of a stochastic parcel–based cumulus parameterization. Air parcels are released from the surface layer and temperature/moisture fluxes effected by the parcels are used to calculate heating/moistening tendencies due to both cumulus convection and boundary layer turbulence. Initial results show that this conceptually simple parameterization produces realistic convective tendencies and also reproduces the LES-simulated mean and variance of cloudy updraft properties, as well as the response of convection to temperature/moisture perturbations.
A Reanalysis of the 1944–53 Atlantic Hurricane Seasons—The First Decade of Aircraft Reconnaissance*
Authors: Hagen Andrew B. , Strahan-Sakoskie Donna , Luckett Christopher 
Published: February 2012

Abstract
The main historical archive of all tropical storms, subtropical storms, and hurricanes in the North Atlantic Ocean, Caribbean Sea, and Gulf of Mexico from 1851 to the present is known as the Atlantic hurricane database (HURDAT), which is the fundamental database for meteorological, engineering, and financial studies of these cyclones. Previous work has demonstrated that a reanalysis of HURDAT is necessary because it contains many random errors and systematic biases. The Atlantic Hurricane Reanalysis Project is an ongoing effort to correct the errors in HURDAT and to make HURDAT as accurate a database as possible with utilization of all available data. For this study, HURDAT is reanalyzed for the period 1944–53, the first decade of the “aircraft reconnaissance era.” The track and intensity of each existing tropical cyclone in HURDAT are reassessed, and previously unrecognized tropical cyclones are discovered, analyzed, and recommended to the HURDAT Best Track Change Committee for inclusion into HURDAT (existing tropical cyclones may be removed from the database as well if analyses indicate evidence that no tropical storm existed). Changes to the number of tropical storms, hurricanes, major hurricanes, accumulated cyclone energy, and U.S. landfalling hurricanes are recommended for most years of the decade. Estimates of uncertainty in the reanalyzed database for the decade are also provided.
Hydrologic Sensitivities of Colorado River Runoff to Changes in Precipitation and Temperature*
Authors: Vano Julie A. , Das Tapash , Lettenmaier Dennis P. 
Published: February 2012

Abstract
The Colorado River is the primary water source for much of the rapidly growing southwestern United States. Recent studies have projected reductions in Colorado River flows from less than 10% to almost 50% by midcentury because of climate change—a range that has clouded potential management responses. These differences in projections are attributable to variations in climate model projections but also to differing land surface model (LSM) sensitivities. This second contribution to uncertainty—specifically, variations in LSM runoff change with respect to precipitation (elasticities) and temperature (sensitivities)—are evaluated here through comparisons of multidecadal simulations from five commonly used LSMs (Catchment, Community Land Model, Noah, Sacramento Soil Moisture Accounting model, and Variable Infiltration Capacity model) all applied over the Colorado River basin at ⅛° latitude by longitude spatial resolution. The annual elasticity of modeled runoff (fractional change in annual runoff divided by fractional change in annual precipitation) at Lees Ferry ranges from two to six for the different LSMs. Elasticities generally are higher in lower precipitation and/or runoff regimes; hence, the highest values are for models biased low in runoff production, and the range of elasticities is reduced to two to three when adjusted to current runoff climatology. Annual temperature sensitivities (percent change in annual runoff per degree change in annual temperature) range from declines of 2% to as much as 9% per degree Celsius increase at Lees Ferry. For some LSMs, small areas, primarily at midelevation, have increasing runoff with increasing temperature; however, on a spatial basis, most sensitivities are negative.
Ensemble Statistics for Diagnosing Dynamics: Tropical Cyclone Track Forecast Sensitivities Revealed by Ensemble Regression
Authors: Gombos Daniel , Hoffman Ross N. , Hansen James A. 
Published: February 2012

Abstract
Ensemble regression (ER) is a simple linear inverse technique that uses correlations from ensemble model output to make inferences about dynamics, models, and forecasts. ER defines a multivariate regression operator in the principal component subspaces of ensemble forecasts and analyses of atmospheric fields. ER uses the ensemble members of a predictor and a predictand field as training samples to compute the ensemble anomaly (with respect to the ensemble mean of the predictand field) with which a dynamically relevant ensemble anomaly (with respect to the ensemble mean of the predictor field) is linearly related. Specifically, an ER operator defined by the Japan Meteorological Agency’s ensemble forecast 500-hPa geopotential height and 1000-hPa potential vorticity is used to show that Supertyphoon Sepat’s (2007) track strongly covaried with the position and strength of the antecedent steering subtropical high to its northeast and the trough to its northwest. The case study illustrates how ER can identify, in real time, the dynamical processes that are particularly relevant for operational forecasters to make specific forecasting decisions and can help researchers to infer physical relationships from multivariate statistical sensitivities.
An Objective Methodology for Configuring and Down-Selecting an NWP Ensemble for Low-Level Wind Prediction
Authors: Lee Jared A. , Kolczynski Walter C. , McCandless Tyler C. , Haupt Sue Ellen 
Published: February 2012

AbstractEnsembles of numerical weather prediction (NWP) model predictions are used for a variety of forecasting applications. Such ensembles quantify the uncertainty of the prediction because the spread in the ensemble predictions is correlated to forecast uncertainty. For atmospheric transport and dispersion and wind energy applications in particular, the NWP ensemble spread should accurately represent uncertainty in the low-level mean wind. To adequately sample the probability density function (PDF) of the forecast atmospheric state, it is necessary to account for several sources of uncertainty. Limited computational resources constrain the size of ensembles, so choices must be made about which members to include. No known objective methodology exists to guide users in choosing which combinations of physics parameterizations to include in an NWP ensemble, however. This study presents such a methodology.The authors build an NWP ensemble using the Advanced Research Weather Research and Forecasting Model (ARW-WRF). This 24-member ensemble varies physics parameterizations for 18 randomly selected 48-h forecast periods in boreal summer 2009. Verification focuses on 2-m temperature and 10-m wind components at forecast lead times from 12 to 48 h. Various statistical guidance methods are employed for down-selection, calibration, and verification of the ensemble forecasts. The ensemble down-selection is accomplished with principal component analysis. The ensemble PDF is then statistically dressed, or calibrated, using Bayesian model averaging. The postprocessing techniques presented here result in a recommended down-selected ensemble that is about half the size of the original ensemble yet produces similar forecast performance, and still includes critical diversity in several types of physics schemes.
Investigation of Microphysical Processes Occurring in Organized Convection during NAME
Authors: Rowe Angela K. , Rutledge Steven A. , Lang Timothy J. 
Published: February 2012

AbstractA major objective of the North American Monsoon Experiment (NAME) was to quantify microphysical processes within convection occurring near the steep topography of northwestern Mexico. A previous study compared examples of isolated convection using polarimetric radar data and noted a dependence on mixed-phase processes via drop freezing and subsequent riming growth along the coastal plain and western slopes, with an even greater role of melting ice in rainfall production over the highest terrain. Despite the higher frequency of these isolated cells compared to organized convective systems, the latter were responsible for 75% of rainfall. Therefore, this study seeks to evaluate the role of mesoscale organization on microphysical processes and describes the evolution of these systems as a function of topography.Similar to isolated convection, both warm-rain and ice-based processes played important roles in producing intense rainfall in organized convection. Although similarities existed between cell types, organized convection was typically deeper and contained greater ice mass, which melted and contributed to the development of outflow boundaries. As convection organized along the slopes, these boundaries spread over the lower terrain, converging with diurnally driven upslope flow, thus allowing for the generation of new convection and propagation toward the coast. Once over lower elevations, additional warm-cloud depth contributed to intense rainfall and allowed for continued ice production. This, along with the development of rear inflow in the trailing stratiform region, led to further development of convective outflow, similar to organized systems in the tropics and midlatitudes.
Export-led Growth in India and the Role of Liberalisation
Authors: Paul Biru Paksha , Das Anupam 
Published: February 2012

The literature on export-led growth in India is voluminous but inconclusive. This study re-examines the export–output relationship over the 1960–2009 period, and finds strong evidence of export-led growth for India. While there is no long-run cointegration relationship between India’s exports and output, tests of causality and impulse responses show a significant positive impact of export growth on output growth in the short run. Autoregressive models of India’s output growth also reveal the significant role of export growth over the same period. This result remains robust regardless of testing exports with different measures of output. The short-run impact of export on output, however, becomes insignificant in all types of estimation once the sample is reduced to the pre-liberalisation era from 1960 to 1991. Hence, liberalisation appears to have significantly contributed to export-led growth in India. We work with quarterly data as well over the liberalisation regime from 1996Q2 to 2010Q4 and find consistent results on export-led growth for India. Thus, export-led growth appears to be a liberalisation phenomenon for India. These findings have implications for other developing economies that aspire to grow fast but confront dilemmas with trade liberalisation policy. JEL Classification: F41, F43, C32, O53
Financial Stability Reports (FSR) of the Reserve Bank of India (RBI), March and December, 2010: A Critical Review with a Long-term Perspective
Authors: Singh Gurbachan 
Published: February 2012

This article considers two aspects in the Reserve Bank of India’s (RBI) first set of reports on financial stability. First, the reports fear sudden and large flows of foreign capital, and rightly so. However, the focus of policy makers has been on foreign exchange reserves and on capital controls to some extent. This article explores the use of an additional instrument—the international credit line. Second, this article reconsiders the reasons for the correlation between stock prices and capital flows. There is some misunderstanding in the interpretation of the evidence. Finally, it is suggested that the government should gradually move in the direction of ‘prescription financial products’ to contain excessive volatility in financial markets. JEL Classification: F33, F41 and G01