bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Statistical Approaches to Evaluate Factors Associated With Metabolic Syndrome
Authors: Fekedulegn Desta , Andrew Michael , Violanti John , Hartley Tara , Charles Luenda , Burchfiel Cecil 
Published: February 2010

J Clin Hypertens (Greenwich).In statistical analyses, metabolic syndrome as a dependent variable is often utilized in a binary form (presence/absence) where the logistic regression model is used to estimate the odds ratio as the measure of association between health‐related factors and metabolic syndrome. Since metabolic syndrome is a common outcome the interpretation of odds ratio as an approximation to prevalence or risk ratio is questionable as it may overestimate its intended target. In addition, dichotomizing a variable that could potentially be treated as discrete may lead to reduced statistical power. In this paper, the authors treat metabolic syndrome as a discrete outcome by defining it as the count of syndrome components. The goal of this study is to evaluate the usefulness of alternative generalized linear models for analysis of metabolic syndrome as a count outcome and compare the results with models that utilize the binary form. Empirical data were used to examine the association between depression and metabolic syndrome. Measures of association were calculated using two approaches; models that treat metabolic syndrome as a binary outcome (the logistic, log‐binomial, Poisson, and the modified Poisson regression) and models that utilize metabolic syndrome as discrete/count data (the Poisson and the negative binomial regression). The method that treats metabolic syndrome as a count outcome (Poisson/negative binomial regression model) appears more sensitive in that it is better able to detect associations and hence can serve as an alternative to analyze metabolic syndrome as count dependent variable and provide an interpretable measure of association.
Rearticulating the myth of human–wildlife conflict
Authors: Peterson M. Nils , Birckhead Jessie L. , Leong Kirsten , Peterson Markus J. , Peterson Tarla Rai 
Published: February 2010

AbstractHuman–wildlife conflict has emerged as the central vocabulary for cases requiring balance between resource demands of humans and wildlife. This phrase is problematic because, given traditional definitions of conflict, it positions wildlife as conscious human antagonists. We used content analysis of wildlife conservation publications and professional meeting presentations to explore the use of the phrase, human–wildlife conflict, and compared competing models explaining its usage. Of the 422 publications and presentations using human–wildlife conflict, only 1 reflected a traditional definition of conflict, >95% referred to reports of animal damage to entities human care about, and <4% referred to human–human conflict. Usage of human–wildlife conflict was related to species type (herbivores with human food, carnivores with human safety, meso‐mammals with property), development level of the nation where the study occurred (less developed nations with human food and more developed nations with human safety and property damage), and whether the study occurred on private lands or protected areas (protected areas with human–human conflict and other areas with property damage). We argue that the phrase, human–wildlife conflict, is detrimental to coexistence between humans and wildlife, and suggest comic reframing to facilitate a more productive interpretation of human–wildlife relationships.
Optimal conservation planning for migratory animals: integrating demographic information across seasons
Authors: Sheehy Justin , Taylor Caz M. , McCann Kevin S. , Norris D. Ryan 
Published: February 2010

AbstractConservation strategies for migratory animals are typically based on ad‐hoc or simple ranking methods and focus on a single period of the annual cycle. We use a density‐dependent population model to examine one‐time land purchase strategies for a migratory population with a breeding and wintering grounds. Under equal rates of habitat loss, we show that it is optimal to invest more, but never solely, in the habitat with the higher density dependence to habitat cost ratio. When there are two habitats that vary in quality within a season, the best strategy is to invest only in one habitat. Whether to purchase high‐ or low‐quality habitat depends on the general life history of the species and the ratio of habitat quality to habitat cost. When carry‐over effects are incorporated, it is almost always optimal to invest in high‐quality habitat during the season that produces the carry‐over effect. We apply this model to a threatened warbler population and show the optimal strategy is to purchase more breeding than wintering habitat despite the fact that breeding habitat is over ten times more expensive. Our model provides a framework for developing year‐round conservation strategies for migratory animals and has important implications for long‐term planning and management.
Transcriptional Regulation of Chitin Synthases by Calcineurin Controls Paradoxical Growth of
Aspergillus fumigatus
in Response to Caspofungin
Authors: Fortwendel Jarrod R. , Juvvadi Praveen R. , Perfect B. Zachary , Rogg Luise E. , Perfect John R. , Steinbach William J. 
Published: February 2010

ABSTRACT

Attenuated activity of echinocandin antifungals at high concentrations, known as the “paradoxical effect,” is a well-established phenomenon in
Candida albicans
and
Aspergillus fumigatus
. In the yeast
C. albicans
, upregulation of chitin biosynthesis via the protein kinase C (PKC), high-osmolarity glycerol response (HOG), and Ca
2+
/calcineurin signaling pathways is an important cell wall stress response that permits growth in the presence of high concentrations of echinocandins. However, nothing is known of the molecular mechanisms regulating the mold
A. fumigatus
and its paradoxical response to echinocandins. Here, we show that the laboratory strain of
A. fumigatus
and five of seven clinical
A. fumigatus
isolates tested display various magnitudes of paradoxical growth in response to caspofungin. Interestingly, none of the eight strains showed paradoxical growth in the presence of micafungin or anidulafungin. Treatment of the Δ
cnaA
and Δ
crzA
strains, harboring gene deletions of the calcineurin A subunit and the calcineurin-dependent transcription factor, respectively, with high concentrations of caspofungin revealed that the
A. fumigatus
paradoxical effect is calcineurin pathway dependent. Exploring a molecular role for CnaA in the compensatory chitin biosynthetic response, we found that caspofungin treatment resulted in increased chitin synthase gene expression, leading to a calcineurin-dependent increase in chitin synthase activity. Taken together, our data suggest a mechanistic role for
A. fumigatus
calcineurin signaling in the chitin biosynthetic response observed during paradoxical growth in the presence of high-dose caspofungin treatment.
Evaluation by Data Mining Techniques of Fluconazole Breakpoints Established by the Clinical and Laboratory Standards Institute (CLSI) and Comparison with Those of the European Committee on Antimicrobial Susceptibility Testing (EUCAST)
Authors: Cuesta Isabel , Bielza Concha , Cuenca-Estrella Manuel , Larrañaga Pedro , Rodríguez-Tudela Juan L. 
Published: February 2010

ABSTRACT

The EUCAST and the CLSI have established different breakpoints for fluconazole and
Candida
spp. However, the reference methodologies employed to obtain the MICs provide similar results. The aim of this work was to apply supervised classification algorithms to analyze the clinical data used by the CLSI to establish fluconazole breakpoints for
Candida
infections and to compare these data with the results obtained with the data set used to set up EUCAST fluconazole breakpoints, where the MIC for detecting failures was >4 mg/liter, with a sensitivity of 87%, a false-positive rate of 8%, and an area under the receiver operating characteristic (ROC) curve of 0.89. Five supervised classifiers (J48 and CART decision trees, the OneR decision rule, the naïve Bayes classifier, and simple logistic regression) were used to analyze the original cohort of patients (Rex's data set), which was used to establish CLSI breakpoints, and a later cohort of candidemia (Clancy's data set), with which CLSI breakpoints were validated. The target variable was the outcome of the infections, and the predictor variable was the MIC or dose/MIC ratio. For Rex's data set, the MIC detecting failures was >8 mg/liter, and for Clancy's data set, the MIC detecting failures was >4 mg/liter, in close agreement with the EUCAST breakpoint (MIC > 4 mg/liter). The sensitivities, false-positive rates, and areas under the ROC curve obtained by means of CART, the algorithm with the best statistical results, were 52%, 18%, and 0.7, respectively, for Rex's data set and 65%, 6%, and 0.72, respectively, for Clancy's data set. In addition, the correlation between outcome and dose/MIC ratio was analyzed for Clancy's data set, where a dose/MIC ratio of >75 was associated with successes, with a sensitivity of 93%, a false-positive rate of 29%, and an area under the ROC curve of 0.83. This dose/MIC ratio of >75 was identical to that found for the cohorts used by EUCAST to establish their breakpoints (a dose/MIC ratio of >75, with a sensitivity of 91%, a false-positive rate of 10%, and an area under the ROC curve of 0.90).
Testing the Efficacy and Toxicity of Adenylyl Cyclase Inhibitors against Enteric Pathogens Using
In Vitro
and
In Vivo
Models of Infection
Authors: Moen Scott T. , Blumentritt Carla A. , Slater Terry M. , Patel Shilpa D. , Tutt Christopher B. , Estrella-Jimenez Maria E. , Pawlik Jennifer , Sower Laurie , Popov Vsevolod L. , Schein Catherine H. , Gilbertson Scott R. , Peterson Johnny W. , Torres Alfredo G. 
Published: February 2010

ABSTRACT

Enterotoxigenic
Escherichia coli
(ETEC) produces the ADP-ribosyltransferase toxin known as heat-labile enterotoxin (LT). In addition to the toxic effect of LT resulting in increases of cyclic AMP (cAMP) and disturbance of cellular metabolic processes, this toxin promotes bacterial adherence to intestinal epithelial cells (A. M. Johnson, R. S. Kaushik, D. H. Francis, J. M. Fleckenstein, and P. R. Hardwidge, J. Bacteriol. 191:178-186, 2009). Therefore, we hypothesized that the identification of a compound that inhibits the activity of the toxin would have a suppressive effect on the ETEC colonization capabilities. Using
in vivo
and
in vitro
approaches, we present evidence demonstrating that a fluorenone-based compound, DC5, which inhibits the accumulation of cAMP in intoxicated cultured cells, significantly decreases the colonization abilities of adenylyl cyclase toxin-producing bacteria, such as ETEC. These findings established that DC5 is a potent inhibitor both of toxin-induced cAMP accumulation and of ETEC adherence to epithelial cells. Thus, DC5 may be a promising compound for treatment of diarrhea caused by ETEC and other adenylyl cyclase toxin-producing bacteria.
Bacterial Guanine Nucleotide Exchange Factors SopE-Like and WxxxE Effectors
Authors: Bulgin Richard , Raymond Benoit , Garnett James A. , Frankel Gad , Crepin Valerie F. , Berger Cedric N. , Arbeloa Ana 
Published: February 2010

ABSTRACTSubversion of Rho family small GTPases, which control actin dynamics, is a common infection strategy used by bacterial pathogens. In particular,Salmonella entericaserovar Typhimurium,Shigella flexneri, enteropathogenicEscherichia coli(EPEC), and enterohemorrhagicEscherichia coli(EHEC) translocate type III secretion system (T3SS) effector proteins to modulate the Rho GTPases RhoA, Cdc42, and Rac1, which trigger formation of stress fibers, filopodia, and lamellipodia/ruffles, respectively. TheSalmonellaeffector SopE is a guanine nucleotide exchange factor (GEF) that activates Rac1 and Cdc42, which induce “the trigger mechanism of cell entry.” Based on a conserved Trp-xxx-Glu motif, the T3SS effector proteins IpgB1 and IpgB2 ofShigella, SifA and SifB ofSalmonella, and Map of EPEC and EHEC were grouped together into a WxxxE family; recent studies identified the T3SS EPEC and EHEC effectors EspM and EspT as new family members. Recent structural and functional studies have shown that representatives of the WxxxE effectors share with SopE a 3-D fold and GEF activity. In this minireview, we summarize contemporary findings related to the SopE and WxxxE GEFs in the context of their role in subverting general host cell signaling pathways and infection.
Expression of the BabA Adhesin during Experimental Infection with
Helicobacter pylori
Authors: Styer Cathy M. , Hansen Lori M. , Cooke Cara L. , Gundersen Amy M. , Choi Sung Sook , Berg Douglas E. , Benghezal Mohammed , Marshall Barry J. , Peek Richard M. , Borén Thomas , Solnick Jay V. 
Published: February 2010

ABSTRACT

The
Helicobacter pylori babA
gene encodes an outer membrane protein that mediates binding to fucosylated ABH antigens of the ABO blood group. We recently demonstrated that BabA expression is lost during experimental infection of rhesus macaques with
H. pylori
J166. We sought to test the generality of this observation by comparison of different
H. pylori
strains and different animal hosts. Challenge of macaques with
H. pylori
J99 yielded output strains that lost BabA expression, either by selection and then expansion of a subpopulation of J99 that had a single-base-pair mutation that encoded a stop codon or by gene conversion of
babA
with a duplicate copy of
babB
, a paralog of unknown function. Challenge of mice with
H. pylori
J166, which unlike J99, has 5′ CT repeats in
babA
, resulted in loss of BabA expression due to phase variation. In the gerbil, Leb binding was lost by replacement of the
babA
gene that encoded Leb binding with a nonbinding allele that differed at six amino acid residues. Complementation experiments confirmed that change in these six amino acids of BabA was sufficient to eliminate binding to Leb and to gastric tissue. These results demonstrate that BabA expression
in vivo
is highly dynamic, and the findings implicate specific amino acid residues as critical for binding to fucosylated ABH antigens. We hypothesize that modification of BabA expression during
H. pylori
infection is a mechanism to adapt to changing conditions of inflammation and glycan expression at the epithelial surface.
Vibrio choleraePhosphoenolpyruvate Phosphotransferase System Control of Carbohydrate Transport, Biofilm Formation, and Colonization of the Germfree Mouse Intestine
Authors: Houot Laetitia , Chang Sarah , Absalon Cedric , Watnick Paula I. 
Published: February 2010

ABSTRACTThe bacterial phosphoenolpyruvate phosphotransferase system (PTS) is a highly conserved phosphotransfer cascade whose components modulate many cellular functions in response to carbohydrate availability. Here, we further elucidate PTS control ofVibrio choleraecarbohydrate transport and activation of biofilm formation on abiotic surfaces. We then define the role of the PTS inV. choleraecolonization of the adult germfree mouse intestine. We report thatV. choleraecolonizes both the small and large intestines of the mouse in a distribution that does not change over the course of a month-long experiment. BecauseV. choleraepossesses many PTS-independent carbohydrate transporters, the PTS is not essential for bacterial growthin vitro. However, we find that the PTS is essential for colonization of the germfree adult mouse intestine and that this requirement is independent of PTS regulation of biofilm formation. Therefore, competition for PTS substrates may be a dominant force in the success ofV. choleraeas an intestinal pathogen. Because the PTS plays a role in colonization of environmental surfaces and the mammalian intestine, we propose that it may be essential to successful transit ofV. choleraethrough its life cycle of pathogenesis and environmental persistence.
NEPI
Authors: Lacage Mathieu , Ferrari Martin , Hansen Mads , Turletti Thierry , Dabbous Walid 
Published: February 2010

Evaluating new network protocols, applications, and architectures uses many kinds of experimentation environments: simulators, emulators, testbeds, and sometimes, combinations of these. As the functionality and complexity of these tools increases, mastering and efficiently using each of them is becoming increasingly difficult.
In this paper, we consider how to make it easier to use multiple tools separately and together to improve the productivity of network researchers. We show how a single object model which encompasses every aspect of a typical experimentation workow can be used to completely describe experiments to be run within very different experimentation environments.
Although Nepi is still in early design and prototyping stage, we expect that its ability to describe and automate easily complex mixed experiments will enable further experimentation with heterogenous networks.
Towards a cost-effective networking testbed
Authors: Knežević Nikola , Schubert Simon , Kostić Dejan 
Published: February 2010

The Internet is suffering from ossification. There has been substantial research on improving current protocols, but the vendors are reluctant to deploy new ones. We believe that this is in part due to the difficulty of evaluating protocols under realistic conditions. Recent wide-area testbeds can help alleviate this problem, but they require substantial resources (equipment, bandwidth) from each participant, and they have difficulty in providing repeatability and full control over the experiments. Existing in-house networking testbeds are capable of running controlled, repeatable experiments, but are typically small-scale (due to various overheads), limited in features, or expensive.
The premise of our work is that it is possible to leverage the recent increases in computational power to improve the researchers' ability to experiment with new protocols in lab settings. We propose a cost-effective testbed, called MX, which emulates many programmable routers running over a realistic topology on multi-core commodity servers. We leverage open source implementations of programmable routers, such as Click, and modify them to allow coexistence of multiple instances in the same kernel in an effort to reduce packet forwarding overheads. Our initial results show that we outperform similar cost-effective solutions by a factor of 2. Next, we demonstrate that grouping and placing routers on to cores which share the L2 cache yields high performance.
Sensitivity of Atmospheric Motion Vectors Height Assignment Methods to Semitransparent Cloud Properties Using Simulated Meteosat-8 Radiances
Authors: Borde Régis , Dubuisson Philippe 
Published: February 2010

Abstract
This paper presents the sensitivity to various atmospheric parameters of two height assignment methods that aim to retrieve the cloud-top height of semitransparent clouds. The use of simulated Meteosat-8 radiances has the advantage that the pressure retrieved by a given method can be compared to the initial pressure set to the cloud in the model, which is exactly known. The methods retrieve the pressure of a perfectly opaque cloud to within a few hectopascals. However, considering more realistic ice clouds, methods are sensitive to all of the tested atmospheric parameters and, especially, to the cloud microphysics, which can bias the results of the CO2-slicing method by several tens of hectopascals. The cloud-top pressure retrieval is especially difficult for thinner clouds with optical thicknesses smaller than 2, for which the errors can reach several tens of hectopascals. The methods have also been tested after introducing realistic perturbations in the temperature and humidity profiles and on the clear-sky surface radiances. The corresponding averages of errors on the retrieved pressures are also very large, especially for thin clouds. In multilayer cloud situations the height assignment methods do not work properly, placing the cloud-top height somewhere between the two cloud layers for most cirrus cloud layers with optical thicknesses between 0.1 and 10.
Topographic Effects on the Surface Radiation Balance in and around Arizona’s Meteor Crater
Authors: Hoch Sebastian W. , Whiteman C. David 
Published: February 2010

Abstract
The individual components of the slope-parallel surface radiation balance were measured in and around Arizona’s Meteor Crater to investigate the effects of topography on the radiation balance. The crater basin has a diameter of 1.2 km and a depth of 170 m. The observations cover the crater floor, the crater rim, four sites on the inner sidewalls on an east–west transect, and two sites outside the crater. Interpretation of the role of topography on radiation differences among the sites on a representative clear day is facilitated by the unique symmetric crater topography. The shortwave radiation balance was affected by the topographic effects of terrain exposure, terrain shading, and terrain reflections, and by surface albedo variations. Terrain exposure caused a site on the steeper upper eastern sidewall of the crater to receive 6% more daily integrated shortwave energy than a site on the lower part of the same slope. Terrain shading had a larger effect on the lower slopes than on the upper slopes. At the lower western slope site the daily total was reduced by 6%. Measurements indicate a diffuse radiation enhancement due to sidewall reflections. The longwave radiation balance was affected by counterradiation from the crater sidewalls and by reduced emissions due to the formation of a nighttime temperature inversion. The total nighttime longwave energy loss at the crater floor was 72% of the loss observed at the crater rim.
Linking Observations of the Asian Monsoon to the Indian Ocean SST: Possible Roles of Indian Ocean Basin Mode and Dipole Mode
Authors: Yang Jianling , Liu Qinyu , Liu Zhengyu 
Published: February 2010

Abstract
The authors investigate the relationship between sea surface temperature (SST) in the tropical Indian Ocean (TIO) and the seasonal atmosphere circulation in the Asian monsoon region (AMR) using the maximum covariance analyses (MCAs). The results show that the Asian monsoon circulation is significantly correlated with two dominant SST anomaly (SSTA) modes: the Indian Ocean Basin mode (IOB) and the Indian Ocean dipole mode (IOD). The peak SSTA of the IOB appears in spring and has a much stronger relationship with the Asian summer monsoon than the peak of the IOD does, whereas the peak SSTA for the IOD appears in fall and shows a stronger link to the Asian winter monsoon than to the Asian summer monsoon. In addition, the IOB in spring has a relatively stronger link with the atmospheric circulation in summer than in other seasons.
The large-scale atmospheric circulation and SSTA patterns of the covariability of the first two dominant MCA modes are described. For the first MCA mode, a warm IOB, persists from spring to summer, and the atmospheric circulation is enhanced by the establishment of the climatological summer monsoon. The increased evaporative moisture associated with the warm IOB is transported to South Asia by the climatological summer monsoon, which increases the moisture convergence toward this region, leading to a significant increase in summer monsoon precipitation. For the second MCA mode, a positive IOD possibly corresponds to a weaker Indian winter monsoon and more precipitation over the southwestern and eastern equatorial TIO.