bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure and Function of a Genetically Engineered Mimic of a Nonenveloped Virus Entry Intermediate
Authors: Banerjee Manidipa , Speir Jeffrey A. , Kwan Maggie H. , Huang Rick , Aryanpur Peyman P. , Bothner Brian , Johnson John E. 
Published: February 2010

ABSTRACT

Divalent metal ions are components of numerous icosahedral virus capsids. Flock House virus (FHV), a small RNA virus of the family
Nodaviridae
, was utilized as an accessible model system with which to address the effects of metal ions on capsid structure and on the biology of virus-host interactions. Mutations at the calcium-binding sites affected FHV capsid stability and drastically reduced virus infectivity, without altering the overall architecture of the capsid. The mutations also altered the conformation of gamma, a membrane-disrupting, virus-encoded peptide usually sequestered inside the capsid, by increasing its exposure under neutral pH conditions. Our data demonstrate that calcium binding is essential for maintaining a pH-based control on gamma exposure and host membrane disruption, and they reveal a novel rationale for the metal ion requirement during virus entry and infectivity. In the light of the phenotypes displayed by a calcium site mutant of FHV, we suggest that this mutant corresponds to an early entry intermediate formed in the endosomal pathway.
Development of an Intergenotypic Hepatitis C Virus (HCV) Cell Culture Method To Assess Antiviral Susceptibilities and Resistance Development of HCV NS3 Protease Genes from HCV Genotypes 1 to 6
Authors: Imhof Ingrid , Simmonds Peter 
Published: February 2010

ABSTRACT

Protease inhibitors (PIs) of hepatitis C virus (HCV) provide an additional or alternative therapy for chronic infection. However, assessment of their efficacy and ability to inhibit replication of different genotypes is hampered by the lack of a convenient animal model or a method for
in vitro
culture of HCV other than the type 1/2-based replicons and the infectious genotype 2a clone JFH1. To address this problem, we constructed a panel of replication-competent chimeric Jc1 (pFK JFH1/J6/C-846) clones containing protease and NS4A coding sequences from all six major genotypes, enabling the determination of replication and the susceptibility to PIs. Chimeras showed substantial variability in replication kinetics, attributable in part to naturally occurring polymorphisms and differing requirements for adaptive mutations in NS3 and NS4A. Through calculation of 50% inhibitory concentrations (IC
50
s) of BILN 2061, measuring reduction in the number of focus-forming units/ml (FFU/ml) and replication inhibition, consistent genotype-associated differences in antiviral susceptibilities were observed. IC
50
s for genotype 1b, 4a, and 6a-derived chimeras (1 to 3 nM) were approximately 100-fold lower than those for genotypes 2a, 3a, and 5a (range, 80 to 720 nM), implying major differences in response to therapy.
In vitro
passage in increasing concentrations of BILN 2061 rapidly induced resistance-associated mutations at position 168 in chimeras of all 6 genotypes and at position 156 in genotypes 1b and 4a, each with substantial variability in the identity of substituted amino acids. The system will allow future comprehensive phenotypic characterization of naturally occurring and treatment-induced mutations for PIs in trial or entering clinical use.
Decadal Shift in El Niño Influences on Indo–Western Pacific and East Asian Climate in the 1970s*
Authors: Xie Shang-Ping , Du Yan , Huang Gang , Zheng Xiao-Tong , Tokinaga Hiroki , Hu Kaiming , Liu Qinyu 
Published: February 2010

Abstract
El Niño’s influence on the subtropical northwest (NW) Pacific climate increased after the climate regime shift of the 1970s. This is manifested in well-organized atmospheric anomalies of suppressed convection and a surface anticyclone during the summer (June–August) of the El Niño decay year [JJA(1)], a season when equatorial Pacific sea surface temperature (SST) anomalies have dissipated. In situ observations and ocean–atmospheric reanalyses are used to investigate mechanisms for the interdecadal change. During JJA(1), the influence of the El Niño–Southern Oscillation (ENSO) on the NW Pacific is indirect, being mediated by SST conditions over the tropical Indian Ocean (TIO). The results here show that interdecadal change in this influence is due to changes in the TIO response to ENSO.
During the postregime shift epoch, the El Niño teleconnection excites downwelling Rossby waves in the south TIO by anticyclonic wind curls. These Rossby waves propagate slowly westward, causing persistent SST warming over the thermocline ridge in the southwest TIO. The ocean warming induces an antisymmetric wind pattern across the equator, and the anomalous northeasterlies cause the north Indian Ocean to warm through JJA(1) by reducing the southwesterly monsoon winds. The TIO warming excites a warm Kelvin wave in tropospheric temperature, resulting in robust atmospheric anomalies over the NW Pacific that include the surface anticyclone. During the preregime shift epoch, ENSO is significantly weaker in variance and decays earlier than during the recent epoch. Compared to the epoch after the mid-1970s, SST and wind anomalies over the TIO are similar during the developing and mature phases of ENSO but are very weak during the decay phase. Specifically, the southern TIO Rossby waves are weaker, so are the antisymmetric wind pattern and the North Indian Ocean warming during JJA(1). Without the anchor in the TIO warming, atmospheric anomalies over the NW Pacific fail to develop during JJA(1) prior to the mid-1970s. The relationship of the interdecadal change to global warming and implications for the East Asian summer monsoon are discussed.
Near-Ground Pressure and Wind Measurements in Tornadoes*
Authors: Karstens Christopher D. , Samaras Timothy M. , Lee Bruce D. , Gallus William A. , Finley Catherine A. 
Published: February 2010

Abstract
Since the spring of 2002, tornadoes were sampled on nine occasions using Hardened In-Situ Tornado Pressure Recorder probes, video probes, and mobile mesonet instrumentation. This study describes pressure and, in some cases, velocity data obtained from these intercepts. In seven of these events, the intercepted tornadoes were within the radar-indicated or visually identified location of the supercell low-level mesocyclone. In the remaining two cases, the intercepted tornadoes occurred outside of this region and were located along either the rear-flank downdraft gust front or an internal rear-flank downdraft surge boundary.
The pressure traces, sometimes augmented with videography, suggest that vortex structures ranged from single-cell to two-cell, quite similar to the swirl-ratio-dependent continuum of vortex structures shown in laboratory and numerical simulations. Although near-ground tornado observations are quite rare, the number of contemporary tornado measurements now available permits a comparative range of observed pressure deficits for a wide variety of tornado sizes and intensities to be presented.
Modeling the Dependence of Tropical Storm Counts in the North Atlantic Basin on Climate Indices
Authors: Villarini Gabriele , Vecchi Gabriel A. , Smith James A. 
Published: February 2010

AbstractThe authors analyze and model time series of annual counts of tropical storms lasting more than 2 days in the North Atlantic basin and U.S. landfalling tropical storms over the period 1878–2008 in relation to different climate indices. The climate indices considered are the tropical Atlantic sea surface temperature (SST), tropical mean SST, the North Atlantic Oscillation (NAO), and the Southern Oscillation index (SOI). Given the uncertainties associated with a possible tropical storm undercount in the presatellite era, two different time series of counts for the North Atlantic basin are employed: one is the original (uncorrected) tropical storm record maintained by the National Hurricane Center and the other one is with a correction for the estimated undercount associated with a changing observation network. Two different SST time series are considered: the Met Office’s HadISSTv1 and NOAA’s Extended Reconstructed SST.Given the nature of the data (counts), a Poisson regression model is adopted. The selection of statistically significant covariates is performed by penalizing models for adding extra parameters and two penalty functions are used. Depending on the penalty function, slightly different models, both in terms of covariates and dependence of the model’s parameter, are obtained, showing that there is not a “single best” model. Moreover, results are sensitive to the undercount correction and the SST time series.Suggestions concerning the model to use are provided, driven by both the outcomes of the statistical analyses and the current understanding of the underlying physical processes responsible for the genesis, development, and tracks of tropical storms in the North Atlantic basin. Although no single model is unequivocally superior to the others, the authors suggest a very parsimonious family of models using as covariates tropical Atlantic and tropical mean SSTs.
Evaluation of Data Reduction Algorithms for Real-Time Analysis
Authors: Lazarus Steven M. , Splitt Michael E. , Lueken Michael D. , Ramachandran Rahul , Li Xiang , Movva Sunil , Graves Sara J. , Zavodsky Bradley T. 
Published: February 2010

Abstract
Data reduction tools are developed and evaluated using a data analysis framework. Simple (nonadaptive) and intelligent (adaptive) thinning algorithms are applied to both synthetic and real data and the thinned datasets are ingested into an analysis system. The approach is motivated by the desire to better represent high-impact weather features (e.g., fronts, jets, cyclones, etc.) that are often poorly resolved in coarse-resolution forecast models and to efficiently generate a set of initial conditions that best describes the current state of the atmosphere. As a precursor to real-data applications, the algorithms are applied to one- and two-dimensional synthetic datasets. Information gleaned from the synthetic experiments is used to create a thinning algorithm that combines the best aspects of the intelligent methods (i.e., their ability to detect regions of interest) while reducing the impacts of spatial irregularities in the data. Both simple and intelligent thinning algorithms are then applied to Atmospheric Infrared Sounder (AIRS) temperature and moisture profiles. For a given retention rate, background, and observation error, the optimal 1D analyses (i.e., lowest MSE) tend to have observations that are near regions of large curvature and gradients. Observation error leads to the selection of spurious data in homogeneous regions of the intelligent algorithms. In the 2D experiments, simple thinning tends to perform better within the homogeneous data regions. Analyses produced using AIRS data demonstrate that observations selected via a combination of the simple and intelligent approaches reduce clustering, provide a more even distribution along the satellite swath edges, and, in general, have lower error and comparable computational requirements compared to standard operational thinning methodologies.
Convection-Allowing and Convection-Parameterizing Ensemble Forecasts of a Mesoscale Convective Vortex and Associated Severe Weather Environment
Authors: Clark Adam J. , Gallus William A. , Xue Ming , Kong Fanyou 
Published: February 2010

Abstract
An analysis of a regional severe weather outbreak that was related to a mesoscale convective vortex (MCV) is performed. The MCV-spawning mesoscale convection system (MCS) formed in northwest Kansas along the southern periphery of a large cutoff 500-hPa low centered over western South Dakota. As the MCS propagated into eastern Kansas during the early morning of 1 June 2007, an MCV that became evident from multiple data sources [e.g., Weather Surveillance Radar-1988 Doppler (WSR-88D) network, visible satellite imagery, wind-profiler data, Rapid Update Cycle 1-hourly analyses] tracked through northwest Missouri and central Iowa and manifested itself as a well-defined midlevel short-wave trough. Downstream of the MCV in southeast Iowa and northwest Illinois, southwesterly 500-hPa winds increased to around 25 m s−1 over an area with southeasterly surface winds and 500–1500 J kg−1 of surface-based convective available potential energy (CAPE), creating a favorable environment for severe weather. In the favorable region, multiple tornadoes occurred, including one rated as a category 3 storm on the enhanced Fujita scale (EF3) that caused considerable damage. In the analysis, emphasis is placed on the role of the MCV in leading to a favorable environment for severe weather. In addition, convection-allowing forecasts of the MCV and associated environmental conditions from the 10-member Storm-Scale Ensemble Forecast (SSEF) system produced for the 2007 NOAA Hazardous Weather Testbed Spring Experiment are compared to those from a similarly configured, but coarser, 30-member convection-parameterizing ensemble. It was found that forecasts of the MCV track and associated environmental conditions (e.g., midlevel winds, low-level wind shear, and instability) were much better in the convection-allowing ensemble. Errors in the MCV track from convection-parameterizing members likely resulted from westward displacement errors in the incipient MCS. Furthermore, poor depiction of MCV structure and maintenance in convection-parameterizing members, which was diagnosed through a vorticity budget analysis, likely led to the relatively poor forecasts of the associated environmental conditions. The results appear to be very encouraging for convection-allowing ensembles, especially when environmental conditions lead to a high degree of predictability for MCSs, which appeared to be the case for this particular event.
Transformation of Fundamental Parameters for Energy Demand and Indoor Temperature from Room Level to Building Level
Authors: Korjenic Azra , Bednar Thomas 
Published: February 2010

Because the thermal optimization of a new building must be done in the planning phase, possible thermal optimizations are sought for the building by varying several parameters. This research article is based on the research of ‘climate surfaces’ by Prof. Keller and Dr Burmeister at the Federal Institute of Technology in Zurich (Burmeister and Keller, 1998). The question should be resolved whether this simplified method using climate surfaces is applicable to the entire building. The most important parameters of the building have been systematically changed and their impact on energy performance during different outdoor climate changes was observed. As a result, the impacts on the following are presented and discussed: Heat energy demands, Cooling energy demands, and Summer indoor temperatures. The results of these investigations showed that the ‘multizone climate surface’ method is a very practical and clear strategy for estimating the thermal behavior of a building by the correct selection of three determining parameters. Already in an early planning stage, it is possible to establish the optimal building data, at a sufficient level of detail, where energy consumption has been concerned. The study is carried out using the monthly energy balance method and dynamic simulation using ‘BuildOpt’ software. The objective was to establish if the much simpler monthly balance method will give sufficiently precise results for this optimization, or if a simulation must be performed. The results of the analysis indicate that the monthly balance method is inaccurate, especially for buildings with low energy demands. Subsequent studies deal with the optimization of the most important construction assembly parameters of a building for specific climates. The results of the optimization studies are presented in this article.
A new plasminogen receptor
Authors: Strickland Dudley K. 
Published: February 2010

AbstractEfficient activation of the fibrinolytic pathway occurs when plasminogen and its activators are sequestered on the cell surface. Identification of receptors responsible for localizing plasminogen to the cell surface has been elusive. Using a proteomics approach, Andronicos and colleagues have identified a novel 17-kDa transmembrane receptor, termed Plg-RKT, that binds plasminogen with high affinity and promotes its activation.1
General and species-specific transcriptional responses to downy mildew infection in a susceptible (Vitis vinifera) and a resistant (V. riparia) grapevine species
Authors: Polesani Marianna , Bortesi Luisa , Ferrarini Alberto , Zamboni Anita , Fasoli Marianna , Zadra Claudia , Lovato Arianna , Pezzotti Mario , Delledonne Massimo , Polverari Annalisa 
Published: February 2010

AbstractBackgroundDowny mildew is a destructive grapevine disease caused byPlasmopara viticola(Berk. and Curt.) Berl. and de Toni, which can only be controlled by intensive fungicide treatments. Natural sources of resistance from wild grapevine (Vitis) species are used in conventional breeding approaches, but the signals and effectors involved in resistance in this important crop species are not well understood.ResultsEarly transcriptional changes associated withP. viticolainfection in susceptibleV. viniferaand resistantV. ripariaplants were analyzed using the Combimatrix microarray platform. Transcript levels were measured 12 and 24 h post-inoculation, reflecting the time points immediately preceding the onset of resistance inV. riparia, as determined by microscopic analysis. Our data indicate that resistance inV. ripariais induced after infection, and is not based on differences in basal gene expression between the two species. The strong and rapid transcriptional reprogramming involves the induction of pathogenesis-related proteins and enzymes required for the synthesis of phenylpropanoid-derived compounds, many of which are also induced, albeit to a lesser extent, inV. vinifera. More interestingly, resistance inV. ripariaalso involves the specific modulation of numerous transcripts encoding components of signal transduction cascades, hypersensitive reaction markers and genes involved in jasmonate biosynthesis. The limited transcriptional modulation inV. viniferarepresents a weak attempted defense response rather than the activation of compatibility-specific pathways.ConclusionsSeveral candidate resistance genes were identified that could be exploited in future biotechnological approaches to increase disease resistance in susceptible grapevine species. Measurements of jasmonic acid and methyl jasmonate in infected leaves suggest that this hormone may also be involved inV. ripariaresistance toP. viticola.
Toxicity of unsaturated fatty acids to the biohydrogenating ruminal bacterium, Butyrivibrio fibrisolvens
Authors: Maia Margarida RG , Chaudhary Lal C , Bestwick Charles S , Richardson Anthony J , McKain Nest , Larson Tony R , Graham Ian A , Wallace Robert J 
Published: February 2010

Background
Health-promoting polyunsaturated fatty acids (PUFA) are abundant in forages grazed by ruminants and in vegetable and fish oils used as dietary supplements, but only a small proportion of PUFA finds its way into meat and milk, because of biohydrogenation in the rumen. Butyrivibrio fibrisolvens plays a major role in this activity. The aim of this study was to investigate the mechanisms by which PUFA affect the growth of B. fibrisolvens, how PUFA are metabolized and the metabolic response to growth in the presence of PUFA.

Results

Linoleic acid (LA; cis-9, cis-12-18:2) and α-linolenic acid (LNA; cis-9, cis-12, cis-15-18:3) increased the lag phase of B. fibrisolvens JW11, LNA having the greater effect. Growth was initiated only when the PUFA had been converted to vaccenic acid (VA; trans- 11-18:1). The major fish oil fatty acids, eicosapentaenoic acid (EPA; 20:5(n- 3)) and docosahexaenoic acid (DHA; 22:6(n- 3)), were not metabolized and prevented growth. Cellular integrity, as determined fluorimetrically by propidium iodide (PI) ingression, was affected as much by 18:1 fatty acids, including VA, as 18:2 fatty acids. The methyl esters of LNA, LA, EPA and DHA had no effect on growth or other measurements. The ATP pool decreased by 2/3 when LA was added to growing bacteria, whereas most acyl CoA pools decreased by >96%.

Conclusions

It was concluded that biohydrogenation occurs to enable B. fibrisolvens to survive the bacteriostatic effects of PUFA, and that the toxicity of PUFA is probably mediated via a metabolic effect rather than disruption of membrane integrity.
Multiple controls affect arsenite oxidase gene expression in Herminiimonas arsenicoxydans
Authors: Koechler Sandrine , Cleiss-Arnold Jessica , Proux Caroline , Sismeiro Odile , Dillies Marie-Agnès , Goulhen-Chollet Florence , Hommais Florence , Lièvremont Didier , Arsène-Ploetze Florence , Coppée Jean-Yves , Bertin Philippe N 
Published: February 2010

Abstract

Background
Both the speciation and toxicity of arsenic are affected by bacterial transformations, i.e. oxidation, reduction or methylation. These transformations have a major impact on environmental contamination and more particularly on arsenic contamination of drinking water. Herminiimonas arsenicoxydans has been isolated from an arsenic- contaminated environment and has developed various mechanisms for coping with arsenic, including the oxidation of As(III) to As(V) as a detoxification mechanism.

Results
In the present study, a differential transcriptome analysis was used to identify genes, including arsenite oxidase encoding genes, involved in the response of H. arsenicoxydans to As(III). To get insight into the molecular mechanisms of this enzyme activity, a Tn5 transposon mutagenesis was performed. Transposon insertions resulting in a lack of arsenite oxidase activity disrupted aoxR and aoxS genes, showing that the aox operon transcription is regulated by the AoxRS two-component system. Remarkably, transposon insertions were also identified in rpoN coding for the alternative N sigma factor (σ54) of RNA polymerase and in dnaJ coding for the Hsp70 co-chaperone. Western blotting with anti-AoxB antibodies and quantitative RT-PCR experiments allowed us to demonstrate that the rpoN and dnaJ gene products are involved in the control of arsenite oxidase gene expression. Finally, the transcriptional start site of the aoxAB operon was determined using rapid amplification of cDNA ends (RACE) and a putative -12/-24 σ54-dependent promoter motif was identified upstream of aoxAB coding sequences.

Conclusion
These results reveal the existence of novel molecular regulatory processes governing arsenite oxidase expression in H. arsenicoxydans. These data are summarized in a model that functionally integrates arsenite oxidation in the adaptive response to As(III) in this microorganism.