bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensitivity of Tropical Cyclone Inner-Core Size and Intensity to the Radial Distribution of Surface Entropy Flux
Authors: Xu Jing , Wang Yuqing 
Published: February 2010

Abstract
The surface energy (entropy) flux is critical to the development and maintenance of a tropical cyclone (TC). However, it is unclear how sensitive the inner-core size and intensity of a TC could be to the radial distribution of the surface entropy flux under the TC. Such a potential sensitivity is examined in this study using the multiply nested, fully compressible, nonhydrostatic TC model TCM4. By artificially eliminating the surface entropy fluxes in different radial extent in different experiments, the effect of the surface entropy flux in the different radial ranges on the inner-core size and intensity of a simulated TC is evaluated. Consistent with recent findings from axisymmetric models, the entropy flux in the eye region of a TC is found to contribute little to the storm intensity, but it plays a role in reducing the radius of maximum wind (RMW). Although surface entropy fluxes under the eyewall contribute greatly to the storm intensity, those outside the eyewall up to a radius of about 2–2.5 times the RMW are also important. Farther outward, the surface entropy fluxes are found to be crucial to the growth of the storm inner-core size but could reduce the storm intensity. The surface entropy flux outside the inner core plays a critical role in maintaining high convective available potential energy (CAPE) outside the eyewall and thus active spiral rainbands. The latent heat release in these rainbands is responsible for the increase in the inner-core size of the simulated TC. A positive feedback is identified to explain changes in the inner-core size of the simulated storms in different experiments. Implications of the results for both observations and numerical prediction of TC structure and intensity changes are briefly discussed.
ENSO Feedbacks and Associated Time Scales of Variability in a Multimodel Ensemble
Authors: Belmadani Ali , Dewitte Boris , An Soon-Il 
Published: February 2010

Abstract
The background state of the equatorial Pacific determines the prevalence of a “slow” recharge oscillator-type ENSO over a “fast” quasi-biennial surface-driven ENSO. The first is controlled to a large extent by the thermocline feedback, whereas the latter is related to enhanced zonal advective feedback. In this study, dynamical diagnostics are used to investigate the relative importance of these two feedbacks in the Coupled Model Intercomparison Project and its relation with the differences in ENSO-like variability among the models. The focus is on the role of the mean oceanic surface circulation in controlling the relative weight of the two feedbacks.
By the means of an intermediate-type ocean model of the tropical Pacific “tuned” from the coupled general circulation model (CGCM) outputs, the contribution of the advection terms (vertical versus zonal) to the rate of SST change is estimated. A new finding is that biases in the advection terms are to a large extent related to the biases in the mean surface circulation. The latter are used to infer the dominant ENSO feedback for each CGCM. This allows for the classification of the CGCMs into three groups that account for the dominant feedback process of the ENSO cycle: horizontal advection (mainly in the western Pacific), vertical advection (mainly in the eastern Pacific), and the combination of both mechanisms.
Based on such classification, the analysis also reveals that the models exhibit distinctive behavior with respect to the characteristics of ENSO: for most models, an enhanced (diminished) contribution of the zonal advective feedback is associated with faster (slower) ENSO and a tendency toward a cooler (warmer) mean state in the western-to-central Pacific Ocean. The results support the interpretation that biases in the mean state are sustained/maintained by the privileged mode of variability associated with the dominant feedback mechanism in the models. In particular, the models having a dominant zonal advective feedback exhibit significant cold SST asymmetry (or negative skewness) in the western equatorial Pacific.
How Much Do Different Land Models Matter for Climate Simulation? Part I: Climatology and Variability
Authors: Wei Jiangfeng , Dirmeyer Paul A. , Guo Zhichang , Zhang Li , Misra Vasubandhu 
Published: February 2010

Abstract
An atmospheric general circulation model (AGCM) is coupled to three different land surface schemes (LSSs), both individually and in combination (i.e., the LSSs receive the same AGCM forcing each time step and the averaged upward surface fluxes are passed back to the AGCM), to study the uncertainty of simulated climatologies and variabilities caused by different LSSs. This tiling of the LSSs is done to study the uncertainty of simulated mean climate and climate variability caused by variations between LSSs. The three LSSs produce significantly different surface fluxes over most of the land, no matter whether they are coupled individually or in combination. Although the three LSSs receive the same atmospheric forcing in the combined experiment, the inter-LSS spread of latent heat flux can be larger or smaller than the individually coupled experiment, depending mostly on the evaporation regime of the schemes in different regions. Differences in precipitation are the main reason for the different latent heat fluxes over semiarid regions, but for sensible heat flux, the atmospheric differences and LSS differences have comparable contributions. The influence of LSS uncertainties on the simulation of surface temperature is strongest in dry seasons, and its influence on daily maximum temperature is stronger than on minimum temperature. Land–atmosphere interaction can dampen the impact of LSS uncertainties on surface temperature in the tropics, but can strengthen their impact in middle to high latitudes. Variations in the persistence of surface heat fluxes exist among the LSSs, which, however, have little impact on the global pattern of precipitation persistence. The results provide guidance to future diagnosis of model uncertainties related to LSSs.
The Impact of Extratropical Atmospheric Variability on ENSO: Testing the Seasonal Footprinting Mechanism Using Coupled Model Experiments
Authors: Alexander Michael A. , Vimont Daniel J. , Chang Ping , Scott James D. 
Published: February 2010

Abstract
Previous studies suggest that extratropical atmospheric variability influences the tropics via the seasonal footprinting mechanism (SFM), in which fluctuations in the North Pacific Oscillation (NPO) impact the ocean via surface heat fluxes during winter and the resulting springtime subtropical SST anomalies alter the atmosphere–ocean system over the tropics in the following summer, fall, and winter. Here, the authors test the SFM hypothesis by imposing NPO-related surface heat flux forcing in an atmospheric GCM coupled to a reduced gravity ocean model in the tropics and a slab ocean in the extratropics. The forcing is only imposed through the first winter, and then the model is free to evolve through the following winter.
The evolution of the coupled model response to the forcing is consistent with the SFM hypothesis: the NPO-driven surface fluxes cause positive SST anomalies to form in the central and eastern subtropics during winter; these anomalies propagate toward the equator along with westerly wind anomalies during spring, reach the equator in summer, and then amplify, which leads to an ENSO event in the following winter. The anomalies reach the equator through a combination of thermodynamically coupled air–sea interactions, namely, the wind–evaporation–SST (WES) feedback and equatorial ocean dynamics. The initial off-equatorial anomaly propagates toward the equator through a relaxation of the climatological easterly winds south of the dominant SST anomalies, which leads to a reduction in upward latent heat flux. These westerly anomalies reach the equator during boreal summer, where they can excite downwelling equatorial Kelvin waves. The connection between off-equatorial variations and tropical ENSO-like conditions may also occur via the excitation of westward-propagating equatorial Rossby waves during spring, which reflect off of the western boundary as Kelvin waves, depressing the thermocline in the eastern Pacific during the following summer. NPO-related anomalies that form during the first winter in the tropical Pacific may also contribute to the development of an El Niño event in the following winter.
The imposition of the NPO-related forcing caused warming in the ENSO region in ∼70% of the ensemble of 60 simulations; therefore, the response depends on the state of the tropical atmosphere–ocean system. For years where the control simulation was poised to develop into a neutral or negative ENSO event, the addition of the NPO heat fluxes tended to cause anomalous warming in the tropical Pacific in the following fall/winter; if the control was heading toward a warm ENSO event, the imposition of NPO forcing tends to reduce the amplitude of that event.
A random effect multiplicative heteroscedastic model for bacterial growth
Authors: Cao Ricardo , Francisco-Fernández Mario , Quinto Emiliano J 
Published: February 2010

AbstractBackgroundPredictive microbiology develops mathematical models that can predict the growth rate of a microorganism population under a set of environmental conditions. Many primary growth models have been proposed. However, when primary models are applied to bacterial growth curves, the biological variability is reduced to a single curve defined by some kinetic parameters (lag time and growth rate), and sometimes the models give poor fits in some regions of the curve. The development of a prediction band (from a set of bacterial growth curves) using non-parametric and bootstrap methods permits to overcome that problem and include the biological variability of the microorganism into the modelling process.ResultsAbsorbance data fromListeria monocytogenescultured at 22, 26, 38, and 42°C were selected under different environmental conditions of pH (4.5, 5.5, 6.5, and 7.4) and percentage of NaCl (2.5, 3.5, 4.5, and 5.5). Transformation of absorbance data to viable count data was carried out. A random effect multiplicative heteroscedastic model was considered to explain the dynamics of bacterial growth. The concept of a prediction band for microbial growth is proposed. The bootstrap method was used to obtain resamples from this model. An iterative procedure is proposed to overcome the computer intensive task of calculating simultaneous prediction intervals, along time, for bacterial growth. The bands were narrower below the inflection point (0-8 h at 22°C, and 0-5.5 h at 42°C), and wider to the right of it (from 9 h onwards at 22°C, and from 7 h onwards at 42°C). A wider band was observed at 42°C than at 22°C when the curves reach their upper asymptote. Similar bands have been obtained for 26 and 38°C.ConclusionsThe combination of nonparametric models and bootstrap techniques results in a good procedure to obtain reliable prediction bands in this context. Moreover, the new iterative algorithm proposed in this paper allows one to achieve exactly the prefixed coverage probability for the prediction band. The microbial growth bands reflect the influence of the different environmental conditions on the microorganism behaviour, helping in the interpretation of the biological meaning of the growth curves obtained experimentally.
An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data
Authors: Wang Congmao , Xu Jie , Zhang Dasheng , Wilson Zoe A , Zhang Dabing 
Published: February 2010

Abstract

Background
ChIP-Seq, which combines chromatin immunoprecipitation (ChIP) with high-throughput massively parallel sequencing, is increasingly being used for identification of protein-DNA interactions in vivo in the genome. However, to maximize the effectiveness of data analysis of such sequences requires the development of new algorithms that are able to accurately predict DNA-protein binding sites.

Results
Here, we present SIPeS (S ite I dentification from P aired-e nd S equencing), a novel algorithm for precise identification of binding sites from short reads generated by paired-end solexa ChIP-Seq technology. In this paper we used ChIP-Seq data from the Arabidopsis basic helix-loop-helix transcription factor ABORTED MICROSPORES (AMS), which is expressed within the anther during pollen development, the results show that SIPeS has better resolution for binding site identification compared to two existing ChIP-Seq peak detection algorithms, Cisgenome and MACS.

Conclusions
When compared to Cisgenome and MACS, SIPeS shows better resolution for binding site discovery. Moreover, SIPeS is designed to calculate the mappable genome length accurately with the fragment length based on the paired-end reads. Dynamic baselines are also employed to effectively discriminate closely adjacent binding sites, for effective binding sites discovery, which is of particular value when working with high-density genomes.
Sp1 and KLF15 regulate basal transcription of the human LRP5 gene
Authors: Li Jiangxia , Yang Yang , Jiang Baichun , Zhang Xiyu , Zou Yongxin , Gong Yaoqin 
Published: February 2010

Abstract

Background
LRP5, a member of the low density lipoprotein receptor superfamily, regulates diverse developmental processes in embryogenesis and maintains physiological homeostasis in adult organisms. However, how the expression of human LRP5 gene is regulated remains unclear.

Results
In order to characterize the transcriptional regulation of human LRP5 gene, we cloned the 5' flanking region and evaluated its transcriptional activity in a luciferase reporter system. We demonstrated that both KLF15 and Sp1 binding sites between -72 bp and -53 bp contribute to the transcriptional activation of human LRP5 promoter. Chromatin immunoprecipitation assay demonstrated that the ubiquitous transcription factors KLF15 and Sp1 bind to this region. Using Drosophila SL2 cells, we showed that KLF15 and Sp1 trans-activated the LRP5 promoter in a manner dependent on the presence of Sp1-binding and KLF15-binding motifs.

Conclusions
Both KLF15 and Sp1 binding sites contribute to the basal activity of human LRP5 promoter. This study provides the first insight into the mechanisms by which transcription of human LRP5 gene is regulated.
Transcriptional profiling of Actinobacillus pleuropneumoniae during the acute phase of a natural infection in pigs
Authors: Deslandes Vincent , Denicourt Martine , Girard Christiane , Harel Josée , Nash John HE , Jacques Mario 
Published: February 2010

Abstract

Background

Actinobacillus pleuropneumoniae is the etiological agent of porcine pleuropneumonia, a respiratory disease which causes great economic losses worldwide. Many virulence factors are involved in the pathogenesis, namely capsular polysaccharides, RTX toxins, LPS and many iron acquisition systems. In order to identify genes that are expressed in vivo during a natural infection, we undertook transcript profiling experiments with an A. pleuropneumoniae DNA microarray, after recovery of bacterial mRNAs from serotype 5b-infected porcine lungs. AppChip2 contains 2033 PCR amplicons based on the genomic sequence of App serotype 5b strain L20, representing more than 95% of ORFs greater than 160 bp in length.

Results
Transcriptional profiling of A. pleuropneumoniae recovered from the lung of a pig suffering from a natural infection or following growth of the bacterial isolate in BHI medium was performed. An RNA extraction protocol combining beadbeating and hot-acid-phenol was developed in order to maximize bacterial mRNA yields and quality following total RNA extraction from lung lesions. Nearly all A. pleuropneumoniae transcripts could be detected on our microarrays, and 150 genes were deemed differentially expressed in vivo during the acute phase of the infection. Our results indicate that, for example, gene apxIVA from an operon coding for RTX toxin ApxIV is highly up-regulated in vivo, and that two genes from the operon coding for type IV fimbriae (APL_0878 and APL_0879) were also up-regulated. These transcriptional profiling data, combined with previous comparative genomic hybridizations performed by our group, revealed that 66 out of the 72 up-regulated genes are conserved amongst all serotypes and that 3 of them code for products that are predicted outer membrane proteins (genes irp and APL_0959, predicted to code for a TonB-dependent receptor and a filamentous hemagglutinin/adhesin respectively) or lipoproteins (gene APL_0920). Only 4 of 72 up-regulated genes had previously been identified in controled experimental infections.

Conclusions
These genes that we have identified as up-regulated in vivo, conserved across serotypes and coding for potential outer membrane proteins represent potential candidates for the development of a cross-protective vaccine against porcine pleuropneumonia.
Genome-wide investigation and functional characterization of the β-ketoadipate pathway in the nitrogen-fixing and root-associated bacterium Pseudomonas stutzeriA1501
Authors: Li Danhua , Yan Yongliang , Ping Shuzhen , Chen Ming , Zhang Wei , Li Liang , Lin Wenna , Geng Lizhao , Liu Wei , Lu Wei , Lin Min 
Published: February 2010

AbstractBackgroundSoil microorganisms are mainly responsible for the complete mineralization of aromatic compounds that usually originate from plant products or environmental pollutants. In many cases, structurally diverse aromatic compounds can be converted to a small number of structurally simpler intermediates, which are metabolized to tricarboxylic acid intermediates via the β-ketoadipate pathway. This strategy provides great metabolic flexibility and contributes to increased adaptation of bacteria to their environment. However, little is known about the evolution and regulation of the β-ketoadipate pathway in root-associated diazotrophs.ResultsIn this report, we performed a genome-wide analysis of the benzoate and 4-hydroxybenzoate catabolic pathways ofPseudomonas stutzeriA1501, with a focus on the functional characterization of the β-ketoadipate pathway. TheP. stutzeriA1501 genome contains sets of catabolic genes involved in the peripheral pathways for catabolism of benzoate (ben) and 4-hydroxybenzoate (pob), and in the catechol (cat) and protocatechuate (pca) branches of the β-ketoadipate pathway. A particular feature of the catabolic gene organization in A1501 is the absence of thecatRandpcaKgenes encoding a LysR family regulator and 4-hydroxybenzoate permease, respectively. Furthermore, the BenR protein functions as a transcriptional activator of thebenoperon, while transcription from thecatBCpromoter can be activated in response to benzoate. Benzoate degradation is subject to carbon catabolite repression induced by glucose and acetate in A1501. The HPLC analysis of intracellular metabolites indicated that low concentrations of 4-hydroxybenzoate significantly enhance the ability of A1501 to degrade benzoate.ConclusionsThe expression of genes encoding proteins involved in the β-ketoadipate pathway is tightly modulated by both pathway-specific and catabolite repression controls in A1501. This strain provides an ideal model system for further study of the evolution and regulation of aromatic catabolic pathways.
Genomic and evolutionary comparisons of diazotrophic and pathogenic bacteria of the order Rhizobiales
Authors: Carvalho Fabíola M , Souza Rangel C , Barcellos Fernando G , Hungria Mariangela , Vasconcelos Ana Tereza R 
Published: February 2010

Abstract

Background
Species belonging to the Rhizobiales are intriguing and extensively researched for including both bacteria with the ability to fix nitrogen when in symbiosis with leguminous plants and pathogenic bacteria to animals and plants. Similarities between the strategies adopted by pathogenic and symbiotic Rhizobiales have been described, as well as high variability related to events of horizontal gene transfer. Although it is well known that chromosomal rearrangements, mutations and horizontal gene transfer influence the dynamics of bacterial genomes, in Rhizobiales, the scenario that determine pathogenic or symbiotic lifestyle are not clear and there are very few studies of comparative genomic between these classes of prokaryotic microorganisms trying to delineate the evolutionary characterization of symbiosis and pathogenesis.

Results
Non-symbiotic nitrogen-fixing bacteria and bacteria involved in bioremediation closer to symbionts and pathogens in study may assist in the origin and ancestry genes and the gene flow occurring in Rhizobiales. The genomic comparisons of 19 species of Rhizobiales, including nitrogen-fixing, bioremediators and pathogens resulted in 33 common clusters to biological nitrogen fixation and pathogenesis, 15 clusters exclusive to all nitrogen-fixing bacteria and bacteria involved in bioremediation, 13 clusters found in only some nitrogen-fixing and bioremediation bacteria, 01 cluster exclusive to some symbionts, and 01 cluster found only in some pathogens analyzed. In BBH performed to all strains studied, 77 common genes were obtained, 17 of which were related to biological nitrogen fixation and pathogenesis. Phylogenetic reconstructions for Fix, Nif, Nod, Vir, and Trb showed possible horizontal gene transfer events, grouping species of different phenotypes.

Conclusions
The presence of symbiotic and virulence genes in both pathogens and symbionts does not seem to be the only determinant factor for lifestyle evolution in these microorganisms, although they may act in common stages of host infection. The phylogenetic analysis for many distinct operons involved in these processes emphasizes the relevance of horizontal gene transfer events in the symbiotic and pathogenic similarity.
Identification of genes associated with growth cessation and bud dormancy entrance using a dormancy-incapable tree mutant
Authors: Jiménez Sergio , Li Zhigang , Reighard Gregory L , Bielenberg Douglas G 
Published: February 2010

Abstract

Background
In many tree species the perception of short days (SD) can trigger growth cessation, dormancy entrance, and the establishment of a chilling requirement for bud break. The molecular mechanisms connecting photoperiod perception, growth cessation and dormancy entrance in perennials are not clearly understood. The peach [Prunus persica (L.) Batsch] evergrowing (evg) mutant fails to cease growth and therefore cannot enter dormancy under SD. We used the evg mutant to filter gene expression associated with growth cessation after exposure to SD. Wild-type and evg plants were grown under controlled conditions of long days (16 h/8 h) followed by transfer to SD (8 h/16 h) for eight weeks. Apical tissues were sampled at zero, one, two, four, and eight weeks of SD and suppression subtractive hybridization was performed between genotypes at the same time points.

Results
We identified 23 up-regulated genes in the wild-type with respect to the mutant during SD exposure. We used quantitative real-time PCR to verify the expression of the differentially expressed genes in wild-type tissues following the transition to SD treatment. Three general expression patterns were evident: one group of genes decreased at the time of growth cessation (after 2 weeks in SD), another that increased immediately after the SD exposure and then remained steady, and another that increased throughout SD exposure.

Conclusions
The use of the dormancy-incapable mutant evg has allowed us to reduce the number of genes typically detected by differential display techniques for SD experiments. These genes are candidates for involvement in the signalling pathway leading from photoperiod perception to growth cessation and dormancy entrance and will be the target of future investigations.