bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of a Serine/Threonine Kinase Involved in Virulence of
Staphylococcus aureus
Authors: Débarbouillé Michel , Dramsi Shaynoor , Dussurget Olivier , Nahori Marie-Anne , Vaganay Elisabeth , Jouvion Grégory , Cozzone Alain , Msadek Tarek , Duclos Bertrand 
Published: April 2009

ABSTRACT

Staphylococcus aureus
is a common human cutaneous and nasal commensal and a major life-threatening pathogen. Adaptation to the different environments encountered inside and outside the host is a crucial requirement for survival and colonization. We identified and characterized a eukaryotic-like serine/threonine kinase with three predicted extracellular PASTA domains (SA1063, or Stk1) and its associated phosphatase (SA1062, or Stp1) in
S. aureus
. Biochemical analyses revealed that Stk1 displays autokinase activity on threonine and serine residues and is localized to the membrane. Stp1 is a cytoplasmic protein with manganese-dependent phosphatase activity toward phosphorylated Stk1. In-frame deletions of the
stk1
and
stp1
genes were constructed in
S. aureus
strain 8325-4. Phenotypic analyses of the mutants revealed reduced growth of the
stk1
mutant in RPMI 1640 defined medium that was restored when adenine was added to the medium. Furthermore, the
stk1
mutant displayed increased resistance to Triton X-100 and to fosfomycin, suggesting modifications in cell wall metabolism. The
stk1
mutant was tested for virulence in a mouse pyelonephritis model and found to be strongly reduced for survival in the kidneys (approximately 2-log-unit decrease) compared to the parental strain. Renal histopathological analyses showed severe inflammatory lesions in mice infected with the parental
S. aureus
SH1000 strain, whereas the Δ
stk1
mutant led to only minimal renal lesions. These results confirm the important role of Stk1 for full expression of
S. aureus
pathogenesis and suggest that phosphorylation levels controlled by
stk1
are essential in controlling bacterial survival within the host.
UNDERSTANDING THE VERY-HIGH-ENERGY EMISSION FROM MICROQUASARS
Authors: BOSCH-RAMON VALENTÍ , KHANGULYAN DMITRY 
Published: April 2009

Microquasars are X-ray binaries with relativistic jets. These jets are powerful energy carriers — thought to be fed by accretion — which produce nonthermal emission at different energy bands. The processes behind the bulk of the nonthermal emission in microquasars may be of leptonic (synchrotron and inverse Compton) and hadronic (proton–proton interactions, photomeson production, and photodisintegration) nature. When leptonic, the fast particle cooling would allow one to obtain relevant information about the properties close to the accelerator, like the radiation and the magnetic field energy densities, and the acceleration efficiency. When hadronic, the extreme conditions required in the emitter would have strong implications for the physics of jets and their surroundings. The very-high-energy part of the spectrum, i.e. > 100 GeV, is a good energy range to explore the physics behind the nonthermal radiation in these compact variable sources. In addition, this energy range, when taken together with lower energy bands, is a key piece for constructing a comprehensive picture of the processes occurring in the emitter. Until recently, the very-high-energy range was hard to probe due to the lack of sensitivity and spatial and spectral resolution of previous instrumentation. Nowadays, however, powerful gamma-ray instruments are operating and the quality of their observations is allowing one, for the first time, to start to understand the production of high-energy emission in microquasars. To date, several galactic sources showing extended radio emission — among them at least one confirmed microquasar, Cygnus X-1 — have shown a TeV signal. All of them show complex patterns of spectral and temporal behavior. In this work, we discuss the physics behind the very-high-energy emission in Cygnus X-1, and also in the other two TeV binaries with detected extended outflows, LS 5039 and LS I +61 303, pointing out relevant aspects of the complex phenomena occurring in them. We conclude that the TeV emission is likely of leptonic origin, although hadrons cannot be discarded. In addition, efficient electromagnetic cascades can hardly develop since even relatively low magnetic fields suppress them. Also, the modeling of the radiation from some of the detected sources points to them as extremely efficient accelerators and/or having the TeV emitter at a distance from the compact object of about ~ 1012 cm. Finally, we point out that the role of a massive and hot stellar companion, due to its strong photon field and wind, cannot be neglected when trying to understand the behavior of microquasars at high and very high energies. The complexity of microquasars precludes straightforward generalizations to a whole population, and are better studied presently on a source-by-source basis. The new and future gamma-ray instrumentation will imply a big step further in our understanding of the processes in microquasars and gamma-ray-emitting binaries.
HIGHLIGHTING RELATIONSHIPS BETWEEN HETEROGENEOUS BIOLOGICAL DATA THROUGH GRAPHICAL DISPLAYS BASED ON REGULARIZED CANONICAL CORRELATION ANALYSIS
Authors: GONZÁLEZ I. , DÉJEAN S. , MARTIN P. G. P. , GONÇALVES O. , BESSE P. , BACCINI A. 
Published: April 2009

Biological data produced by high throughput technologies are becoming more and more abundant and are arousing many statistical questions. This paper addresses one of them; when gene expression data are jointly observed with other variables with the purpose of highlighting significant relationships between gene expression and these other variables. One relevant statistical method to explore these relationships is Canonical Correlation Analysis (CCA). Unfortunately, in the context of postgenomic data, the number of variables (gene expressions) is usually greater than the number of units (samples) and CCA cannot be directly performed: a regularized version is required.We applied regularized CCA on data sets from two different studies and show that its interpretation evidences both previously validated relationships and new hypothesis. From the first data sets (nutrigenomic study), we generated interesting hypothesis on the transcription factor pathways potentially linking hepatic fatty acids and gene expression. From the second data sets (pharmacogenomic study on the NCI-60 cancer cell line panel), we identified new ABC transporter candidate substrates which relevancy is illustrated by the concomitant identification of several known substrates.In conclusion, the use of regularized CCA is likely to be relevant to a number and a variety of biological experiments involving the generation of high throughput data. We demonstrated here its ability to enhance the range of relevant conclusions that can be drawn from these relatively expensive experiments.
Verification of Tropical Cyclone–Related Satellite Precipitation Estimates in Mainland China
Authors: Yu Zifeng , Yu Hui , Chen Peiyan , Qian Chuanhai , Yue Caijun 
Published: April 2009

Abstract
To evaluate the abilities of satellite retrievals in reflecting precipitation features related to tropical cyclones (TCs) affecting mainland China, four years of 6- and 24-h precipitation retrievals from three datasets, namely the Tropical Rainfall Measuring Mission satellite algorithm 3B42, version 6 (3B42), Climate Prediction Center morphed (CMORPH) product, and one based on the Geostationary Meteorological Satellite-5 infrared brightness temperature (GMS5-TBB), are compared statistically with direct measurements from surface gauge rainfall data during the periods affected by TCs. The GMS5-TBB dataset was set up by a method of considering the GMS5-TBB characteristics, hourly precipitation intensity, and horizontal distribution for landfalling TCs. The results show that in a general sense, all three satellite-retrieved rainfall datasets give quite reasonable 6- and 24-h rainfall distributions, with skill decreasing with the increase in both latitude and rainfall amount. The 3B42 has a little bit better skill than CMORPH, which is likely related to the fact that the 3B42 product has a rain gauge adjustment and CMORPH does not. Further analyses show that both 3B42 and CMORPH considerably underestimate the moderate and heavy rainfall and overestimate the very light precipitation. The overestimation of the GMS5-TBB data for the light rain is larger than that for 3B42 and CMORPH, probably due to the fact that the GMS5-TBB method considers stratiform and convective rainfall separately with a fixed stratiform rain rate of 2 mm h−1. For the heavy rainfall events, the GMS5-TBB data perform much better than the 3B42 and CMORPH data with an almost halved bias, owing to the fact that the GMS5-TBB method adopted the adjustment of the convective rain rate by considering TBB characteristics of landfalling TCs and using hourly gauge rainfall in the setup process. Since the heavy rainfall events associated with landfalling TCs are of the most concern, the compared GMS5-TBB data could be useful as an operational/research reference.
Interannual Variability of the Global Radiation Budget
Authors: Kato Seiji 
Published: April 2009

Abstract
Interannual variability of the global radiation budget, regions that contribute to its variability, and what limits albedo variability are investigated using Clouds and the Earth’s Radiant Energy System (CERES) data taken from March 2000 through February 2004. Area-weighted mean top-of-atmosphere (TOA) reflected shortwave, longwave, and net irradiance standard deviations computed from monthly anomalies over a 1° × 1° region are 9.6, 7.6, and 7.6 W m−2, respectively. When standard deviations are computed from global monthly anomalies, they drop to 0.5, 0.4, and 0.4 W m−2, respectively. Clouds are mostly responsible for the variation. Regions with a large standard deviation of TOA shortwave and longwave irradiance at TOA are the tropical western and central Pacific, which is caused by shifting from La Niña to El Niño during this period. However, a larger standard deviation of 300–1000-hPa thickness anomalies occurs in the polar region instead of the tropics. The correlation coefficient between atmospheric net irradiance anomalies and 300–1000-hPa thickness anomalies is negative. These indicate that temperature anomalies in the atmosphere are mostly a result of anomalies in longwave and dynamical processes that transport energy poleward, instead of albedo anomalies by clouds directly affecting temperature anomalies in the atmosphere. With simple zonal-mean thermodynamic energy equations it is demonstrated that temperature anomalies decay exponentially with time by longwave emission and by dynamical processes. As a result, the mean meridional temperature gradient is maintained. Therefore, mean meridional circulations are not greatly altered by albedo anomalies on an annual time scale, which in turn provides small interannual variability of the global mean albedo.
Diurnal Cycle of Precipitation in the Tropics Simulated in a Global Cloud-Resolving Model
Authors: Sato Tomonori , Miura Hiroaki , Satoh Masaki , Takayabu Yukari N. , Wang Yuqing 
Published: April 2009

Abstract
This study analyzes the diurnal cycle of precipitation simulated in a global cloud-resolving model (GCRM) named the Nonhydrostatic Icosahedral Atmospheric Model (NICAM). A 30-day integration of NICAM successfully simulates the precipitation diurnal cycle associated with the land–sea breeze and the thermally induced topographic circulations as well as the horizontal propagation of diurnal cycle signals. The first harmonic of the diurnal cycle of precipitation in the 7-km run agrees well with that from satellite observations in its geographical distributions although its amplitude is slightly overestimated. The NICAM simulation revealed that the precipitation diurnal cycle over the Maritime Continent is strongly coupled with the land–sea breeze that controls the convergence/divergence pattern in the lower troposphere around the islands. The analysis also suggests that the cold pool often forms over the open ocean where the precipitation intensity is high, and the propagation of the cold pool events is related to the precipitation diurnal cycle as well as the land–sea breeze.
Sensitivity experiments suggest a prominent horizontal resolution dependence of the simulated precipitation diurnal cycle. Over continental areas the 14-km run induces the diurnal peak about three hours later than the 7-km run. The 3.5-km run produces the peak time and amplitude that are very similar to those in Tropical Rainfall Measuring Mission (TRMM) precipitation radar (PR) observations. Meanwhile, the resolution dependence in phase and amplitude is negligibly small over the open oceans. This contrast sensitivity to the horizontal resolution is attributed to the differences in structure and life cycle of convective systems over land and ocean.
Diurnal peaks of precipitable water vapor, precipitation, and outgoing longwave radiation (OLR) are compared over land areas using the NICAM 7-km run. The daily precipitable water vapor maximum appears around 1500 local time (LT), which is followed by the precipitation peak around 1630 LT. The diurnal cycle of high clouds tends to peak around 1930 LT, three hours later than the precipitation peak. These results from NICAM simulations can explain the cause of the phase differences among precipitation products based on several satellite observations. The authors demonstrate that the GCRM is a promising tool for realistically simulating the precipitation diurnal cycle and could be quite useful for studying the role of the diurnal cycle in the climate systems in a global context.
The Psychrometric Constant Is Not Constant: A Novel Approach to Enhance the Accuracy and Precision of Latent Energy Fluxes through Automated Water Vapor Calibrations
Authors: Loescher H. W. , Hanson C. V. , Ocheltree T. W. 
Published: April 2009

Abstract
Numerous agencies, programs, and national networks are focused on improving understanding of water and energy fluxes across temporal and spatial scales and on enhancing confidence to synthesize data across multiple sites. Enhancing the accuracy and precision in the surface energy balance and the latent energy (λE) flux lies, in part, with being able to uniformly calibrate water vapor measurements at and among sites to traceable standards. This paper examines (i) the traceable physical controls on field applications of chilled-mirror hygrometers and (ii) an automated means to accurately and precisely calibrate infrared gas analyzers for water vapor concentrations and eddy covariance (λE) data. The environmental physics and gas handling were examined in a theoretical and applied manner that found that chilled-mirror technologies can be a robust measure of dewpoint temperatures and ambient water vapor only if the unit conversions are accounted for between inlet and body temperatures. Psychrometers were also examined and a functional relationship (exponential) was developed for the psychrometric constant against the wet-bulb temperature depression (Tdb − Twb), across a wider range of temperature depressions than previously reported. These empirical estimates of the psychrometer constant for small temperature depressions are much lower than other reported values—that is, ∼0.000 52 K−1 for a wet-bulb temperature depression (Tdb − Twb) of 4.3 K.
Evaluations of NAM Forecasts on Midtropospheric Perturbation-Induced Convective Storms over the U.S. Northern Plains
Authors: Wang Shih-Yu , Chen Tsing-Chang , Taylor S. Elwynn 
Published: April 2009

Abstract
In the U.S. northern plains, summer progressive convective storms that occur in weakly forced environments are often coupled with short-wave perturbations that are embedded in the midlevel northwesterly flow. These midtropospheric perturbations (MPs) are capable of inducing propagating convection that contributes to a majority of the rainfall over the northern plains during July and August. There is a possibility that the difficulties of numerical weather prediction models in forecasting summer convective rainfall over the northern plains are partly attributed to their deficiency in forecasting MPs. The present study tests this possibility through examining operational forecasts by the North American Mesoscale (NAM) model during the summers of 2005 and 2006.
Forecasted MPs exhibit slower propagation speeds and weaker relative vorticity than the observations leading to systematic position errors. Underpredicted vorticity magnitudes weaken horizontal vorticity advection that influences the vorticity tendency throughout the MP life cycle and, in turn, slows the propagation speed of MPs. Moreover, biases of weak ambient flow speed and vortex stretching contribute to the magnitude and propagation speed errors of MPs. Skill scores of precipitation forecasts associated with MPs are low, but can be considerably improved after removing the MP position error that displaces the rainfall pattern. The NAM also tends to underpredict precipitation amounts. A modified water vapor budget analysis reveals that the NAM insufficiently generates atmospheric humidity over the central United States. The shortage of moisture in the forecast reduces the water vapor flux convergence that is part of the precipitation process. The precipitation bias may feed back to affect the MP growth through the bias in heating, thus further slowing the perturbation.
Characterisation of the effects of caffeine on sleep in the rat: a potential model of sleep disruption
Authors: Paterson LM , Wilson SJ , Nutt DJ , Hutson PH , Ivarsson M 
Published: April 2009

AbstractCaffeine is known to disrupt sleep and its administration to human subjects has been used to model sleep disruption. We previously showed that its effects on sleep onset latency are comparable between rats and humans. This study evaluated the potential use of caffeine as a model of sleep disruption in the rat, by assessing its effects on sleep architecture and electroencephalogram (EEG) frequency spectrum, and using sleep-promoting drugs to reverse these effects. Rats were implanted with radiotelemetry devices for body temperature, EEG, electromyogram and locomotor activity. Following recovery, animals were dosed with caffeine (10 mg/kg) alone or in combination with zolpidem (10 mg/kg) or trazodone (20 mg/kg). Sleep was scored for the subsequent 12 h using automated analysis software. Caffeine dose-dependently disrupted sleep: it increased WAKE time, decreased NREM (non-REM) sleep time and NREM bout duration (but not bout number), and decreased delta activity in NREM sleep. It also dose-dependently increased locomotor activity and body temperature. When given alone, zolpidem suppressed REM whilst trazodone increased NREM sleep time at the expense of WAKE, increased NREM bout duration, increased delta activity in NREM sleep and reduced body temperature. In combination, zolpidem attenuated caffeine’s effects on WAKE, whilst trazodone attenuated its effects on NREM sleep, NREM bout duration, delta activity, body temperature and locomotor activity. Caffeine administration produced many of the signs of insomnia that were improved by two of its most successful current treatments. This model may therefore be useful in the study of new drugs for the treatment of sleep disturbance.
Learning and Innovation
Authors: Lorentzen Jo 
Published: April 2009

Much innovation research views catch-up as a process that at low levels of development starts with imitation, and whose end point is innovation; and it posits that different stages require different frameworks to explain what is going on. In its more extreme versions it adds a horizontal to the over-time differentiation and demands that individual or groups of countries be appreciated for their contextual dissimilarities, requiring in each case yet another tailor-made model. The purpose of this review essay is to argue that to derive and justify different sui-generis frameworks from differential catch-up experiences is a non-sequitur, theoretically unsatisfactory, empirically unhelpful and not constructive for policy. Conceptually, all the pieces for a more unified approach are in place. We know how firms gain competitiveness through dynamic capabilities and complementary assets. We also know that firm-level technological capabilities are related to national (and perhaps regional) technological capabilities. Finally, we know that governing and supporting institutions matter in addressing the uncertainty resulting from problems of information, coordination, and so forth. This provides an opportunity to apply insights from theories of firm behaviour and new evolutionary thinking on technologies and institutions to historically informed, comparative studies of firm-based catch-up over the last decade or so.
The ITP syndrome: pathogenic and clinical diversity
Authors: Cines Douglas B. , Bussel James B. , Liebman Howard A. , Luning Prak Eline T. 
Published: April 2009

AbstractImmune thrombocytopenia (ITP) is mediated by platelet autoantibodies that accelerate platelet destruction and inhibit their production. Most cases are considered idiopathic, whereas others are secondary to coexisting conditions. Insights from secondary forms suggest that the proclivity to develop platelet-reactive antibodies arises through diverse mechanisms. Variability in natural history and response to therapy suggests that primary ITP is also heterogeneous. Certain cases may be secondary to persistent, sometimes inapparent, infections, accompanied by coexisting antibodies that influence outcome. Alternatively, underlying immune deficiencies may emerge. In addition, environmental and genetic factors may impact platelet turnover, propensity to bleed, and response to ITP-directed therapy. We review the pathophysiology of several common secondary forms of ITP. We suggest that primary ITP is also best thought of as an autoimmune syndrome. Better understanding of pathogenesis and tolerance checkpoint defects leading to autoantibody formation may facilitate patient-specific approaches to diagnosis and management.
FlyPhy: a phylogenomic analysis platform for Drosophila genes and gene families
Authors: Wu Jinyu , Xu Xiang , Xiao Jian , Xu Long , Yi Huiguang , Gao Shengjie , Liu Jing , Bao Qiyu , Zhao Fangqing , Li Xiaokun 
Published: April 2009

Abstract

Background
The availability of 12 fully sequenced Drosophila species genomes provides an excellent opportunity to explore the evolutionary mechanism, structure and function of gene families in Drosophila. Currently, several important resources, such as FlyBase, FlyMine and DroSpeGe, have been devoted to integrating genetic, genomic, and functional data of Drosophila into a well-organized form. However, all of these resources are gene-centric and lack the information of the gene families in Drosophila.

Description
FlyPhy is a comprehensive phylogenomic analysis platform devoted to analyzing the genes and gene families in Drosophila. Genes were classified into families using a graph-based Markov Clustering algorithm and extensively annotated by a number of bioinformatic tools, such as basic sequence features, functional category, gene ontology terms, domain organization and sequence homolog to other databases. FlyPhy provides a simple and user-friendly web interface to allow users to browse and retrieve the information at multiple levels. An outstanding feature of the FlyPhy is that all the retrieved results can be added to a workset for further data manipulation. For the data stored in the workset, multiple sequence alignment, phylogenetic tree construction and visualization can be easily performed to investigate the sequence variation of each given family and to explore its evolutionary mechanism.

Conclusion
With the above functionalities, FlyPhy will be a useful resource and convenient platform for the Drosophila research community. The FlyPhy is available at http://bioinformatics.zj.cn/fly/.