bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Arabidopsis Mitogen-Activated Protein Kinase Phosphatase PP2C5 Affects Seed Germination, Stomatal Aperture, and Abscisic Acid-Inducible Gene Expression
Authors: Brock Anita K. , Willmann Roland , Kolb Dagmar , Grefen Laure , Lajunen Heini M. , Bethke Gerit , Lee Justin , Nürnberger Thorsten , Gust Andrea A. 
Published: May 2010

AbstractAbscisic acid (ABA) is an important phytohormone regulating various cellular processes in plants, including stomatal opening and seed germination. Although protein phosphorylation via mitogen-activated protein kinases (MAPKs) has been suggested to be important in ABA signaling, the corresponding phosphatases are largely unknown. Here, we show that a member of the Protein Phosphatase 2C (PP2C) family in Arabidopsis (Arabidopsis thaliana), PP2C5, is acting as a MAPK phosphatase. The PP2C5 protein colocalizes and directly interacts with stress-induced MPK3, MPK4, and MPK6, predominantly in the nucleus. Importantly, altered PP2C5 levels affect MAPK activation. Whereas Arabidopsis plants depleted of PP2C5 show an enhanced ABA-induced activation of MPK3 and MPK6, ectopic expression of PP2C5 in tobacco (Nicotiana benthamiana) resulted in the opposite effect, with the two MAPKs salicylic acid-induced protein kinase and wound-induced protein kinase not being activated any longer after ABA treatment. Moreover, depletion of PP2C5, whose gene expression itself is affected by ABA treatment, resulted in altered ABA responses. Loss-of-function mutation in PP2C5 or AP2C1, a close PP2C5 homolog, resulted in an increased stomatal aperture under normal growth conditions and a partial ABA-insensitive phenotype in seed germination that was most prominent in the pp2c5 ap2c1 double mutant line. In addition, the response of ABA-inducible genes such as ABI1, ABI2, RD29A, and Erd10 was reduced in the mutant plants. Thus, we suggest that PP2C5 acts as a MAPK phosphatase that positively regulates seed germination, stomatal closure, and ABA-inducible gene expression.
Vascularization of testicular germ cell tumours: evidence from experimental teratocarcinomas
Authors: Silván U. , Díez‐Torre A. , Jiménez‐Rojo L. , Aréchaga J. 
Published: May 2010

SummaryTesticular germ cell tumours (TGCTs) represent about 2% of male malignancies, being the most common cancer among adolescents and young adults. As in most neoplasias, TGCTs show a chaotic vascular architecture, altered blood supply and over‐expression of pro‐angiogenic factors, aspects closely related to tumour overgrowth and metastasis. Following this trend, our laboratory has analysed the effect of the hypoxic tumour microenvironment on cancer stem cells, particularly the expression of factors related to vascularization, such as matrix metalloproteinases, adhesion molecules, vascular endothelial growth factors (VEGF) and VEGF receptors. This review also summarizes our present knowledge on vascularization in the normal and neoplastic testis, the potential role of the factors involved in TGCT neovascularization and their importance as possible therapeutic targets.
Artificial neural network‐based analysis of effective crack model in concrete fracture
Authors: INCE R. 
Published: May 2010

ABSTRACTMany non‐linear fracture models have been proposed by design codes and investigators to determine fracture parameters of cement‐based materials. To characterise failure of concrete structures, the effective crack model (ECM) needs two fracture parameters: the effective crack length ae and the critical stress intensity factor . Nevertheless, ECM requires a closed‐loop testing system and the calculation of ae needs considerable computational effort. For this reason, ECM is simulated with an artificial neural network (ANN) in this study. The main benefit of using an ANN approach is that the network is built directly on experimental data by using the self‐organizing capabilities of the ANN. The presented fracture model was developed by utilising 464 noisy test data taken from the literature, which were obtained via different test methods in different laboratories. The results of an ANN‐based ECM look viable and very promising.
Analysis of Intraseasonal and Interannual Variability of the Asian Summer Monsoon Using a Hidden Markov Model
Authors: Yoo Jin Ho , Robertson Andrew W. , Kang In-Sik 
Published: May 2010

AbstractIntraseasonal and interannual variability of Asian summer monsoon rainfall in pentad precipitation data is examined using a hidden Markov model (HMM). The spatial patterns of discrete rainfall states derived with the HMM and the associated transition probabilities between the states are shown to represent well the principal Asian summer monsoon intraseasonal oscillation (ISO), propagating eastward and northward with a period of 40–50 days. Stochastic simulations made with the HMM reasonably reproduce the canonical ISO propagation and its observed statistics such as the frequency of ISO events.The interannual modulation of the ISO associated with El Niño–Southern Oscillation (ENSO) is assessed by employing a nonhomogeneous HMM (NHMM) with summer-mean Niño-3.4 index prescribed as an input variable. ENSO influence on the ISO is found to manifest as preferences toward particular ISO phases depending on the ENSO condition, thus adding an asymmetry to the ISO. In the presence of seasonal mean anomalies, it is shown that the El Niño seasonal mean rainfall anomaly pattern is identified by the HMM as a distinct state, in addition to the ISO states, whereas the La Niña seasonal mean rainfall anomaly pattern does not appear distinct from the ISO states.
Multiscale Momentum Flux and Diffusion due to Whitecapping in Wave–Current Interactions
Authors: Restrepo Juan M. , Ramírez Jorge M. , McWilliams James C. , Banner Michael 
Published: May 2010

Abstract
Whitecapping affects the Reynolds stresses near the ocean surface. A model for the conservative dynamics of waves and currents is modified to include the averaged effect of multiple, short-lived, and random wave-breaking events on large spatiotemporal scales. In this study’s treatment, whitecapping is parameterized stochastically as an additive uncertainty in the fluid velocity. It is coupled to the Stokes drift as well as to the current velocity in the form of nonlinear momentum terms in the vortex force and the Bernoulli head. The effects of whitecapping on tracer dynamics, mass balances, and boundary conditions are also derived here. Whitecapping also modifies the dynamics and the size of the sea surface boundary layer. This study does not resolve the boundary layer, however, the authors appeal to traditional viscosity parameterizations to include these diffusive effects, modified for the context of wave–current interactions.
The parameterized breaking velocity field is endowed with empirical rules that link their generation in space and time to properties and dynamics of wave groups. The energy convergence rate of wave groups is used as an indicator for the onset of wave breaking. A methodology is proposed for evaluating this criterion over an evolving random Gaussian model for the ocean surface. The expected spatiotemporal statistics of the breaking events are not imposed, but rather computed, and are found to agree with the general expectation of its Poisson character. The authors also compute, rather than impose, the shear stress associated with the breaking events and find it to agree with theoretical expectations.
When the relative role played by waves and breaking events on currents is compared, this study finds that waves, via the vortex force, purely advect the vorticity of currents that are essentially only dependent on transverse coordinates. The authors show that currents will tend to get rougher in the direction of steady wind, when whitecapping is present. Breaking events can alter and even suppress the rate of advection in the vortex force. When comparing the rates of transport, the waves will tend to dominate the short term and the whitecapping of the long-term rate.
Optical Characteristics of OTD Flashes and the Implications for Flash-Type Discrimination
Authors: Koshak W. J. 
Published: May 2010

Abstract
Flashes detected by the Optical Transient Detector (OTD) that occur over the continental United States (CONUS) are intercompared with data from the National Lightning Detection Network (NLDN) in order to partition the OTD flashes into ground and cloud flashes. The entire 5-yr OTD dataset for CONUS is analyzed. The statistical distributions of a variety of optical characteristics are examined, including five flash-level attributes (radiance, area, duration, number of optical groups, and number of optical events), and two group-level attributes [the maximum number of events in a group (MNEG), and a closely related parameter, the maximum group area (MGA)]. On average, there were 5.6 optical groups per return stroke in a ground flash, which is in part due to the likelihood that OTD detects interstroke K changes. It was found that return strokes within ground flashes typically produce large optical groups; hence, the MNEG and MGA parameters serve as useful “return-stroke detectors.” The results of this study provide insight on how to construct an algorithm for retrieving the fraction of ground flashes in a set of flashes observed from a satellite lightning imager. Specifically, even though it is shown that the statistical distributions of the optical characteristics for ground and cloud flashes overlap substantially, the mean values of these distributions differ. Hence, a retrieval method that is based on an analysis of the distribution of the means, and that employs the central limit theorem of statistics, is recommended. As the sample size used to compute the means is increased, the overlap in the distributions of the means for ground and cloud flashes is diminished, making ground flash fraction retrieval feasible. Of the seven optical characteristics examined here, the mean MNEG and mean MGA parameters are suggested as being the most useful for discriminating between ground and cloud flashes in the context of this “central limit theorem” approach.
Wave Heights during Hurricane Katrina: An Evaluation of PPP and PPK Measurements of the Vertical Displacement of the GPS Antenna
Authors: Bender L. C. , Howden S. D. , Dodd D. , Guinasso N. L. 
Published: May 2010

Abstract
In August 2005 the eye of Hurricane Katrina passed 49 n mi to the west of a 3-m discus buoy operated by the Central Gulf of Mexico Ocean Observing System (CenGOOS). Buoy motions were measured with a strapped-down 6 degrees of freedom accelerometer, a three-axis magnetometer, and a survey-grade GPS receiver. The significant wave heights were computed from the buoy’s accelerometer record and from the dual-frequency GPS measurements that were processed in two different ways. The first method was postprocessed kinematic (PPK) GPS, which requires another GPS receiver at a fixed known location, and the other was precise point positioning (PPP) GPS, which is another postprocessed positioning technique that yields absolute rather than differential positions. Unlike inertial measurement units, either GPS technique can be used to obtain both waves and water levels. The purpose of this note is to demonstrate the excellent reliability and accuracy of both methods for determining wave heights and periods from a GPS record. When the motion of the GPS antenna is properly understood as the motion of the buoy deck and not the true vertical motion of the sea surface, the GPS wave heights are as reliable as a strapped-down 1D accelerometer.
Formation of Charge Structures in a Supercell
Authors: Bruning Eric C. , Rust W. David , MacGorman Donald R. , Biggerstaff Michael I. , Schuur Terry J. 
Published: May 2010

Abstract
Lightning mapping, electric field, and radar data from the 26 May 2004 supercell in central Oklahoma are used to examine the storm’s charge structure. An initial arc-shaped maximum in lightning activity on the right flank of the storm’s bounded weak echo region was composed of an elevated normal polarity tripole in the region of precipitation lofted above the storm’s weak echo region. Later in the storm, two charge structures were associated with precipitation that reached the ground. To the left of the weak echo region, six charge regions were inferred, with positive charge carried on hail at the bottom of the stack. Farther forward in the storm’s precipitation region, four charge regions were inferred, with negative charge at the bottom of the stack. There were different charge structures in adjacent regions of the storm at the same time, and regions of opposite polarity charge were horizontally adjacent at the same altitude. Flashes occasionally lowered positive charge to ground from the forward charge region. A conceptual model is presented that ties charge structure in different regions of the storm to storm structure inferred from radar reflectivity.
Evolutionary ancestry and novel functions of the mammalian glucose transporter (GLUT) family
Authors: Wilson-O'Brien Amy L , Patron Nicola , Rogers Suzanne 
Published: May 2010

Abstract

Background
In general, sugar porters function by proton-coupled symport or facilitative transport modes. Symporters, coupled to electrochemical energy, transport nutrients against a substrate gradient. Facilitative carriers transport sugars along a concentration gradient, thus transport is dependent upon extracellular nutrient levels. Across bacteria, fungi, unicellular non-vertebrates and plants, proton-coupled hexose symport is a crucial process supplying energy under conditions of nutrient flux. In mammals it has been assumed that evolution of whole body regulatory mechanisms would eliminate this need. To determine whether any isoforms bearing this function might be conserved in mammals, we investigated the relationship between the transporters of animals and the proton-coupled hexose symporters found in other species.

Results
We took a comparative genomic approach and have performed the first comprehensive and statistically supported phylogenetic analysis of all mammalian glucose transporter (GLUT) isoforms. Our data reveals the mammalian GLUT proteins segregate into five distinct classes. This evolutionary ancestry gives insight to structure, function and transport mechanisms within the groups. Combined with biological assays, we present novel evidence that, in response to changing nutrient availability and environmental pH, proton-coupled, active glucose symport function is maintained in mammalian cells.

Conclusions
The analyses show the ancestry, evolutionary conservation and biological importance of the GLUT classes. These findings significantly extend our understanding of the evolution of mammalian glucose transport systems. They also reveal that mammals may have conserved an adaptive response to nutrient demand that would have important physiological implications to cell survival and growth.
Adenosine thiamine triphosphate accumulates in Escherichia coli cells in response to specific conditions of metabolic stress
Authors: Gigliobianco Tiziana , Lakaye Bernard , Wins Pierre , El Moualij Benaïssa , Zorzi Willy , Bettendorff Lucien 
Published: May 2010

Abstract

Background

E. coli cells are rich in thiamine, most of it in the form of the cofactor thiamine diphosphate (ThDP). Free ThDP is the precursor for two triphosphorylated derivatives, thiamine triphosphate (ThTP) and the newly discovered adenosine thiamine triphosphate (AThTP). While, ThTP accumulation requires oxidation of a carbon source, AThTP slowly accumulates in response to carbon starvation, reaching ~15% of total thiamine. Here, we address the question whether AThTP accumulation in E. coli is triggered by the absence of a carbon source in the medium, the resulting drop in energy charge or other forms of metabolic stress.

Results
In minimal M9 medium, E. coli cells produce AThTP not only when energy substrates are lacking but also when their metabolization is inhibited. Thus AThTP accumulates in the presence of glucose, when glycolysis is blocked by iodoacetate, or in the presence lactate, when respiration is blocked by cyanide or anoxia. In both cases, ATP synthesis is impaired, but AThTP accumulation does not appear to be a direct consequence of reduced ATP levels. Indeed, in the CV2 E. coli strain (containing a thermolabile adenylate kinase), the ATP content is very low at 37°C, even in the presence of metabolizable substrates (glucose or lactate) and under these conditions, the cells produce ThTP but not AThTP. Furthermore, we show that ThTP inhibits AThTP accumulation. Therefore, we conclude that a low energy charge is not sufficient to trigger AThTP accumulation and the latter can only accumulate under conditions where no ThTP is synthesized. We further show that AThTP production can also be induced by the uncoupler CCCP but, unexpectedly, this requires the presence of pyruvate or a substrate yielding pyruvate (such a D-glucose or L-lactate). Under the conditions described, AThTP production is not different when RelA or SpoT mutants are used.

Conclusions
In E. coli, AThTP accumulates in response to two different conditions of metabolic stress: lack of energy substrates (or inhibition of their metabolization) and uncoupled pyruvate oxidation. Both conditions prevent bacterial growth. There is no obvious link with the stringent response or catabolite repression.
A descriptive analysis of child-relevant systematic reviews in the Cochrane Database of Systematic Reviews
Authors: Bow Simon , Klassen Jeffrey , Chisholm Annabritt , Tjosvold Lisa , Thomson Denise , Klassen Terry P , Moher David , Hartling Lisa 
Published: May 2010

Abstract

Background
Systematic reviews (SRs) are considered an important tool for decision-making. There has been no recent comprehensive identification or description of child-relevant SRs. A description of existing child-relevant SRs would help to identify the extent of available child-relevant evidence available in SRs and gaps in the evidence base where SRs are required. The objective of this study was to describe child-relevant SRs from the Cochrane Database of Systematic Reviews (CDSR, Issue 2, 2009).

Methods
SRs were assessed for relevance using pre-defined criteria. Data were extracted and entered into an electronic form. Univariate analyses were performed to describe the SRs overall and by topic area.

Results
The search yielded 1666 SRs; 793 met the inclusion criteria. 38% of SRs were last assessed as up-to-date prior to 2007. Corresponding authors were most often from the UK (41%). Most SRs (59%) examined pharmacological interventions. 53% had at least one external source of funding. SRs included a median of 7 studies (IQR 3, 15) and 679 participants (IQR 179, 2833). Of all studies, 48% included only children, and 27% only adults. 94% of studies were published in peer-reviewed journals. Primary outcomes were specified in 72% of SRs. Allocation concealment and the Jadad scale were used in 97% and 25% of SRs, respectively. Adults and children were analyzed separately in 12% of SRs and as a subgroup analysis in 14%. Publication bias was assessed in only 14% of SRs. A meta-analysis was conducted in 68% of SRs with a median of 5 trials (IQR 3, 9) each. Variations in these characteristics were observed across topic areas.

Conclusions
We described the methodological characteristics and rigour of child-relevant reviews in the CDSR. Many SRs are not up-to-date according to Cochrane criteria. Our study describes variation in conduct and reporting across SRs and reveals clinicians' ability to access child-specific data.
Design of the Anti-tuberculosis Drugs induced Adverse Reactions in China National Tuberculosis Prevention and Control Scheme Study (ADACS)
Authors: Xia Yin Yin , Hu Dai Yu , Liu Fei Ying , Wang Xiao Meng , Yuan Yan Li , Tu De Hua , Chen Yi Xin , Zhou Lin , Zhu Li Zhen , Gao Wei Wei , Wang Hong Yuan , Chen Da Fang , Yang Li , He Ping Ping , Li Xiao Ting , He Ying Jian , Sun Feng , Zhan Si Yan 
Published: May 2010

Abstract

Background
More than 1 million tuberculosis (TB) patients are receiving the standard anti-TB treatment provided by China National Tuberculosis Prevention and Control Scheme (CNTS) in China every year. Adverse reactions (ADRs) induced by anti-TB drugs could both do harm to patients and lead to anti-TB treatment failure. The ADACS aimed to explore ADRs' incidences, prognoses, economical and public health impacts for TB patients and TB control, and build a DNA bank of TB patients.

Methods/Design
Multiple study designs were adopted. Firstly, a prospective cohort with 4488 sputum smears positive pulmonary tuberculosis patients was established. Patients were followed up for 6-9 months in 52 counties of four regions. Those suspected ADRs should be checked and confirmed by Chinese State Food and Drug Administration (SFDA). Secondly, if the suspected ADR was anti-TB drug induced liver injury (ATLI), a nested case-control study would be performed which comprised choosing a matched control and doing a plus questionnaire inquiry. Thirdly, health economical data of ADRs would be collected to analyze financial burdens brought by ADRs and cost-effectiveness of ADRs' treatments. Fourthly, a drop of intravenous blood for each patient was taken and saved in FTA card for DNA banking and genotyping. Finally, the demographic, clinical, environmental, administrative and genetic data would be merged for the comprehensive analysis.

Discussion
ADACS will give an overview of anti-TB drugs induced ADRs' incidences, risk factors, treatments, prognoses, and clinical, economical and public health impacts for TB patients applying CNTS regimen in China, and provide suggestions for individualized health care and TB control policy.
Reduced evolvability of Escherichia coli MDS42, an IS-less cellular chassis for molecular and synthetic biology applications
Authors: Umenhoffer Kinga , Fehér Tamás , Balikó Gabriella , Ayaydin Ferhan , Pósfai János , Blattner Frederick R , Pósfai György 
Published: May 2010

Abstract

Background
Evolvability is an intrinsic feature of all living cells. However, newly emerging, evolved features can be undesirable when genetic circuits, designed and fabricated by rational, synthetic biological approaches, are installed in the cell. Streamlined-genome E. coli MDS42 is free of mutation-generating IS elements, and can serve as a host with reduced evolutionary potential.

Results
We analyze an extreme case of toxic plasmid clone instability, and show that random host IS element hopping, causing inactivation of the toxic cloned sequences, followed by automatic selection of the fast-growing mutants, can prevent the maintenance of a clone developed for vaccine production. Analyzing the molecular details, we identify a hydrophobic protein as the toxic byproduct of the clone, and show that IS elements spontaneously landing in the cloned fragment relieve the cell from the stress by blocking transcription of the toxic gene. Bioinformatics analysis of sequence reads from early shotgun genome sequencing projects, where clone libraries were constructed and maintained in E. coli, suggests that such IS-mediated inactivation of ectopic genes inhibiting the growth of the E. coli cloning host might happen more frequently than generally anticipated, leading to genomic instability and selection of altered clones.

Conclusions
Delayed genetic adaptation of clean-genome, IS-free MDS42 host improves maintenance of unstable genetic constructs, and is suggested to be beneficial in both laboratory and industrial settings.