bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distribution of Helicity, CAPE, and Shear in Tropical Cyclones
Authors: Molinari John , Vollaro David 
Published: August 2009

Abstract
The previous study of helicity, CAPE, and shear in Hurricane Bonnie (1998) was extended to all eight tropical cyclones sampled by NASA during the Convection and Moisture Experiments (CAMEX). Storms were categorized as having large or small ambient vertical wind shear, with 10 m s−1 as the dividing line. In strongly sheared storms, the downshear mean helicity exceeded the upshear mean by a factor of 4. As in the previous study, the helicity differences resulted directly from the tropical cyclone response to ambient shear, with enhanced in-up-out flow and veering of the wind with height present downshear. CAPE in strongly sheared storms was 60% larger downshear. Mean inflow near the surface and the depth of the inflow layer each were 4 times larger downshear. At more than 30% of observation points outside the 100-km radius in the downshear right quadrant, midlatitude empirical parameters indicated a strong likelihood of supercells. No such points existed upshear in highly sheared storms. Much smaller upshear–downshear differences and little likelihood of severe cells occurred in storms with ambient wind shear below 10 m s−1. In addition to these azimuthal asymmetries, highly sheared storms produced 30% larger area-averaged CAPE and double the area-averaged helicity versus relatively unsheared storms. The vortex-scale increase in these quantities lessens the negative impact of large vertical wind shear.
Cold Events over Southern Australia: Synoptic Climatology and Hemispheric Structure
Authors: Ashcroft Linden Claire , Pezza Alexandre Bernardes , Simmonds Ian 
Published: August 2009

Abstract
Cold events (CEs) are an important feature of southern Australian weather. Unseasonably cold conditions can have a significant impact on Australia’s agricultural industry and other aspects of society. In this study the bottom 0.4% of maximum temperatures in Melbourne and Perth from the 1958–2006 period are defined as CEs, representing the large-scale patterns affecting most of extratropical Australia. Compiling 6-hourly progressions of the tracks of the cyclones and anticyclones that are geostrophically associated with CEs gives for the first time a detailed synoptic climatology over the area.
The anticyclone tracks display a “cloud” of high density across the Indian Ocean, which is linked, in the mean, to weak but significant negative SST anomalies in the region. The cyclone tracks display much variability, with system origins ranging from subpolar to tropical. Several CEs are found to involve tropical and extratropical interaction or extratropical transition of originally tropical cyclones (hurricanes). CE-associated systems travel farther and exhibit longer life spans than similar, non-CE systems. Upper-level analyses indicate the presence of a wave train originating more than 120° west of the CE. This pattern greatly intensifies over the affected area in conjunction with a merging of the subpolar and subtropical jets. The upper-level wave train is present up to five days before the CE. The absence of large orographic features in Australia highlights the importance of wave amplification in CE occurrence. No consistent trend in CE intensity over the period is found, but a significant negative trend in event frequency is identified for both Melbourne and Perth.
An Object-Oriented Multiscale Verification Scheme
Authors: Lack Steven A. , Limpert George L. , Fox Neil I. 
Published: August 2009

Abstract
Object-oriented verification methodology is becoming more and more common in the evaluation of model performance on high-resolution grids. The research herein describes an advanced version of an object-oriented approach that involves a combination of object identification on multiple scales with Procrustes shape analysis techniques. The multiscale object identification technique relies heavily on a novel Fourier transform approach to associate the signals within convection to different spatial scales. Other features of this new verification scheme include using a weighted cost function that can be user defined for object matching using different criteria, delineating objects that are more linear in character from those that are more cellular, and tagging object matches as hits, misses, or false alarms. Although the scheme contains a multiscale approach for identifying convective objects, standard minimum intensity and minimum size thresholds can be set when desirable. The method was tested as part of a spatial verification intercomparison experiment utilizing a combination of synthetic data and real cases from the Storm Prediction Center (SPC)/NSSL Weather Research and Forecasting (WRF) model Spring Program 2005. The resulting metrics, including error measures from differences in matched objects due to displacement, dilation, rotation, and intensity, from these cases run through this new, robust verification scheme are shown.
Ensemble-Based Sensitivity Analysis Applied to African Easterly Waves
Authors: Torn Ryan D. 
Published: August 2009

Abstract
An ensemble Kalman filter (EnKF) coupled to the Advanced Research version of the Weather Research and Forecasting (WRF) model is used to generate ensemble analyses and forecasts of a strong African easterly wave (AEW) during the African Monsoon Multidisciplinary Analysis field campaign. Ensemble sensitivity analysis is then used to evaluate the impacts of initial condition errors on AEW amplitude and position forecasts at two different initialization times.
WRF forecasts initialized at 0000 UTC 8 September 2006, prior to the amplification of the AEW, are characterized by large variability in evolution as compared to forecasts initialized 48 h later when the AEW is within a denser observation network. Short-lead-time amplitude forecasts are most sensitive to the midtropospheric meridional winds, while at longer lead times, midtropospheric θe errors have equal or larger impacts. For AEW longitude forecasts, the largest sensitivities are associated with the θe downstream of the AEW and, to a lesser extent, the meridional winds. Ensemble predictions of how initial condition errors impact the AEW amplitude and position compare qualitatively well with perturbed integrations of the WRF model.
Much of the precipitation associated with the AEW is generated by the Kain–Fritsch cumulus parameterization, thus the initial-condition sensitivities are also computed for ensemble forecasts that employ the Betts–Miller–Janjić and Grell cumulus parameterization schemes, and for a high-resolution nested domain with explicit convection, but with the same initial conditions. While the 12-h AEW amplitude forecast is characterized by consistent initial-condition sensitivity among the different schemes, there is greater variability among methods beyond 24 h. In contrast, the AEW longitude forecast is sensitive to the downstream thermodynamic profile with all cumulus schemes.
Working in the Public Sector
Authors: Coffey Margaret , Dugdill Lindsey , Tattersall Andy 
Published: August 2009

• Summary: This article explores working conditions and quality of life in social services. The article focuses on the qualitative findings generated throughout a phased study comprising: in-depth interviews ( n = 8) used to develop an original questionnaire; a large survey ( n = 1237) of staff in two social service departments in the UK; and focus groups ( n = 4) used in Children and Families Division to develop a better understanding of the difficulties experienced and develop context-specific interventions aimed at reducing or eliminating these stressors. It also reports quantitative findings in respect stress (measured using the General Health Questionnaire — GHQ-12). • Findings: The survey findings indicated that 36 percent ( n = 392) of the respondents were considered to be suffering from mental distress. Children and Families Division was worst affected, reporting the highest levels of absenteeism and poorest well-being. The qualitative findings were summarized into five broad themes: organizational culture and function; control; lack of resources; responsibility for people; and the rate and pace of change, which were incorporated into a model. • Application: The article suggests that during times of change a thorough understanding of working conditions in the public sector are a fundamental prerequisite to developing interventions aimed at improving them. Additionally, the model clearly identifies a number of factors that are ‘organizational’, rather than being intrinsic to working in social services.
Regulation of myelopoiesis through syntenin-mediated modulation of IL-5 receptor output
Authors: Beekman Jeffrey M. , Verhagen Liesbeth P. , Geijsen Niels , Coffer Paul J. 
Published: August 2009

AbstractThe granulocyte-macrophage colony-stimulating factor (GM-CSF)/interleukin (IL)–3/IL-5 receptor family regulates the production and function of myeloid cells. These cytokines signal through receptor complexes that consist of unique ligand-binding α-chains and common signaling β-chains. IL-5 is distinct from IL-3 and GM-CSF in its capacity to induce eosinophil development, however, the molecular mechanisms that generate functional diversity within this receptor family are mostly unknown. Here, we characterized the selective IL-5Rα–binding adapter protein syntenin in IL-5R function. Syntenin and IL-5Rα colocalize at the plasma membrane and in early endosomal compartments. Manipulation of syntenin expression by ectopic expression or knockdown selectively modulated IL-5R but not GM-CSF receptor signaling, and severely affected IL-5–induced eosinophil differentiation from primary human CD34+ hematopoietic progenitor cells. We found syntenin up-regulated during eosinophilopoiesis but down-regulated during neutropoiesis. Syntenin forms complexes with multiple IL-5Rα chains, suggesting that syntenin-enhanced IL-5R output may result from stabilization of an IL-5–induced oligomeric receptor complex. These data demonstrate that cytokine-specific functions can be transduced by unique receptor α-chain–associating adapter proteins.
Donor-recipient mismatches in MHC class I chain-related gene A in unrelated donor transplantation lead to increased incidence of acute graft-versus-host disease
Authors: Parmar Simrit , del Lima Marcos , Zou Yizhou , Patah Poliana A. , Liu Ping , Cano Pedro , Rondon Gabriela , Pesoa Susana , de Padua Silva Leandro , Qazilbash Muzaffar H. , Hosing Chitra , Popat Uday , Kebriaei Partow , Shpall Elizabeth J. , Giralt Sergio , Champlin Richard E. , Stastny Peter , Fernandez-Vina Marcelo 
Published: August 2009

AbstractThe polymorphic products of major histocompatibility complex class I–related chain A (MICA) genes are important in solid organ transplantation rejection. MICA expression is limited to gut epithelium and may play a role in triggering acute graft-versus-host disease (aGVHD). A total of 236 recipients of unrelated donor transplantation were studied. Donor-recipient human leukocyte antigen (HLA) match was 10/10 human leukocyte antigen (HLA-A, -B, -C, -DRB1, -DQB1) in 73% and MICA mismatch in 8.4%. Because of physical vicinity of the loci, MICA mismatch was significantly associated with mismatch at HLA-B and HLA-C. A higher rate of grade II-IV aGVHD was seen in MICA-mismatched patients (80% vs 40%, P = .003) irrespective of degree of HLA matching (HLA 10/10 match: 75% vs 39%, P = .02) and HLA any mismatch (83% vs 46%, P = .003). The rate of grade II-IV gastrointestinal aGVHD was also higher in MICA-mismatched patients (35% vs 17%, P = .05). We conclude that MICA may represent novel a transplantation antigen recognized by human allogeneic T cells. This study was registered at ClinicalTrials.gov (Identifier NCT00506922).
Resolving deconvolution ambiguity in gene alternative splicing
Authors: She Yiyuan , Hubbell Earl , Wang Hui 
Published: August 2009

Abstract

Background
For many gene structures it is impossible to resolve intensity data uniquely to establish abundances of splice variants. This was empirically noted by Wang et al. in which it was called a "degeneracy problem". The ambiguity results from an ill-posed problem where additional information is needed in order to obtain an unique answer in splice variant deconvolution.

Results
In this paper, we analyze the situations under which the problem occurs and perform a rigorous mathematical study which gives necessary and sufficient conditions on how many and what type of constraints are needed to resolve all ambiguity. This analysis is generally applicable to matrix models of splice variants. We explore the proposal that probe sequence information may provide sufficient additional constraints to resolve real-world instances. However, probe behavior cannot be predicted with sufficient accuracy by any existing probe sequence model, and so we present a Bayesian framework for estimating variant abundances by incorporating the prediction uncertainty from the micro-model of probe responsiveness into the macro-model of probe intensities.

Conclusion
The matrix analysis of constraints provides a tool for detecting real-world instances in which additional constraints may be necessary to resolve splice variants. While purely mathematical constraints can be stated without error, real-world constraints may themselves be poorly resolved. Our Bayesian framework provides a generic solution to the problem of uniquely estimating transcript abundances given additional constraints that themselves may be uncertain, such as regression fit to probe sequence models. We demonstrate the efficacy of it by extensive simulations as well as various biological data.
Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels
Authors: Yip Kevin Y , Kim Philip M , McDermott Drew , Gerstein Mark 
Published: August 2009

Abstract

Background
Proteins interact through specific binding interfaces that contain many residues in domains. Protein interactions thus occur on three different levels of a concept hierarchy: whole-proteins, domains, and residues. Each level offers a distinct and complementary set of features for computationally predicting interactions, including functional genomic features of whole proteins, evolutionary features of domain families and physical-chemical features of individual residues. The predictions at each level could benefit from using the features at all three levels. However, it is not trivial as the features are provided at different granularity.

Results
To link up the predictions at the three levels, we propose a multi-level machine-learning framework that allows for explicit information flow between the levels. We demonstrate, using representative yeast interaction networks, that our algorithm is able to utilize complementary feature sets to make more accurate predictions at the three levels than when the three problems are approached independently. To facilitate application of our multi-level learning framework, we discuss three key aspects of multi-level learning and the corresponding design choices that we have made in the implementation of a concrete learning algorithm. 1) Architecture of information flow: we show the greater flexibility of bidirectional flow over independent levels and unidirectional flow; 2) Coupling mechanism of the different levels: We show how this can be accomplished via augmenting the training sets at each level, and discuss the prevention of error propagation between different levels by means of soft coupling; 3) Sparseness of data: We show that the multi-level framework compounds data sparsity issues, and discuss how this can be dealt with by building local models in information-rich parts of the data. Our proof-of-concept learning algorithm demonstrates the advantage of combining levels, and opens up opportunities for further research.

Availability
The software and a readme file can be downloaded at http://networks.gersteinlab.org/mll. The programs are written in Java, and can be run on any platform with Java 1.4 or higher and Apache Ant 1.7.0 or higher installed. The software can be used without a license.
Comparative genomic analysis uncovers 3 novel loci encoding type six secretion systems differentially distributed in Salmonella serotypes
Authors: Blondel Carlos J , Jiménez Juan C , Contreras Inés , Santiviago Carlos A 
Published: August 2009

Abstract

Background
The recently described Type VI Secretion System (T6SS) represents a new paradigm of protein secretion in bacteria. A number of bioinformatic studies have been conducted to identify T6SS gene clusters in the available bacterial genome sequences. According to these studies, Salmonella harbors a unique T6SS encoded in the Salmonella Pathogenicity Island 6 (SPI-6). Since these studies only considered few Salmonella genomes, the present work aimed to identify novel T6SS loci by in silico analysis of every genome sequence of Salmonella available.

Results
The analysis of sequencing data from 44 completed or in progress Salmonella genome projects allowed the identification of 3 novel T6SS loci. These clusters are located in differentially-distributed genomic islands we designated SPI-19, SPI-20 and SPI-21, respectively. SPI-19 was identified in a subset of S. enterica serotypes including Dublin, Weltevreden, Agona, Gallinarum and Enteritidis. In the later, an internal deletion eliminated most of the island. On the other hand, SPI-20 and SPI-21 were restricted to S. enterica subspecies arizonae (IIIa) serotype 62:z4,z23:-. Remarkably, SPI-21 encodes a VgrG protein containing a C-terminal extension similar to S-type pyocins of Pseudomonas aeruginosa. This is not only the first evolved VgrG described in Salmonella, but also the first evolved VgrG including a pyocin domain described so far in the literature. In addition, the data indicate that SPI-6 T6SS is widely distributed in S. enterica and absent in serotypes Enteritidis, Gallinarum, Agona, Javiana, Paratyphi B, Virchow, IIIa 62:z4,z23:- and IIIb 61:1,v:1,5,(7). Interestingly, while some serotypes harbor multiple T6SS (Dublin, Weltvreden and IIIa 62:z4,z23:-) others do not encode for any (Enteritidis, Paratyphi B, Javiana, Virchow and IIIb 61:1,v:1,5,(7)). Comparative and phylogenetic analyses indicate that the 4 T6SS loci in Salmonella have a distinct evolutionary history. Finally, we identified an orphan Hcp-like protein containing the Hcp/COG3157 domain linked to a C-terminal extension. We propose to designate this and related proteins as "evolved Hcps".

Conclusion
Altogether, our data suggest that (i) the Salmonella T6SS loci were acquired by independent lateral transfer events and (ii) evolved to contribute in the adaptation of the serotypes to different lifestyles and environments, including animal hosts. Notably, the presence of an evolved VgrG protein related to pyocins suggests a novel role for T6SS in bacterial killing. Future studies on the roles of the identified T6SS loci will expand our knowledge on Salmonella pathogenesis and host specificity.
Genome-wide computational identification of functional RNA elements in Trypanosoma brucei
Authors: Mao Yuan , Najafabadi Hamed Shateri , Salavati Reza 
Published: August 2009

Abstract

Background
Post-transcriptional regulation of gene expression is the dominant regulatory mechanism in trypanosomatids as their mRNAs are transcribed from polycistronic units. A few cis-acting RNA elements in 3'-untranslated regions of mRNAs have been identified in trypanosomatids, which affect the mRNA stability or translation rate in different life stages of these parasites. Other functional RNAs (fRNAs) also play essential roles in these organisms. However, there has been no genome-wide analysis for identification of fRNAs in trypanosomatids.

Results
Functional RNAs, including non-coding RNAs (ncRNAs) and cis-acting RNA elements involved in post-transcriptional gene regulation, were predicted based on two independent computational analyses of the genome of Trypanosoma brucei. In the first analysis, the predicted candidate ncRNAs were identified based on conservation with the related trypanosomatid Leishmania braziliensis. This prediction had a substantially low estimated false discovery rate, and a considerable number of the predicted ncRNAs represented novel classes with unknown functions. In the second analysis, we identified a number of function-specific regulatory motifs, based on which we devised a classifier that can be used for homology-independent function prediction in T. brucei.

Conclusion
This first genome-wide analysis of fRNAs in trypanosomatids restricts the search space of experimental approaches and, thus, can significantly expedite the process of characterization of these elements. Our classifier for function prediction based on cis-acting regulatory elements can also, in combination with other methods, provide the means for homology-independent annotation of trypanosomatid genomes.
Moderate strength (0.23–0.28 T) static magnetic fields (SMF) modulate signaling and differentiation in human embryonic cells
Authors: Wang Zhiyun , Sarje Anshu , Che Pao-Lin , Yarema Kevin J 
Published: August 2009

Abstract

Background
Compelling evidence exists that magnetic fields modulate living systems. To date, however, rigorous studies have focused on identifying the molecular-level biosensor (e.g., radical ion pairs or membranes) or on the behavior of whole animals leaving a gap in understanding how molecular effects are translated into tissue-wide and organism-level responses. This study begins to bridge this gulf by investigating static magnetic fields (SMF) through global mRNA profiling in human embryonic cells coupled with software analysis to identify the affected signaling pathways.

Results
Software analysis of gene expression in cells exposed to 0.23–0.28 T SMF showed that nine signaling networks responded to SMF; of these, detailed biochemical validation was performed for the network linked to the inflammatory cytokine IL-6. We found the short-term (<24 h) activation of IL-6 involved the coordinate up-regulation of toll-like receptor-4 (TLR4) with complementary changes to NEU3 and ST3GAL5 that reduced ganglioside GM3 in a manner that augmented the activation of TLR4 and IL-6. Loss of GM3 also provided a plausible mechanism for the attenuation of cellular responses to SMF that occurred over longer exposure periods. Finally, SMF-mediated responses were manifest at the cellular level as morphological changes and biochemical markers indicative of pre-oligodendrocyte differentiation.

Conclusion
This study provides a framework describing how magnetic exposure is transduced from a plausible molecular biosensor (lipid membranes) to cell-level responses that include differentiation toward neural lineages. In addition, SMF provided a stimulus that uncovered new relationships – that exist even in the absence of magnetic fields – between gangliosides, the time-dependent regulation of IL-6 signaling by these glycosphingolipids, and the fate of embryonic cells.