bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating Low-Cloud Simulation from an Upgraded Multiscale Modeling Framework Model. Part II: Seasonal Variations over the Eastern Pacific
Authors: Xu Kuan-Man , Cheng Anning 
Published: January 2013

Abstract
The eastern Pacific is a climatologically important region. Conventional coupled atmosphere–ocean general circulation models produce positive sea surface temperature biases of 2–5 K in this region because of insufficient stratocumulus clouds. In this study, a global multiscale modeling framework (MMF), which replaces traditional cloud parameterizations with a 2D cloud-resolving model (CRM) in each atmospheric column, is used to examine the seasonal variations of this Pacific region. The CRM component contains an advanced third-order turbulence closure, helping it to better simulate boundary layer turbulence and low-level clouds. Compared to available satellite observations of cloud amount, liquid water path, cloud radiative effects, and precipitation, this MMF produces realistic seasonal variations of the eastern Pacific region, although there are some disagreements in the exact location of maximum cloudiness centers in the Peruvian region and the intensity of ITCZ precipitation. Analyses of profile- and subcloud-based decoupling measures reveal very small amplitudes of seasonal variations in the decoupling strength in the subtropics except for those regions off the subtropical coasts where the decoupling measures suggest that the boundary layers should be well coupled in all four seasons. In the Peruvian and Californian regions, the seasonal variations of low clouds are related to those in the boundary layer height and the strength of inversion. Factors that influence the boundary layer and the inversion, such as solar incident radiation, subcloud-layer turbulent mixing, and large-scale subsidence, can collectively explain the seasonal variations of low clouds rather than the deepening–warming mechanism of Bretherton and Wyant cited in earlier studies.
Evaluation of ASCAT-Based Daily Gridded Winds in the Tropical Indian Ocean*
Authors: Sivareddy S. , Ravichandran M. , Girishkumar M. S. 
Published: January 2013

AbstractThe quality of daily gridded Advanced Scatterometer (ASCAT; DASCAT) blended winds is examined in the tropical Indian Ocean using 3-day running mean gridded Quick Scatterometer (QuikSCAT; QSCAT) winds and in situ daily winds from the Research Moored Array for African–Asian–Australian Monsoon Analysis and Prediction (RAMA). The primary objective of this study is to examine whether DASCAT is a reliable replacement for the widely used QSCAT wind products. Spatial distributions of DASCAT and QSCAT winds show good agreement in speed and direction, except over a few localized regions. The study finds a significant spatial coherence between rainfall and the regions of discrepancy between DASCAT and QSCAT. Comparison of DASCAT and QSCAT wind products with RAMA moorings indicates that DASCAT better captures the overall wind variability compared to QSCAT, especially during rainy and low wind (&lt;5 m s−1) conditions. The root-mean-square of the RAMA–DASCAT (RAMA–QSCAT) difference during rainfall in the zonal and meridional winds is 1.4 and 1.6 m s−1 (2.7 and 2.0 m s−1), respectively. The present study indicates that the DASCAT blended wind product is a reliable alternative to QSCAT in the tropical Indian Ocean.
Large-Scale Influences on the Evolution of Winter Subtropical Maritime Cyclones Affecting Australia’s East Coast
Authors: Browning Stuart A. , Goodwin Ian D. 
Published: January 2013

Abstract
Subtropical maritime low pressure systems frequently impact Australia’s eastern seaboard. Closed circulation lows in the Tasman Sea region are termed East Coast Cyclones (ECC); they can evolve in a range of climatic environments and have proven most destructive during the late autumn–winter period. Using criteria based on pressure gradients, inferred wind field, and duration, an objectively determined database of ECC occurrences is established to explore large-scale influences on ECC evolution. Subclassification based on evolutionary trajectory reveals two dominant storm types during late autumn–winter: easterly trough lows (ETL) and southern secondary lows (SSL). Synoptic composites are used to investigate the climatological evolution of each storm type. ETL cyclogenesis occurs along the eastern seaboard at the confluence of warm moist subtropical easterlies and cool air over the continent that is advected from higher latitudes. SSL develop when a cold extratropical cyclone moves equatorward and interacts with warm moist conditions in the Tasman Sea. At seasonal time scales, a complex interplay of tropical and extratropical influences contributes to high-frequency storm seasons. ETL are more frequent during neutral or positive phases of the El Niño–Southern Oscillation, cool sea surface temperature anomalies (SSTAs) in the tropical Indian Ocean, and neutral to positive southern annular mode phases. SSL are more frequent during years with warm SSTAs in the eastern Indian Ocean, warm SSTAs in the western Pacific, and high-latitude blocking.
Ensemble-Based Exigent Analysis. Part I: Estimating Worst-Case Weather-Related Forecast Damage Scenarios
Authors: Gombos Daniel , Hoffman Ross N. 
Published: January 2013

AbstractExigent analysis supplements an ensemble forecast of weather-related damage with a map of the worst-case scenario (WCS), a multivariate confidence bound of the damage. For multivariate Gaussian ensembles, ensemble-based exigent analysis uses a Lagrange multiplier technique to identify the unique maximizing damage map at a given uncertainty level based on the ensemble-estimated covariance of the damage. Exigent analysis is applied to two case studies. First, using ensemble forecasts of 2-m temperature and estimates of the number of inhabitants at each location, exigent analysis is applied to forecast the worst-case heating demand for a large portion of the United States on 8–9 January 2010. The WCS at the 90th percentile results in only 1.26% more heating demand than the ensemble mean. Second, using ensemble forecasts of 2-m temperature and estimates of the number of citrus trees at each location, exigent analysis is applied to forecast the worst-case freeze damage to Florida citrus trees on 11 January 2010. For this case study, the WCS at the 90th percentile damages about 14.2 million trees, about 4.3 times more than the ensemble mean.
Ensemble-Based Exigent Analysis. Part II: Using Ensemble Regression to Estimate Conditions Antecedent to Worst-Case Forecast Damage Scenarios
Authors: Gombos Daniel , Hoffman Ross N. 
Published: January 2013

Abstract
In Part I of this series on ensemble-based exigent analysis, a Lagrange multiplier minimization technique is used to estimate the exigent damage state (ExDS), the “worst case” with respect to a user-specified damage function and confidence level. Part II estimates the conditions antecedent to the ExDS using ensemble regression (ER), a linear inverse technique that employs an ensemble-estimated mapping matrix to propagate a predictor perturbation state into a predictand perturbation state. By propagating the exigent damage perturbations (ExDPs) from the heating degree days (HDD) and citrus tree case studies of Part I into their respective antecedent forecast state vectors, ER estimates the most probable antecedent perturbations expected to evolve into these ExDPs. Consistent with the physical expectations of a trough that precedes and coincides with the anomalously cold temperatures during the HDD case study, the ER-estimated antecedent 300-hPa geopotential height trough is approximately 59 and 17 m deeper than the ensemble mean at around the time of the ExDP as well as 24 h earlier, respectively. Statistics of the explained variance and from leave-one-out cross-validation runs indicate that the expected errors of these ER-estimated perturbations are smaller for the HDD case study than for the citrus tree case study.
Sports participation styles revisited: A time-trend study in Belgium from the 1970s to the 2000s
Authors: Borgers Julie , Thibaut Erik , Vandermeerschen Hanne , Vanreusel Bart , Vos Steven , Scheerder Jeroen 
Published: January 2013

Social changes have been influencing determinants for sports participation since the introduction of the Sport for All ideology in the early 1970s. Consistent with Crum’s sportisation theory, today’s modes of sports practices, as well as the network of sport services, have diversified and de-traditionalised. As part of a research tradition, this contribution aims at analysing changes in sports participation styles in kinesiology students in Belgium during the past four decades (1972–2009). The distinct target group was supposed to fulfil a trend-setting role in the area of active sports participation. Data were obtained from a standardised retrospective questionnaire on leisure-time sports participation. Using standardised methods, Principal Component Analysis was used to identify patterns of sports participation. The results show a diversification of sports participation styles until the 1980s, followed by an intensification of basic style components since the 1990s. Sports participation styles between 1999 and 2009 are subdivided into multiple distinct traditional and non-traditional components, with growing emphasis on non-traditional, alternative practices. Newly observed components in 2009 are discussed in relation to previous time intervals and trends in sports participation.
Standardization of bleeding assessment in immune thrombocytopenia: report from the International Working Group
Authors: Rodeghiero Francesco , Michel Marc , Gernsheimer Terry , Ruggeri Marco , Blanchette Victor , Bussel James B. , Cines Douglas B. , Cooper Nichola , Godeau Bertrand , Greinacher Andreas , Imbach Paul , Khellaf Mehdi , Klaassen Robert J. , Kühne Thomas , Liebman Howard , Mazzucconi Maria Gabriella , Newland Adrian , Pabinger Ingrid , Tosetto Alberto , Stasi Roberto 
Published: January 2013

Abstract
In a previous publication on new terminology, definitions, and outcome criteria for immune thrombocytopenia (ITP), the International Working Group (IWG) on ITP acknowledged that response to treatment should consist of clinically meaningful end points such as bleeding manifestations and that platelet count may not be the ideal parameter for capturing the benefits of therapy. The IWG now proposes a consensus-based ITP-specific bleeding assessment tool (ITP-BAT) with definitions and terminology consistent with those adopted for other bleeding disorders. Bleeding manifestations were grouped into three major domains: skin (S), visible mucosae (M), and organs (O), with gradation of severity (SMOG). Each bleeding manifestation is assessed at the time of examination. Severity is graded from 0 to 3 or 4, with grade 5 for any fatal bleeding. Bleeding reported by the patient without medical documentation is graded 1. Within each domain, the same grade is assigned to bleeding manifestations of similar clinical impact. The “worst bleeding manifestation since the last visit” (observation period) is graded (a suitable database collection form is provided), and the highest grade within each domain is recorded. The SMOG system provides a consistent description of the bleeding phenotype in ITP, and the IWG unanimously supports its adoption and validation in future clinical studies.
Neurokinin-1 receptor agonists bias therapeutic dendritic cells to induce type 1 immunity by licensing host dendritic cells to produce IL-12
Authors: Janelsins Brian M. , Sumpter Tina L. , Tkacheva Olga A. , Rojas-Canales Darling M. , Erdos Geza , Mathers Alicia R. , Shufesky William J. , Storkus Walter J. , Falo Louis D. , Morelli Adrian E. , Larregina Adriana T. 
Published: January 2013

Key Points
Therapeutic DCs stimulated via NK1R stimulate type 1–biased immunity.
Autologous stem cell transplantation for enteropathy-associated T-cell lymphoma: a retrospective study by the EBMT
Authors: Jantunen Esa , Boumendil Ariane , Finel Herve , Luan Jian-Jian , Johnson Peter , Rambaldi Alessandro , Haynes Andrew , Duchosal Michel A. , Bethge Wolfgang , Biron Pierre , Carlson Kristina , Craddock Charles , Rudin Claudius , Finke Jurgen , Salles Gilles , Kroschinsky Frank , Sureda Anna , Dreger Peter 
Published: January 2013

Key Points
ASCT provides long-term remission in the majority of EATL patients transplanted in first complete or partial remission. ASCT should be considered in transplant-eligible EATL patients.
Exploring biological interaction networks with tailored weighted quasi-bicliques
Authors: Chang Wen-Chieh , Vakati Sudheer , Krause Roland , Eulenstein Oliver 
Published: January 2013

Abstract

Background
Biological networks provide fundamental insights into the functional characterization of genes and their products, the characterization of DNA-protein interactions, the identification of regulatory mechanisms, and other biological tasks. Due to the experimental and biological complexity, their computational exploitation faces many algorithmic challenges.

Results
We introduce novel weighted quasi-biclique problems to identify functional modules in biological networks when represented by bipartite graphs. In difference to previous quasi-biclique problems, we include biological interaction levels by using edge-weighted quasi-bicliques. While we prove that our problems are NP-hard, we also describe IP formulations to compute exact solutions for moderately sized networks.

Conclusions
We verify the effectiveness of our IP solutions using both simulation and empirical data. The simulation shows high quasi-biclique recall rates, and the empirical data corroborate the abilities of our weighted quasi-bicliques in extracting features and recovering missing interactions from biological networks.
High-performance blob-based iterative three-dimensional reconstruction in electron tomography using multi-GPUs
Authors: Wan Xiaohua , Zhang Fa , Chu Qi , Liu Zhiyong 
Published: January 2013

Abstract

Background
Three-dimensional (3D) reconstruction in electron tomography (ET) has emerged as a leading technique to elucidate the molecular structures of complex biological specimens. Blob-based iterative methods are advantageous reconstruction methods for 3D reconstruction in ET, but demand huge computational costs. Multiple graphic processing units (multi-GPUs) offer an affordable platform to meet these demands. However, a synchronous communication scheme between multi-GPUs leads to idle GPU time, and a weighted matrix involved in iterative methods cannot be loaded into GPUs especially for large images due to the limited available memory of GPUs.

Results
In this paper we propose a multilevel parallel strategy combined with an asynchronous communication scheme and a blob-ELLR data structure to efficiently perform blob-based iterative reconstructions on multi-GPUs. The asynchronous communication scheme is used to minimize the idle GPU time so as to asynchronously overlap communications with computations. The blob-ELLR data structure only needs nearly 1/16 of the storage space in comparison with ELLPACK-R (ELLR) data structure and yields significant acceleration.

Conclusions
Experimental results indicate that the multilevel parallel scheme combined with the asynchronous communication scheme and the blob-ELLR data structure allows efficient implementations of 3D reconstruction in ET on multi-GPUs.
GxcC connects Rap and Rac signaling during Dictyostelium development
Authors: Plak Katarzyna , Veltman Douwe , Fusetti Fabrizia , Beeksma Jetze , Rivero Francisco , Van Haastert Peter JM , Kortholt Arjan 
Published: January 2013

Abstract

Background
Rap proteins belong to the Ras family of small G-proteins. Dictyostelium RapA is essential and implicated in processes throughout the life cycle. In early development and chemotaxis competent cells RapA induces pseudopod formation by activating PI3K and it regulates substrate attachment and myosin disassembly via the serine/threonine kinase Phg2. RapA is also important in late development, however so far little is known about the downstream effectors of RapA that play a role in this process.

Results
Here we show that cells expressing constitutively active RapA exhibit a high level of Rac activation. With a pull-down screen coupled to mass spectrometry, we identified the Rac specific guanine nucleotide exchange factor, GxcC, as Rap binding partner. GxcC binds directly and specifically to active RapA and binds to a subset of Dictyostelium Rac proteins. Deletion studies revealed that this pathway is involved in regulating Dictyostelium development.

Conclusions
GxcC provides a novel link between Rap and Rac signalling and is one of the Rap effectors regulating the progression of multicellular development.
Comparison and contrast of genes and biological pathways responding to Marek’s disease virus infection using allele-specific expression and differential expression in broiler and layer chickens
Authors: Perumbakkam Sudeep , Muir William M , Black-Pyrkosz Alexis , Okimoto Ron , Cheng Hans H 
Published: January 2013

Abstract

Background
Marek’s disease (MD) is a commercially important neoplastic disease of chickens caused by the Marek’s disease virus (MDV), a naturally occurring oncogenic alphaherpesvirus. Enhancing MD genetic resistance is desirable to augment current vaccines and other MD control measures. High throughput sequencing was used to profile splenic transcriptomes from individual F1 progeny infected with MDV at 4 days of age from both outbred broilers (meat-type) and inbred layer (egg-type) chicken lines that differed in MD genetic resistance. The resulting information was used to identify SNPs, genes, and biological pathways exhibiting allele-specific expression (ASE) in response to MDV infection in each type of chicken. In addition, we compared and contrasted the results of pathway analyses (ASE and differential expression (DE)) between chicken types to help inform on the biological response to MDV infection.

Results
With 7 individuals per line and treatment group providing high power, we identified 6,132 single nucleotide polymorphisms (SNPs) in 4,768 genes and 4,528 SNPs in 3,718 genes in broilers and layers, respectively, that exhibited ASE in response to MDV infection. Furthermore, 548 and 434 genes in broilers and layers, respectively, were found to show DE following MDV infection. Comparing the datasets, only 72 SNPs and 850 genes for ASE and 20 genes for DE were common between the two bird types. Although the chicken types used in this study were genetically different, at the pathway level, both TLR receptor and JAK/STAT signaling pathways were enriched as well as exhibiting a high proportion of ASE genes, especially at the beginning of both above mentioned regulatory pathways.

Conclusions
RNA sequencing with adequate biological replicates is a powerful approach to identify high confidence SNPs, genes, and pathways that are associated with transcriptional response to MDV infection. In addition, the SNPs exhibiting ASE in response to MDV infection provide a strong foundation for determining the extent to which variation in expression influences MD incidence plus yield genetic markers for genomic selection. However, given the paucity of overlap among ASE SNP sets (broilers vs. layers), it is likely that separate screens need to be incorporated for each population. Finally, comparison of gene lists obtained between these two diverse chicken types indicate the TLR and JAK/STAT signaling are conserved when responding to MDV infection and may be altered by selection of genes exhibiting ASE found at the start of each pathway.
UtroUp is a novel six zinc finger artificial transcription factor that recognises 18 base pairs of the utrophin promoter and efficiently drives utrophin upregulation
Authors: Onori Annalisa , Pisani Cinzia , Strimpakos Georgios , Monaco Lucia , Mattei Elisabetta , Passananti Claudio , Corbi Nicoletta 
Published: January 2013

Abstract

Background
Duchenne muscular dystrophy (DMD) is the most common X-linked muscle degenerative disease and it is due to the absence of the cytoskeletal protein dystrophin. Currently there is no effective treatment for DMD. Among the different strategies for achieving a functional recovery of the dystrophic muscle, the upregulation of the dystrophin-related gene utrophin is becoming more and more feasible.

Results
We have previously shown that the zinc finger-based artificial transcriptional factor “Jazz” corrects the dystrophic pathology in mdx mice by upregulating utrophin gene expression. Here we describe a novel artificial transcription factor, named “UtroUp”, engineered to further improve the DNA-binding specificity. UtroUp has been designed to recognise an extended DNA target sequence on both the human and mouse utrophin gene promoters. The UtroUp DNA-binding domain contains six zinc finger motifs in tandem, which is able to recognise an 18-base-pair DNA target sequence that statistically is present only once in the human genome. To achieve a higher transcriptional activation, we coupled the UtroUp DNA-binding domain with the innovative transcriptional activation domain, which was derived from the multivalent adaptor protein Che-1/AATF. We show that the artificial transcription factor UtroUp, due to its six zinc finger tandem motif, possesses a low dissociation constant that is consistent with a strong affinity/specificity toward its DNA-binding site. When expressed in mammalian cell lines, UtroUp promotes utrophin transcription and efficiently accesses active chromatin promoting accumulation of the acetylated form of histone H3 in the utrophin promoter locus.

Conclusions
This novel artificial molecule may represent an improved platform for the development of future applications in DMD treatment.
Characterizing the emergence and persistence of drug resistant mutations in HIV-1 subtype C infections using 454 ultra deep pyrosequencing
Authors: Bansode Vijay , McCormack Grace P , Crampin Amelia C , Ngwira Bagrey , Shrestha Ram K , French Neil , Glynn Judith R , Travers Simon A 
Published: January 2013

Abstract

Background
The role of HIV-1 RNA in the emergence of resistance to antiretroviral therapies (ARTs) is well documented while less is known about the role of historical viruses stored in the proviral DNA. The primary focus of this work was to characterize the genetic diversity and evolution of HIV drug resistant variants in an individual’s provirus during antiretroviral therapy using next generation sequencing.

Methods
Blood samples were collected prior to antiretroviral therapy exposure and during the course of treatment from five patients in whom drug resistance mutations had previously been identified using consensus sequencing. The spectrum of viral variants present in the provirus at each sampling time-point were characterized using 454 pyrosequencing from multiple combined PCR products. The prevalence of viral variants containing drug resistant mutations (DRMs) was characterized at each time-point.

Results
Low abundance drug resistant viruses were identified in 14 of 15 sampling time-points from the five patients. In all individuals DRMs against current therapy were identified at one or more of the sampling time-points. In two of the five individuals studied these DRMs were present prior to treatment exposure and were present at high prevalence within the amplified and sequenced viral population. DRMs to drugs other than those being currently used were identified in four of the five individuals.

Conclusion
The presence of DRMs in the provirus, regardless of their observed prevalence did not appear to have an effect on clinical outcomes in the short term suggesting that the drug resistant viral variants present in the proviral DNA do not appear to play a role in the short term in facilitating the emergence of drug resistance.