bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Scheme to Identify Loops from Trajectories of Oceanic Surface Drifters: An Application in the Kuroshio Extension Region
Authors: Dong Changming , Liu Yu , Lumpkin Rick , Lankhorst Matthias , Chen Dake , McWilliams James C. , Guan Yuping 
Published: May 2011

Abstract
When a drifter is trapped in an eddy, it makes either a cycloidal or a looping trajectory. The former case takes place when the translating speed is larger than the eddy spinning speed. When the background mean velocity is removed, drifter trajectories make loops. Thus, eddies can be detected from a drifter trajectory by identifying looping segments. In this paper, an automated scheme is developed to identify looping segments from Lagrangian trajectories, based on a geometric definition of a loop, that is, a closing curve with its starting point overlapped by its ending point. The scheme is to find the first returning point, if it exists, along a trajectory of a surface drifter with a few other criteria. To further increase the chance that detected loops are eddies, it is considered that a loop identifies an eddy only when the loop’s spinning period is longer than the local inertial period and shorter than the seasonal scale, and that at least two consecutive loops with the same polarity that stay sufficiently close are found. Five parameters that characterize an eddy are estimated by the scheme: location (eddy center), time (starting and ending time), period, polarity, and intensity. As an example, the scheme is applied to surface drifters in the Kuroshio Extension region. Results indicate that numbers of eddies are symmetrically distributed for cyclonic and anticyclonic eddies, mean eddy sizes are 40–50 km, and eddy abundance is the highest along the Kuroshio path with more cyclonic eddies along its southern flank.
A Fuzzy Logic Method for Lightning Prediction Using Thermodynamic and Kinematic Parameters from Radio Sounding Observations in South Korea
Authors: Kuk Bongjae , Kim Hongil , Ha Jongsung , Lee Hyokeun , Lee Gyuwon 
Published: May 2011

Abstract
Lightning is one of the most troubling weather phenomena for weather forecasters at space centers. In this study, proximity sounding and lightning data were used to evaluate the utility of thermodynamic and kinematic parameters for forecasting lightning prior to launch operations. Various parameters from 4138 radio sounding observations at five sites and cloud-to-ground (CG) stroke data from the Korea Meteorological Administration’s Lightning Detection Network (KLDN) over South Korea during 2004–09 were used. To support launch operations, forecasts of the total membership function for lightning (TMF) were derived from the combination of membership functions of selected thermodynamic and kinematic parameters with each objective weight using a fuzzy logic algorithm. The forecast skill of TMF was evaluated by computing several skill statistics, which include probability of detection (POD), false alarm rate (FAR), percent correct (PC), critical success index (CSI), and the true skill statistic (TSS). The lightning forecasting method for Gwangju, South Korea (site nearest to the Naro Space Center), was found to have a POD of 0.68, an FAR of 0.45, a PC of 0.76, a CSI of 0.44, and a TSS of 0.47.
Serving inland rural communities through university clinics
Authors: Allan Julaine , Pope Rod , O’Meara Peter , Higgs Joy , Kent Jenny 
Published: May 2011

Aim: To effectively provide clinical placements for students and increase healthcare options for rural communities, an investigation of university clinics was conducted. Method: This project adopted a consultative inquiry strategy and involved two processes: (1) a review of literature; and (2) interviews with existing health sciences clinic staff. Results: Low income population groups are more likely to find student-provided services acceptable and have a reliable demand for these services if they are accessible. University clinics reporting high client numbers had a consistent flow of low income clients with chronic problems. Private healthcare providers were often unable to meet the demand from this group. However, multiple methods and flexibility of delivery that fitted in with local services were required rather than single point of access clinics. Discussion: University clinics are an effective way of providing clinical placements for students and some healthcare for rural communities. Key aspects of the community context that make a university clinic viable are the degree of disadvantage in a community, the population density (or dispersion), the workforce available to supply health services in the public and private sectors, and the types of services that are demanded by policy or lobby groups and not yet supplied.
Relationship of blood pressure and obesity with inflammatory cytokines among African Americans
Authors: DeLoach Stephanie , Huan Yonghong , Keith Scott W. , Martinez Cantarin Maria P. , Falkner Bonita 
Published: May 2011

Objectives: Hypertension and obesity are major public health issues. Both conditions are highly prevalent among African Americans and contribute to the increased burden of cardiovascular disease in this group. Inflammation is considered to be an underlying process in both conditions. The authors sought to determine if there is an interaction between high blood pressure (HBP) and obesity that is associated with markedly elevated plasma levels of proinflammatory cytokines in African American adults. Methods: This study examined 484 African Americans, aged 18–45 years, including people with and without obesity, and also with and without HBP. People known to have diabetes were not enrolled. Plasma levels of high-sensitivity C-reactive protein (hsCRP), interleukin-6 (IL-6), plasminogen activator inhibitor 1, tumor necrosis factor alpha (TNF-α), and adiponectin were measured. Participants also underwent an oral glucose tolerance test and measurement of blood pressure and body mass index (BMI). Results: There was no statistically significant interaction between obesity and HBP on plasma levels of adiponectin or the inflammatory cytokines. When both conditions were present, HBP and obesity had additive associations with the expected geometric mean ratios for IL-6 (1.44, 95% CI 1.18 to 1.75), TNF-α (1.31, 95% CI 1.11 to 1.53), hsCRP (2.55, 95% CI 1.99 to 3.26) and negative association with adiponectin (0.61, 95% CI 0.52 to 0.71). Compared with HBP, obesity had the predominant association with cytokine levels. An increase in cytokine plasma levels was detectable when BMI exceeded 25 kg/m2. Conclusions: Biomarkers of inflammation in African Americans are strongly associated with BMI. A modest additive effect is found with HBP. Interventions to reduce obesity-related inflammation may impact cardiovascular disease outcomes.
Crebbp haploinsufficiency in mice alters the bone marrow microenvironment, leading to loss of stem cells and excessive myelopoiesis
Authors: Zimmer Stephanie N. , Zhou Qing , Zhou Ting , Cheng Ziming , Abboud-Werner Sherry L. , Horn Diane , Lecocke Mike , White Ruth , Krivtsov Andrei V. , Armstrong Scott A. , Kung Andrew L. , Livingston David M. , Rebel Vivienne I. 
Published: May 2011

AbstractCREB-binding protein (CREBBP) is important for the cell-autonomous regulation of hematopoiesis, including the stem cell compartment. In the present study, we show that CREBBP plays an equally pivotal role in microenvironment-mediated regulation of hematopoiesis. We found that the BM microenvironment of Crebbp+/− mice was unable to properly maintain the immature stem cell and progenitor cell pools. Instead, it stimulates myeloid differentiation, which progresses into a myeloproliferation phenotype. Alterations in the BM microenvironment resulting from haploinsufficiency of Crebbp included a marked decrease in trabecular bone that was predominantly caused by increased osteoclastogenesis. Although CFU-fibroblast (CFU-F) and total osteoblast numbers were decreased, the bone formation rate was similar to that found in wild-type mice. At the molecular level, we found that the known hematopoietic modulators matrix metallopeptidase-9 (MMP9) and kit ligand (KITL) were decreased with heterozygous levels of Crebbp. Lastly, potentially important regulatory proteins, endothelial cell adhesion molecule 1 (ESAM1) and cadherin 5 (CDH5), were increased on Crebbp+/− endothelial cells. Our findings reveal that a full dose of Crebbp is essential in the BM microenvironment to maintain proper hematopoiesis and to prevent excessive myeloproliferation.
Redirecting αβT cells against cancer cells by transfer of a broadly tumor-reactive γδT-cell receptor
Authors: Marcu-Malina Victoria , Heijhuurs Sabine , van Buuren Marit , Hartkamp Linda , Strand Susanne , Sebestyen Zsolt , Scholten Kirsten , Martens Anton , Kuball Jürgen 
Published: May 2011

AbstractMajor limitations of currently investigated αβT cells redirected against cancer by transfer of tumor-specific αβTCR arise from their low affinity, MHC restriction, and risk to mediate self-reactivity after pairing with endogenous α or βTCR chains. Therefore, the ability of a defined γ9δ2TCR to redirect αβT cells selectively against tumor cells was tested and its molecular interaction with a variety of targets investigated. Functional analysis revealed that a γ9δ2TCR efficiently reprograms both CD4+ and CD8+ αβT cells against a broad panel of cancer cells while ignoring normal cells, and substantially reduces but does not completely abrogate alloreactivity. γ9δ2TCR-transduced αβT cells reduced colony formation of progenitor cells of primary acute myeloid leukemia blasts and inhibited leukemia growth in a humanized mouse model. Thereby, metabolites of a dysregulated mevalonate pathway are targeted and the additional application of widely used biphosphonates is crucial for in vivo efficacy most likely because of its modulating effect on cytokine secretion of γ9δ2TCR-transduced αβT cells. Expression of NKG2D ligands and F1-ATPase contributed to the activity of γ9δ2TCR-transduced αβT cells but were not mandatory. In summary, γ9δ2 TCRs are an attractive alternative to broadly redirect αβT cells against cancer cells with both an improved efficacy and safety profile compared with currently used αβTCRs.
To aggregate or not to aggregate high-dimensional classifiers
Authors: Xu Cheng-Jian , Hoefsloot Huub CJ , Smilde Age K 
Published: May 2011

Abstract

Background
High-throughput functional genomics technologies generate large amount of data with hundreds or thousands of measurements per sample. The number of sample is usually much smaller in the order of ten or hundred. This poses statistical challenges and calls for appropriate solutions for the analysis of this kind of data.

Results
Principal component discriminant analysis (PCDA), an adaptation of classical linear discriminant analysis (LDA) for high-dimensional data, has been selected as an example of a base learner. The multiple versions of PCDA models from repeated double cross-validation were aggregated, and the final classification was performed by majority voting. The performance of this approach was evaluated by simulation, genomics, proteomics and metabolomics data sets.

Conclusions
The aggregating PCDA learner can improve the prediction performance, provide more stable result, and help to know the variability of the models. The disadvantage and limitations of aggregating were also discussed.
A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus
Authors: Neves Leandro G , MC Mamani Eva , Alfenas Acelino C , Kirst Matias , Grattapaglia Dario 
Published: May 2011

Abstract
Background
Technological advances are progressively increasing the application of genomics to a wider array of economically and ecologically important species. High-density maps enriched for transcribed genes facilitate the discovery of connections between genes and phenotypes. We report the construction of a high-density linkage map of expressed genes for the heterozygous genome of Eucalyptus using Single Feature Polymorphism (SFP) markers.

Results
SFP discovery and mapping was achieved using pseudo-testcross screening and selective mapping to simultaneously optimize linkage mapping and microarray costs. SFP genotyping was carried out by hybridizing complementary RNA prepared from 4.5 year-old trees xylem to an SFP array containing 103,000 25-mer oligonucleotide probes representing 20,726 unigenes derived from a modest size expressed sequence tags collection. An SFP-mapping microarray with 43,777 selected candidate SFP probes representing 15,698 genes was subsequently designed and used to genotype SFPs in a larger subset of the segregating population drawn by selective mapping. A total of 1,845 genes were mapped, with 884 of them ordered with high likelihood support on a framework map anchored to 180 microsatellites with average density of 1.2 cM. Using more probes per unigene increased by two-fold the likelihood of detecting segregating SFPs eventually resulting in more genes mapped. In silico validation showed that 87% of the SFPs map to the expected location on the 4.5X draft sequence of the Eucalyptus grandis genome.

Conclusions
The Eucalyptus 1,845 gene map is the most highly enriched map for transcriptional information for any forest tree species to date. It represents a major improvement on the number of genes previously positioned on Eucalyptus maps and provides an initial glimpse at the gene space for this global tree genome. A general protocol is proposed to build high-density transcript linkage maps in less characterized plant species by SFP genotyping with a concurrent objective of reducing microarray costs. HIgh-density gene-rich maps represent a powerful resource to assist gene discovery endeavors when used in combination with QTL and association mapping and should be especially valuable to assist the assembly of reference genome sequences soon to come for several plant and animal species.
PHENOPSIS DB: an Information System for Arabidopsis thalianaphenotypic data in an environmental context
Authors: Fabre Juliette , Dauzat Myriam , Nègre Vincent , Wuyts Nathalie , Tireau Anne , Gennari Emilie , Neveu Pascal , Tisné Sébastien , Massonnet Catherine , Hummel Irène , Granier Christine 
Published: May 2011

Abstract

Background
Renewed interest in plant × environment interactions has risen in the post-genomic era. In this context, high-throughput phenotyping platforms have been developed to create reproducible environmental scenarios in which the phenotypic responses of multiple genotypes can be analysed in a reproducible way. These platforms benefit hugely from the development of suitable databases for storage, sharing and analysis of the large amount of data collected. In the model plant Arabidopsis thaliana, most databases available to the scientific community contain data related to genetic and molecular biology and are characterised by an inadequacy in the description of plant developmental stages and experimental metadata such as environmental conditions. Our goal was to develop a comprehensive information system for sharing of the data collected in PHENOPSIS, an automated platform for Arabidopsis thaliana phenotyping, with the scientific community.

Description
PHENOPSIS DB is a publicly available (URL: http://bioweb.supagro.inra.fr/phenopsis/) information system developed for storage, browsing and sharing of online data generated by the PHENOPSIS platform and offline data collected by experimenters and experimental metadata. It provides modules coupled to a Web interface for (i) the visualisation of environmental data of an experiment, (ii) the visualisation and statistical analysis of phenotypic data, and (iii) the analysis of Arabidopsis thaliana plant images.

Conclusions
Firstly, data stored in the PHENOPSIS DB are of interest to the Arabidopsis thaliana community, particularly in allowing phenotypic meta-analyses directly linked to environmental conditions on which publications are still scarce. Secondly, data or image analysis modules can be downloaded from the Web interface for direct usage or as the basis for modifications according to new requirements. Finally, the structure of PHENOPSIS DB provides a useful template for the development of other similar databases related to genotype × environment interactions.
Becoming a general practitioner - Which factors have most impact on career choice of medical students?
Authors: Kiolbassa Kathrin , Miksch Antje , Hermann Katja , Loh Andreas , Szecsenyi Joachim , Joos Stefanie , Goetz Katja 
Published: May 2011

Abstract

Background
In Germany, there is a shortage of young physicians in several specialties, the situation of general practitioners (GP) being especially precarious. The factors influencing the career choice of German medical students are poorly understood. This study aims to identify factors influencing medical students' specialty choice laying a special focus on general practice.

Methods
The study was designed as a cross-sectional survey. In 2010, students at the five medical schools in the federal state of Baden-Wuerttemberg (Germany) filled out an online-questionnaire. On 27 items with 5-point Likert scales, the students rated the importance of specified individual and occupational aspects. Furthermore, students were asked to assign their intended medical specialty.

Results
1,299 students participated in the survey. Thereof, 1,114 students stated a current choice for a specialty, with 708 students choosing a career in one of the following 6 specialties: internal medicine, surgery, gynaecology and obstetrics, paediatrics, anaesthetics and general practice. Overall, individual aspects ('Personal ambition', 'Future perspective', 'Work-life balance') were rated as more important than occupational aspects (i.e. 'Variety in job', 'Job-related ambition') for career choice. For students favouring a career as a GP individual aspects and the factor 'Patient orientation' among the occupational aspects were significantly more important and 'Job-related ambition' less important compared to students with other specialty choices.

Conclusions
This study confirms that future GPs differ from students intending to choose other specialties particularly in terms of patient-orientation and individual aspects such as personal ambition, future perspective and work-life balance. Improving job-conditions in terms of family compatibility and work-life balance could help to increase the attractiveness of general practice. Due to the shortage of GPs those factors should be made explicit at an early stage at medical school to increase the number of aspirants for general practice.
The association of HLA-DQB1, -DQA1 and -DPB1 alleles with anti- glomerular basement membrane (GBM) disease in Chinese patients
Authors: Luo Huan , Chen Min , Cui Zhao , Yang Rui , Xu Peng-Cheng , Zhou Xu-Jie , Zhao Ming-Hui 
Published: May 2011

Abstract

Background
Human leukocyte antigen (HLA) alleles are associated with many autoimmune diseases, including anti-glomerular basement membrane (GBM) disease. In our previous study, it was demonstrated that HLA-DRB1*1501 was strongly associated with anti-GBM disease in Chinese. However, the association of anti-GBM disease and other HLA class II genes, including HLA-DQB1, -DQA1,-DPB1 alleles, has rarely been investigated in Asian, especially Chinese patients. The present study further analyzed the association between anti-GBM disease and HLA-DQB1, -DQA1, and -DPB1 genes. Apart from this, we tried to locate the potential risk amino acid residues of anti-GBM disease.

Methods
This study included 44 Chinese patients with anti-GBM disease and 200 healthy controls. The clinical and pathological data of the patients were collected and analyzed. Typing of HLA-DQB1, -DQA1 and -DPB1 alleles were performed by bi-directional sequencing of exon 2 using the SeCoreTM Sequencing Kits.

Results
Compared with normal controls, the prevalence of HLA-DPB1*0401 was significantly lower in patients with anti-GBM disease (3/88 vs. 74/400, p = 4.4 × 10-4, pc = 0.039). Comparing with normal controls, the combination of presence of DRB1*1501 and absence of DPB1*0401 was significantly prominent among anti-GBM patients (p = 2.0 × 10-12, pc = 1.7 × 10-10).

Conclusions
HLA-DPB1*0401 might be a protective allele to anti-GBM disease in Chinese patients. The combined presence of DRB1*1501 and absence of DPB1*0401 might have an even higher risk to anti-GBM disease than HLA-DRB1*1501 alone.
CD248 facilitates tumor growth via its cytoplasmic domain
Authors: Maia Margarida , DeVriese Astrid , Janssens Tom , Moons Michaël , Lories Rik J , Tavernier Jan , Conway Edward M 
Published: May 2011

AbstractBackgroundStromal fibroblasts participate in the development of a permissive environment for tumor growth, yet molecular pathways to therapeutically target fibroblasts are poorly defined. CD248, also known as endosialin or tumor endothelial marker 1 (TEM1), is a transmembrane glycoprotein expressed on activated fibroblasts. We recently showed that the cytoplasmic domain of CD248 is important in facilitating an inflammatory response in a mouse model of arthritis. Others have reported thatCD248gene inactivation in mice results in dampened tumor growth. We hypothesized that the conserved cytoplasmic domain of CD248 is important in regulating tumor growth.MethodsMice lacking the cytoplasmic domain of CD248 (CD248CyD/CyD) were generated and evaluated in tumor models, comparing the findings with wild-type mice (CD248WT/WT).ResultsAs compared to the response in CD248WT/WTmice, growth of T241 fibrosarcomas and Lewis lung carcinomas was significantly reduced in CD248CyD/CyDmice. Tumor size was similar to that seen with CD248-deficient mice. Conditioned media from CD248CyD/CyDfibroblasts were less effective at supporting T241 fibrosarcoma cell survival. In addition to our previous observation of reduced release of activated matrix metalloproteinase (MMP)-9, CD248CyD/CyDfibroblasts also had impaired PDGF-BB-induced migration and expressed higher transcripts of tumor suppressor factors, transgelin (SM22α), Hes and Hey1.ConclusionsThe multiple pathways regulated by the cytoplasmic domain of CD248 highlight its potential as a therapeutic target to treat cancer.