bluuebunny/crossref_metadata_2025_split huggingface dataset:
Homogenization and Trend Analysis of Canadian Near-Surface Wind Speeds
Authors: Wan Hui , Wang Xiaolan L. , Swail Val R. 
Published: October 2009

Abstract
Near-surface wind speeds recorded at 117 stations in Canada for the period from 1953 to 2006 were analyzed in this study. First, metadata and a logarithmic wind profile were used to adjust hourly wind speeds measured at nonstandard anemometer heights to the standard 10-m level. Monthly mean near-surface wind speed series were then derived and subjected to a statistical homogeneity test, with homogeneous monthly mean geostrophic wind (geowind) speed series being used as reference series. Homogenized monthly mean near-surface wind speed series were obtained by adjusting all significant mean shifts, using the results of the statistical test and modeling along with all available metadata, and were used to assess the long-term trends.
This study shows that station relocation and anemometer height change are the main causes for discontinuities in the near-surface wind speed series, followed by instrumentation problems or changes, and observing environment changes. It also shows that the effects of artificial mean shifts on the results of trend analysis are remarkable, and that the homogenized near-surface wind speed series show good spatial consistency of trends, which are in agreement with long-term trends estimated from independent datasets, such as surface winds in the United States and cyclone activity indices and ocean wave heights in the region. These indicate success in the homogenization of the wind data. During the period analyzed, the homogenized near-surface wind speed series show significant decreases throughout western Canada and most parts of southern Canada (except the Maritimes) in all seasons, with significant increases in the central Canadian Arctic in all seasons and in the Maritimes in spring and autumn.
Relative Short-Range Forecast Impact from Aircraft, Profiler, Radiosonde, VAD, GPS-PW, METAR, and Mesonet Observations via the RUC Hourly Assimilation Cycle
Authors: Benjamin Stanley G. , Jamison Brian D. , Moninger William R. , Sahm Susan R. , Schwartz Barry E. , Schlatter Thomas W. 
Published: October 2009

Abstract
An assessment is presented on the relative forecast impact on the performance of a numerical weather prediction model from eight different observation data types: aircraft, profiler, radiosonde, velocity azimuth display (VAD), GPS-derived precipitable water, aviation routine weather report (METAR; surface), surface mesonet, and satellite-based atmospheric motion vectors. A series of observation sensitivity experiments was conducted using the Rapid Update Cycle (RUC) model/assimilation system in which various data sources were denied to assess the relative importance of the different data types for short-range (3–12 h) wind, temperature, and relative humidity forecasts at different vertical levels and near the surface. These experiments were conducted for two 10-day periods, one in November–December 2006 and one in August 2007. These experiments show positive short-range forecast impacts from most of the contributors to the heterogeneous observing system over the RUC domain. In particular, aircraft observations had the largest overall impact for forecasts initialized 3–6 h before 0000 or 1200 UTC, considered over the full depth (1000–100 hPa), followed by radiosonde observations, even though the latter are available only every 12 h. Profiler data (including at a hypothetical 8-km depth), GPS-precipitable water estimates, and surface observations also led to significant improvements in short-range forecast skill.
The Psychiatric Profession: an Expertise Under Siege?
Authors: De Waal Hugo , Malik Amit , Bhugra Dinesh 
Published: October 2009

Background: Psychiatry along with other medical disciplines has been under siege in the UK and the USA for a number of years and for a number of reasons. These have varied from various medical scandals and funding changes to political imperatives and public expectations. Changes in the knowledge base have added yet another dimension to this debate. Material: The subject is explored using historical figures and their writings and an overview of historic views on the psychiatry profession. Discussion: The demise of the psychiatrist as an expert and the profession of psychiatry as an expertise can be related to both real and perceived factors. Unlike, for instance, the language used by cardio-thoracic surgeons, the language used in and for professional communications in pyschiatry has become very similar to that used in lay discourses on psychological and relationship matters in the general population — partly as a result of the Freudian project successfully insinuating itself into ‘common knowledge’ and partly as the influence of media grows across the globe. This language has been misappropriated by a wide variety of non-experts, who then speak and interpret it as if they are specialists and any challenge from professionals is seen as self-protection and heresy. As psychiatrists, we do not use technology in a persuasive way as other branches of medicine tend to and this takes away a powerful symbolic conveying ‘expertise’. Increased consumerism adds yet another dimension to this discourse. Conclusions: The patient is definitely the expert on how their illness affects their life, but it is the psychiatrist who is the expert on the illness rather than simply focusing on disease. It is time for the profession loudly to proclaim itself for what it is and what it can and cannot do.
Glenohumeral, Scapular, and Thoracic Angles at Maximum Shoulder External Rotation in Throwing
Authors: Miyashita Koji , Kobayashi Hirokazu , Koshida Sentaro , Urabe Yukio 
Published: October 2009

Background Because a majority of throwing injuries occur near the maximum external rotation (MER) of the throwing shoulder, sports medicine practitioners and researchers have paid special attention to the shoulder kinematics at the MER in throwing. However, little is known about the individual kinematics of the glenohumeral, scapulothoracic, and thoracic joints at the MER. Purpose To demonstrate the glenohumeral, scapulothoracic, and thoracic joint movements and their contribution to the MER in throwing for baseball players. Study Design Descriptive laboratory study. Methods We collected throwing motion data for 20 collegiate baseball players by using 3 high-speed cameras and established 3-dimensional coordinates of each landmark with a direct linear translation method. We then obtained the MER of the shoulder complex, the external rotation angle of the glenohumeral joint, the posterior tipping angle of the scapula, and the thoracic extension angles at the MER in throwing. Results The mean (± standard deviation) value of the MER was 144.2° ± 11.0°. The mean (± standard deviation) values of the glenohumeral external rotation, the scapular posterior tipping, and the thoracic extension angles at the MER were 105.7° ± 15.5°, 23.5° ± 13.9°, and 8.9° ± 7.3°, respectively. Conclusion Our results indicate that not only the glenohumeral joint movement but also the scapular and thoracic movements make major contributions to the MER angle. Clinical Relevance To better understand the pathomechanics of the shoulder complex in throwing, we need to take into account the individual contributions of the glenohumeral, scapulothoracic, and thoracic extension movements to the MER.
ATG-induced expression of FOXP3 in human CD4+ T cells in vitro is associated with T-cell activation and not the induction of FOXP3+ T regulatory cells
Authors: Broady Raewyn , Yu Jie , Levings Megan K. 
Published: October 2009

Abstract
Several recent reports have suggested that in vitro exposure of CD4+ T cells to rabbit antithymocyte globulin (rATG), which is commonly used to prevent and treat graft-versus-host disease and allograft rejection, is an effective method to induce CD4+CD25+FOXP3+ T regulatory cells (Tregs). We and others, however, have shown that FOXP3 is also expressed in activated T cells. We therefore investigated whether the induction of FOXP3 expression by rATG resulted in a stable population of suppressive Tregs. We found that exposure of peripheral blood mononuclear cells (PBMCs) or conventional T cells to rATG resulted in induction of transient rather than stable expression of CD25 and FOXP3. Furthermore, rATG-treated T effector cells acquired neither an immunosuppressive profile of cytokine production nor suppressive capacity, even at the time of maximal FOXP3 expression. These findings indicate that the notion that rATG can be used to induce Tregs in vitro for cellular therapy in vivo should be re-evaluated.
Differential roles for ETS, CREB, and EGR binding sites in mediating VEGF receptor 1 expression in vivo
Authors: Jin Enjing , Liu Ju , Suehiro Jun-ichi , Yuan Lei , Okada Yoshiaki , Nikolova-Krstevski Vesna , Yano Kiichiro , Janes Lauren , Beeler David , Spokes Katherine C. , Li Dan , Regan Erzsébet , Shih Shou-Ching , Oettgen Peter , Minami Takashi , Aird William C. 
Published: October 2009

Abstract
Vascular endothelial growth factor receptor 1 (VEGFR1) is a marker for endothelial-specific gene expression. We previously reported that the human VEGFR1 promoter (between −748 and +284) contains information for expression in the intact endothelium of transgenic mice. The objective of this study was to dissect the cis-regulatory elements underlying VEGFR1 promoter activity in vitro and in vivo. In primary endothelial cells, binding sites for E74-like factor 1 (ELF-1; between −49 and −52), cyclic adenosine monophosphate response element binding (CREB; between −74 and −81), and early growth response factor 1/3 (EGR-1/3; between −16 to −25) were shown to play a positive role in gene transcription, whereas a putative E26 transformation-specificsequence (ETS) motif between −36 and −39 had a net negative effect on promoter activity. When targeted to the Hprt locus of mice, mutations of the ELF-1 binding site and the CRE element reduced promoter activity in the embryonic vasculature and resulted in a virtual loss of expression in adult endothelium. Postnatally, the EGR binding site mutant displayed significantly reduced promoter activity in a subset of vascular beds. In contrast, mutation of the −39 ETS site resulted in increased LacZ staining in multiple vascular beds. Together, these results provide new insights into the transcriptional regulatory mechanisms of VEGFR1.
Pericyte recruitment during vasculogenic tube assembly stimulates endothelial basement membrane matrix formation
Authors: Stratman Amber N. , Malotte Kristine M. , Mahan Rachel D. , Davis Michael J. , Davis George E. 
Published: October 2009

AbstractWe show that endothelial cell (EC)–generated vascular guidance tunnels (ie, matrix spaces created during tube formation) serve as conduits for the recruitment and motility of pericytes along EC ablumenal surfaces to facilitate vessel maturation events, including vascular basement membrane matrix assembly and restriction of EC tube diameter. During quail development, pericyte recruitment along microvascular tubes directly correlates with vascular basement membrane matrix deposition. Pericyte recruitment to EC tubes leads to specific induction of fibronectin and nidogen-1 (ie, matrix-bridging proteins that link together basement membrane components) as well as perlecan and laminin isoforms. Coincident with these events, up-regulation of integrins, α5β1, α3β1, α6β1, and α1β1, which bind fibronectin, nidogens, laminin isoforms, and collagen type IV, occurs in EC-pericyte cocultures, but not EC-only cultures. Integrin-blocking antibodies to these receptors, disruption of fibronectin matrix assembly, and small interfering RNA suppression of pericyte tissue inhibitor of metalloproteinase (TIMP)-3 (a known regulator of vascular tube stabilization) all lead to decreased EC basement membrane, resulting in increased vessel lumen diameter, a key indicator of dysfunctional EC-pericyte interactions. Thus, pericyte recruitment to EC-lined tubes during vasculogenesis is a stimulatory event controlling vascular basement membrane matrix assembly, a fundamental maturation step regulating the transition from vascular morphogenesis to stabilization.
The impact of prophylactic fresh-frozen plasma and cryoprecipitate on the incidence of central nervous system thrombosis and hemorrhage in children with acute lymphoblastic leukemia receiving asparaginase
Authors: Abbott Lesleigh S. , Deevska Mariana , Fernandez Conrad V. , Dix David , Price Victoria E. , Wang Hao , Parker Louise , Yhap Margaret , Fitzgerald Colleen , Barnard Dorothy R. , Berman Jason N. 
Published: October 2009

AbstractAsparaginase (ASP) therapy is associated with depletion of antithrombin (AT) and fibrinogen (FG). Potential toxicities include central nervous system thrombosis (CNST) and hemorrhage. Historical practice at the Izaak Walton Killam Health Centre (IWK) involves measuring AT and FG levels after ASP administration and transfusing fresh-frozen plasma (FFP) or cryoprecipitate (CRY) to prevent thrombotic and hemorrhagic complications. To determine whether this reduced these complications in children with acute lymphoblastic leukemia (ALL), incidence, outcome, and clinical characteristics of ASP-related CNST in ALL patients at IWK were compared with a similar cohort from BC Children's Hospital (BCCH), where prophylaxis was not performed. Costs associated with preventative versus expectant management were estimated. From 1990 to 2005, 240 patients were treated at IWK and 479 at BCCH. Seven BCCH patients developed venous CNST (1.5%), compared with none at IWK. CNST occurred exclusively during induction. Six patients received anticoagulation and continued ASP. All 7 patients remain in remission. National Cancer Institute high-risk ALL predicted CNST risk (P = .02), whereas sex, age, race, and body mass index did not. Neither FFP nor CRY protected against CNST, suggesting prophylaxis is unwarranted for unselected ALL patients. However, prophylactic replacement for HR patients in induction may be cost-effective.
Immunoglobulin aggregation leading to Russell body formation is prevented by the antibody light chain
Authors: Corcos Daniel , Osborn Michael J. , Matheson Louise S. , Santos Fatima , Zou Xiangang , Smith Jennifer A. , Morgan Geoff , Hutchings Amanda , Hamon Maureen , Oxley David , Brüggemann Marianne 
Published: October 2009

AbstractRussell bodies (RBs) are intracellular inclusions filled with protein aggregates. In diverse lymphoid disorders these occur as immunoglobulin (Ig) deposits, accumulating in abnormal plasma or Mott cells. In heavy-chain deposition disease truncated antibody heavy-chains (HCs) are found, which bear a resemblance to diverse polypeptides produced in Ig light-chain (LC)–deficient (L−/−) mice. In L−/− animals, the known functions of LC, providing part of the antigen-binding site of an antibody and securing progression of B-cell development, may not be required. Here, we show a novel function of LC in preventing antibody aggregation. L−/− mice produce truncated HC naturally, constant region (C)γ and Cα lack CH1, and Cμ is without CH1 or CH1 and CH2. Most plasma cells found in these mice are CD138+ Mott cells, filled with RBs, formed by aggregation of HCs of different isotypes. The importance of LC in preventing HC aggregation is evident in knock-in mice, expressing Cμ without CH1 and CH2, which only develop an abundance of RBs when LC is absent. These results reveal that preventing antibody aggregation is a major function of LC, important for understanding the physiology of heavy-chain deposition disease, and in general recognizing the mechanisms, which initiate protein conformational diseases.
VANLO - Interactive visual exploration of aligned biological networks
Authors: Brasch Steffen , Linsen Lars , Fuellen Georg 
Published: October 2009

Abstract

Background
Protein-protein interaction (PPI) is fundamental to many biological processes. In the course of evolution, biological networks such as protein-protein interaction networks have developed. Biological networks of different species can be aligned by finding instances (e.g. proteins) with the same common ancestor in the evolutionary process, so-called orthologs. For a better understanding of the evolution of biological networks, such aligned networks have to be explored. Visualization can play a key role in making the various relationships transparent.

Results
We present a novel visualization system for aligned biological networks in 3D space that naturally embeds existing 2D layouts. In addition to displaying the intra-network connectivities, we also provide insight into how the individual networks relate to each other by placing aligned entities on top of each other in separate layers. We optimize the layout of the entire alignment graph in a global fashion that takes into account inter- as well as intra-network relationships. The layout algorithm includes a step of merging aligned networks into one graph, laying out the graph with respect to application-specific requirements, splitting the merged graph again into individual networks, and displaying the network alignment in layers. In addition to representing the data in a static way, we also provide different interaction techniques to explore the data with respect to application-specific tasks.

Conclusion
Our system provides an intuitive global understanding of aligned PPI networks and it allows the investigation of key biological questions. We evaluate our system by applying it to real-world examples documenting how our system can be used to investigate the data with respect to these key questions. Our tool VANLO (Visualization of Aligned Networks with Layout Optimization) can be accessed at http://www.math-inf.uni-greifswald.de/VANLO.
miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression
Authors: Wang Wei-Chi , Lin Feng-Mao , Chang Wen-Chi , Lin Kuan-Yu , Huang Hsien-Da , Lin Na-Sheng 
Published: October 2009

Abstract

Background
MicroRNAs (miRNAs), small non-coding RNAs of 19 to 25 nt, play important roles in gene regulation in both animals and plants. In the last few years, the oligonucleotide microarray is one high-throughput and robust method for detecting miRNA expression. However, the approach is restricted to detecting the expression of known miRNAs. Second-generation sequencing is an inexpensive and high-throughput sequencing method. This new method is a promising tool with high sensitivity and specificity and can be used to measure the abundance of small-RNA sequences in a sample. Hence, the expression profiling of miRNAs can involve use of sequencing rather than an oligonucleotide array. Additionally, this method can be adopted to discover novel miRNAs.

Results
This work presents a systematic approach, miRExpress, for extracting miRNA expression profiles from sequencing reads obtained by second-generation sequencing technology. A stand-alone software package is implemented for generating miRNA expression profiles from high-throughput sequencing of RNA without the need for sequenced genomes. The software is also a database-supported, efficient and flexible tool for investigating miRNA regulation. Moreover, we demonstrate the utility of miRExpress in extracting miRNA expression profiles from two Illumina data sets constructed for the human and a plant species.

Conclusion
We develop miRExpress, which is a database-supported, efficient and flexible tool for detecting miRNA expression profile. The analysis of two Illumina data sets constructed from human and plant demonstrate the effectiveness of miRExpress to obtain miRNA expression profiles and show the usability in finding novel miRNAs.
BASE - 2nd generation software for microarray data management and analysis
Authors: Vallon-Christersson Johan , Nordborg Nicklas , Svensson Martin , Häkkinen Jari 
Published: October 2009

Abstract

Background
Microarray experiments are increasing in size and samples are collected asynchronously over long time. Available data are re-analysed as more samples are hybridized. Systematic use of collected data requires tracking of biomaterials, array information, raw data, and assembly of annotations. To meet the information tracking and data analysis challenges in microarray experiments we reimplemented and improved BASE version 1.2.

Results
The new BASE presented in this report is a comprehensive annotable local microarray data repository and analysis application providing researchers with an efficient information management and analysis tool. The information management system tracks all material from biosource, via sample and through extraction and labelling to raw data and analysis. All items in BASE can be annotated and the annotations can be used as experimental factors in downstream analysis. BASE stores all microarray experiment related data regardless if analysis tools for specific techniques or data formats are readily available. The BASE team is committed to continue improving and extending BASE to make it usable for even more experimental setups and techniques, and we encourage other groups to target their specific needs leveraging on the infrastructure provided by BASE.

Conclusion
BASE is a comprehensive management application for information, data, and analysis of microarray experiments, available as free open source software at http://base.thep.lu.se under the terms of the GPLv3 license.
A tamoxifen inducible knock-in allele for investigation of E2A function
Authors: Jones Mary E , Kondo Motonari , Zhuang Yuan 
Published: October 2009

Abstract

Background
E-proteins are transcription factors important for the development of a variety of cell types, including neural, muscle and lymphocytes of the immune system. E2A, the best characterized E-protein family member in mammals, has been shown to have stage specific roles in cell differentiation, lineage commitment, proliferation, and survival. However, due to the complexity of E2A function, it is often difficult to separate these roles using conventional genetic approaches. Here, we have developed a new genetic model for reversible control of E2A protein activity at physiological levels. This system was created by inserting a tamoxifen-responsive region of the estrogen receptor (ER) at the carboxyl end of the tcfe2a gene to generate E2AER fusion proteins. We have characterized and analyzed the efficiency and kinetics of this inducible E2AER system in the context of B cell development.

Results
B cell development has been shown previously to be blocked at an early stage in E2A deficient animals. Our E2AER/ER mice demonstrated this predicted block in B cell development, and E2AER DNA binding activity was not detected in the absence of ligand. In vitro studies verified rapid induction of E2AER DNA binding activity upon tamoxifen treatment. While tamoxifen treatment of E2AER/ER mice showed inefficient rescue of B cell development in live animals, direct exposure of bone marrow cells to tamoxifen in an ex vivo culture was sufficient to rescue and support early B cell development from the pre-proB cell stage.

Conclusion
The E2AER system provides inducible and reversible regulation of E2A function at the protein level. Many previous studies have utilized over-expression systems to induce E2A function, which are complicated by the toxicity often resulting from high levels of E2A. The E2AER model instead restores E2A activity at an endogenous level and in addition, allows for tight regulation of the timing of induction. These features make our E2AER
ex vivo culture system attractive to study both immediate and gradual downstream E2A-mediated events.