bluuebunny/crossref_metadata_2025_split huggingface dataset:
Numerical Simulation of Tornadogenesis in an Outer-Rainband Minisupercell of Typhoon Shanshan on 17 September 2006
Authors: Mashiko Wataru , Niino Hiroshi , Kato Teruyuki 
Published: July 2009

Abstract
On 17 September 2006, three tornadoes occurred along the east coast of Kyusyu Island in western Japan during the passage of an outer rainband in the right-front quadrant of Typhoon Shanshan. To clarify the structure of the tornado-producing storms and the mechanism of tornadogenesis, quadruply nested numerical simulations were performed using a nonhydrostatic model with an innermost horizontal grid spacing of 50 m. Several simulated convective storms in the outermost rainband exhibited characteristics of a minisupercell. One storm had a strong rotating updraft of more than 30 m s−1 and a large vertical vorticity exceeding 0.06 s−1. This storm spawned a tornado when the low-level mesocyclone intensified. The tornado was generated on the rear-flank gust front near the mesocyclone center when a secondary rear-flank downdraft (RFD) surge advanced cyclonically around the low-level mesocyclone and overtook the rear-flank gust front at its left-front edge. Backward trajectories and vorticity budget analysis along the trajectories indicate that the secondary RFD surge played a key role in tornadogenesis by barotropically transporting the large streamwise vorticity associated with the environmental low-level veering shear toward the surface. When the secondary RFD outflow surge boundary reached the rear-flank gust front, the horizontal convergence was enhanced, contributing to the rapid amplification of the vertically tilted streamwise vorticity. The diagnostics of the vertical momentum equation and several sensitivity experiments demonstrated that precipitation loading in the area of a hook-shaped precipitation pattern was crucial to the behavior of the RFD and the subsequent tornadogenesis.
Long-term follow-up of benign multiple sclerosis in Hordaland County, Western Norway
Authors: Glad SB , Nyland HI , Aarseth JH , Riise T , Myhr KM 
Published: July 2009

Objective To study the frequency of benign multiple sclerosis (MS) after 20 years disease duration and identify early clinical and demographic prognostic factors of a benign course. Methods A population-based cohort including all 230 MS patients with clinical disease onset during 1976–1986 in Hordaland County, Western Norway was followed up with clinical examination in 1995 and 2003. Benign MS was defined as an Expanded Disability Status Scale (EDSS) score ≤3.0, at least 10 years after disease onset. Results A relapsing–remitting disease course at onset, female gender, and younger age at onset were significantly associated with a benign course, but could only explain 23.0% of the variation in the benign course. A low annual relapse rate was also associated with a benign course. When including this variable in the model, 42.3% of the variation could be explained. The number of benign MS cases decreased significantly from 37.6% in 1995 to 24.2% in 2003. Conclusion Benign MS is frequently a temporary condition. Only a small part of the variation in the long-term benign course could be explained by clinical data present in the early phase of the disease. With several new emerging therapies in MS, the need for more reliable prognostic factors is increasing, to improve and individualize patient treatment.
Mighty mouse
Authors: Johnson Amy J. 
Published: July 2009

Abstract
In this issue of Blood, ter Brugge and colleagues describe the results of their efforts to express SV40 T antigen in mature B cells of mice.1 As a consequence of T antigen expression, B cells develop normally but, upon aging, mice show an accumulation of monoclonal CD5+ B cells and have a chronic lymphocytic leukemia-like phenotype.
Megakaryocytes survive without survivin
Authors: Ravid Katya 
Published: July 2009

Abstract
Survivin has been described as an important regulator of late mitosis and as antiapoptotic in various cells. In this issue of Blood, Wen and colleagues describe a megakaryocyte-specific knockout of survivin, with no influence on megakaryocyte survival, and a stimulating effect on polyploidy.1
Identification of valid reference genes during the differentiation of human myoblasts
Authors: Stern-Straeter Jens , Bonaterra Gabriel A , Hörmann Karl , Kinscherf Ralf , Goessler Ulrich R 
Published: July 2009

Abstract

Background
Analysis of RNA expression using real-time PCR (qRT-PCR) traditionally includes reference genes (RG) as an internal control. This practice is being questioned as it becomes increasingly clear that RG may vary considerably under certain experimental conditions. Thus, the validity of a particular RG must be determined for each experimental setting. We used qRT-PCR to measure the levels of six RG, which have been reported in the literature to be invariant. The RG were analyzed in human myoblast cultures under differentiation conditions. We examined the expression by qRT-PCR of mRNA encoding Beta-actin (ACTB), Beta-2-microglobulin (B2M), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), peptidylprolyl isomerase A (PPIA), TATA box binding protein (TBP) and ribosomal protein, large, P0 (RPLPO). The mRNA expression of the following genes of interest (GOI) were analyzed: skeletal muscle alpha 1 actin (ACTA1), myogenin/myogenic factor 4 (MYOG), embryonic skeletal muscle myosin heavy chain 3 (MYH3) and the activity of creatine phosphokinase (CK). The geNorm, NormFinder and BestKeeper software programs were used to ascertain the most suitable RG to normalize the RNA input.

Results
Using the geNorm program, RPLPO and TBP were found to be the most stable genes, additionally a suitable normalization factor (NF) was calculated. The NormFinder software showed that RPLPO was the most stable, whereas TBP ranked second. BestKeeper program also revealed that RPLPO and TBP as stable genes, but PPIA was the most stable reference gene, whereas GAPDH and ACTB were the worst ranked.

Conclusion
RNA expression analyses including three independent softwares revealed that RPLPO, TBP as reference genes or NF calculated by geNorm software, are suitable to normalize the mRNA expression in myoblast after culture under differentiation conditions. Significant correlations can be identified between the differentiations markers ACTA1, MYOG, MYH3 and creatine phosphokinase (CK) activity, when the expression is normalized with the NF calculated with RPLPO and TBP.
Optimizing expression of the pregnancy malaria vaccine candidate, VAR2CSA in Pichia pastoris
Authors: Avril Marion , Hathaway Marianne J , Cartwright Megan M , Gose Severin O , Narum David L , Smith Joseph D 
Published: June 2009

Abstract

Background
VAR2CSA is the main candidate for a vaccine against pregnancy-associated malaria, but vaccine development is complicated by the large size and complex disulfide bonding pattern of the protein. Recent X-ray crystallographic information suggests that domain boundaries of VAR2CSA Duffy binding-like (DBL) domains may be larger than previously predicted and include two additional cysteine residues. This study investigated whether longer constructs would improve VAR2CSA recombinant protein secretion from Pichia pastoris and if domain boundaries were applicable across different VAR2CSA alleles.

Methods
VAR2CSA sequences were bioinformatically analysed to identify the predicted C11 and C12 cysteine residues at the C-termini of DBL domains and revised N- and C-termimal domain boundaries were predicted in VAR2CSA. Multiple construct boundaries were systematically evaluated for protein secretion in P. pastoris and secreted proteins were tested as immunogens.

Results
From a total of 42 different VAR2CSA constructs, 15 proteins (36%) were secreted. Longer construct boundaries, including the predicted C11 and C12 cysteine residues, generally improved expression of poorly or non-secreted domains and permitted expression of all six VAR2CSA DBL domains. However, protein secretion was still highly empiric and affected by subtle differences in domain boundaries and allelic variation between VAR2CSA sequences. Eleven of the secreted proteins were used to immunize rabbits. Antibodies reacted with CSA-binding infected erythrocytes, indicating that P. pastoris recombinant proteins possessed native protein epitopes.

Conclusion
These findings strengthen emerging data for a revision of DBL domain boundaries in var-encoded proteins and may facilitate pregnancy malaria vaccine development.
Survey of smokers' reasons for not switching to safer sources of nicotine and their willingness to do so in the future
Authors: Heavner Karyn K , Rosenberg Zale , Phillips Carl V 
Published: July 2009

Abstract
Despite the well-known risks of smoking, policy, social pressure, and accessible cessation programs, tens of millions of North American adults continue smoking rather than quitting or switching to less harmful non-combustion nicotine products. We surveyed people smoking in public in Edmonton, Canada (n = 242, year = 2007) to investigate smokers' reasons for resisting switching to low-risk nicotine sources. 43% had used low-risk products (mostly pharmaceutical nicotine). 75% indicated willingness to consider switching to low-risk products. Smokers cited similar reasons for not switching to smokeless tobacco and pharmaceutical nicotine, largely based on misinformation. Accurate risk information may lead many to try low-risk nicotine products.
Primary hepatic embryonal sarcoma masquerading as metastatic ovarian cancer
Authors: Kullar Peter , Stonard Christopher , Jamieson Neville , Huguet Emmanuel , Praseedom Raaj , Jah Asif 
Published: July 2009

Abstract

Background
Hepatic embryonal sarcoma (HES) is a rare but aggressive primary tumor of the liver occurring most frequently in childhood.

Case presentation
We report a case of a 52 year old woman having previously undergone treatment for ovarian serous papillary carcinoma who subsequently presented with a large solitary mass in the liver. Initially this was presumed to be metastasis from the ovarian primary however, on further examination it was shown to be a primary hepatic embryonal sarcoma.

Conclusion
Primary liver tumors should be considered in differential diagnoses in patients with ovarian cancer who subsequently present with liver tumors. This is particularly important when there is no direct evidence of recurrence of ovarian cancer.
Plasma TF activity predicts cardiovascular mortality in patients with acute myocardial infarction
Authors: Steppich Birgit A , Braun Siegmund Lorenz , Stein Andreas , Demetz Gabriele , Groha Philip , Schömig Albert , von Beckerath Nicolas , Kastrati Adnan , Ott Ilka 
Published: July 2009

Abstract

Objectives and Background
Tissue factor (TF) contributes to thrombosis following plaque disruption in acute coronary syndromes (ACS). Aim of the study was to investigate the impact of plasma TF activity on prognosis in patients with ACS.

Methods and Results
One-hundred seventy-four patients with unstable Angina pectoris (uAP) and 112 patients with acute myocardial infarction (AMI) were included with a mean follow up time of 3.26 years. On admission, plasma TF activity was assessed. Patients were categorized into 2 groups: a high-TF activity group with TF >24 pmol/L and low TF activity group with TF ≤ 24 pmol/L. Fifteen cardiovascular deaths occurred in the uAP group and 16 in the AMI group. In AMI TF activity was 24,9 ± 2,78 pmol/l (mean ± SEM) in survivors and 40,9 ± 7,96 pmol/l in nonsurvivors (P = 0.024). In uAP no differences were observed (25.0 ± 8.04 pmol/L nonsurvivors vs. 25.7 ± 2.14 pmol/L survivors; P = 0.586). Kaplan-Meier estimates of survival at 3.26 years regarding TF activity in AMI were 81.3% and 92.2% with an hazard ratio of 3.02 (95% CI [1.05–8.79], P = 0.03). The Cox proportional hazards model adjusting for correlates of age and risk factors showed that plasma TF activity was an independent correlate of survival (hazard ratio 9.27, 95% CI [1.24–69.12], P = 0.03). In an additional group of patients with uAP and AMI, we identified circulating microparticles as the prevailing reservoir of plasma TF activity in acute coronary syndromes.

Conclusion
Systemic TF activity in AMI has an unfavorable prognostic value and as a marker for dysregulated coagulation may add to predict the atherothrombotic risk.
Studies on membrane topology, N-glycosylation and functionality of SARS-CoV membrane protein
Authors: Voß Daniel , Pfefferle Susanne , Drosten Christian , Stevermann Lea , Traggiai Elisabetta , Lanzavecchia Antonio , Becker Stephan 
Published: July 2009

Abstract
The glycosylated membrane protein M of the severe acute respiratory syndrome associated coronavirus (SARS-CoV) is the main structural component of the virion and mediates assembly and budding of viral particles. The membrane topology of SARS-CoV M and the functional significance of its N-glycosylation are not completely understood as is its interaction with the surface glycoprotein S. Using biochemical and immunofluorescence analyses we found that M consists of a short glycosylated N-terminal ectodomain, three transmembrane segments and a long, immunogenic C-terminal endodomain. Although the N-glycosylation site of M seems to be highly conserved between group 1 and 3 coronaviruses, studies using a recombinant SARS-CoV expressing a glycosylation-deficient M revealed that N-glycosylation of M neither influence the shape of the virions nor their infectivity in cell culture. Further functional analysis of truncated M proteins showed that the N-terminal 134 amino acids comprising the three transmembrane domains are sufficient to mediate accumulation of M in the Golgi complex and to enforce recruitment of the viral spike protein S to the sites of virus assembly and budding in the ERGIC.
CSF/serum quotient graphs for the evaluation of intrathecal C4synthesis
Authors: Padilla-Docal Barbara , Dorta-Contreras Alberto J , Bu-Coifiu-Fanego Raisa , Rey Alexis Rodriguez 
Published: July 2009

AbstractBackgroundCerebrospinal fluid (CSF)/serum quotient graphs have been used previously to determine local synthesis in brain of immunoglobulins and C3complement component. The aim of this study was to use the same technique to construct quotient graphs, or Reibergrams, for the beta globulin C4and to evaluate the method for assessing intrathecal synthesis in neurological disease.MethodsThe constants in the previously-defined Reibergram for immunoglobulin IgA were used to calculate the CSF/serum quotient for C4. CSF and serum were analyzed for C4, IgA and albumin from a total of 12 patients with meningoencephalitis caused by encapsulated microorganisms and 10 subjects without infections or inflammatory neurological disease, some of which had dysfunction of the blood-CSF barrier,ResultsThe formula and C4Reibergram with the constants previously found for IgA, determined the intrathecal C4synthesis in CSF. The intrathecal C4fraction in CSF (C4loc in mg/l) was compared to the C4-Index (fraction of CSF: serum for C4/fraction of CSF: serum for albumin). There was a significant correlation between the two formulae. The CSF/Serum quotient graph was superior for detecting intrathecal synthesis of C4under variable conditions of blood-CSF barrier permeability.ConclusionThe C4Reibergram can be used to quantify the intrathecal synthesis of this component of the complement system in different infectious diseases of the central nervous system and is especially useful for patients with blood-brain barrier dysfunction.
Unstable angina early after aortic valve replacement surgery in a female patient with normal coronary arteries preoperatively – a case report
Authors: Gruber Sybille , Ng Choi-Keung , Schwarz Christian , Auer Johann 
Published: July 2009

Abstract

Background
Angina pectoris early after aortic valve replacement surgery in patients with previously normal coronary arteries may be life threatening and has to be assessed immediately.

Case report
12 weeks after aortic valve replacement surgery, a 60-year-old female patient was referred for evaluation of recent onset of severe chest pain on mild exertion and at rest. Coronary angiography showed severe stenosis nvolving the left coronary ostium and the left main stem. The patient was urgently referred for bypass surgery and had an uneventful postoperative recovery.

Conclusion
A high degree of suspicion is needed for early recognition and aggressive management of this rare but serious complication.
Effects of triptolide from Radix Tripterygium wilfordii (Leigongteng) on cartilage cytokines and transcription factor NF-κB: a study on induced arthritis in rats
Authors: Xiao Cheng , Zhou Jing , He Yinghui , Jia Hongwei , Zhao Linhua , Zhao Ning , Lu Aiping 
Published: July 2009

AbstractBackgroundTriptolide, an active compound ofRadix Tripterygium wilfordii, is immunosuppressive, cartilage protective and anti-inflammatory both in human and animal studies of various inflammatory and autoimmune diseases, including rheumatoid arthritis, but its therapeutic mechanism remains unclear. The aim of this study is to investigate the effects of triptolide on cartilage cytokines in the CIA model.MethodsSprague Dawley rats were immunized with type II collagen and orally administered with triptolide. The arthritic scores and incidence changes of the rats were observed. The expression of TNF-α, IL-6, COX-2 and NF-κB in paw cartilage was studied with immunohistochemical staining.ResultsTriptolide, at both high and low doses, significantly lowered the arthritic scores, delayed the onset of arthritis and lowered the arthritis incidence. Triptolide treatment at both high and low doses lowered the expression of TNF-α, IL-6, COX-2 and NF-κB in paw cartilage in arthritic rats.ConclusionTriptolide lowers the arthritic scores, delays the onset of collagen induced arthritis and reduces the expressions of TNF-α, IL-6, NF-κB and COX-2 in paw cartilage in arthritic rats.
Application of an iterative Bayesian variable selection method in a genome-wide association study of rheumatoid arthritis
Authors: Kwon Soonil , Wang Dai , Guo Xiuqing 
Published: June 2009

Abstract
Genome-wide association studies usually involve several hundred thousand of single-nucleotide polymorphisms (SNPs). Conventional approaches face challenges when there are enormous number of SNPs but a relatively small number of samples and, in some cases, are not feasible. We introduce here an iterative Bayesian variable selection method that provides a unique tool for association studies with a large number of SNPs (p) but a relatively small sample size (n). We applied this method to the simulated case-control sample provided by the Genetic Analysis Workshop 15 and compared its performance with stepwise variable selection method. We demonstrated that the results of iterative Bayesian variable selection applied to when p » n are as comparable as those of stepwise variable selection implemented to when n » p. When n > p, the iterative Bayesian variable selection performs better than stepwise variable selection does.
Cladistic analysis of genotype data-application to GAW15 Problem 3
Authors: Jung Hsuan , Zhao Keyan , Marjoram Paul 
Published: June 2009

Abstract
Given the increasing size of modern genetic data sets and, in particular, the move towards genome-wide studies, there is merit in considering analyses that gain computational efficiency by being more heuristic in nature. With this in mind, we present results of cladistic analyses methods on the Genetic Analysis Workshop 15 Problem 3 simulated data (answers known). Our analysis attempts to capture similarities between individuals using a series of trees, and then looks for regions in which mutations on those trees can successfully explain a phenotype of interest. Existing varieties of such algorithms assume haplotypes are known, or have been inferred, an assumption that is often unrealistic for genome-wide data. We therefore present an extension of these methods that can successfully analyze genotype, rather than haplotype, data.
A logistic mixture model for a family-based association study
Authors: Xing Guan , Xing Chao , Lu Qing , Elston Robert C 
Published: June 2009

Abstract
A family-based association study design is not only able to localize causative genes more precisely than linkage analysis, but it also helps explain the genetic mechanism underlying the trait under study. Therefore, it can be used to follow up an initial linkage scan. For an association study of binary traits in general pedigrees, we propose a logistic mixture model that regresses the trait value on the genotypic values of markers under investigation and other covariates such as environmental factors. We first tested both the validity and power of the new model by simulating nuclear families inheriting a simple Mendelian trait. It is powerful when the correct disease model is specified and shows much loss of power when the dominance of a model is inversely specified, i.e., a dominant model is wrongly specified as recessive or vice versa. We then applied the new model to the Genetic Analysis Workshop (GAW) 15 simulation data to test the performance of the model when adjusting for covariates in the case of complex traits. Adjusting for the covariate that interacts with disease loci improves the power to detect association. The simplest version of the model only takes monogenic inheritance into account, but analysis of the GAW simulation data shows that even this simple model can be powerful for complex traits.
The role of heritability in mapping expression quantitative trait loci
Authors: Huang Song , Ballard David , Zhao Hongyu 
Published: June 2009

Abstract
Gene expression, as a heritable complex trait, has recently been used in many genome-wide linkage studies. The estimated overall heritability of each trait may be considered as evidence of a genetic contribution to the total phenotypic variation, which implies the possibility of mapping genome regions responsible for the gene expression variation via linkage analysis. However, heritability has been found to be an inconsistent predictor of significant linkage signals. To investigate this issue in human studies, we performed genome-wide linkage analysis on the 3554 gene expression traits of 194 Centre d'Etude du Polymorphisme Humain individuals provided by Genetic Analysis Workshop 15. Out of the 422 expression traits with significant linkage signals identified (LOD > 5.3), 89 traits have low estimated heritability (h
2 < 10%), among which 23 traits have an estimated heritability equal to 0. The linkage analysis on individual pedigree shows that the overall LOD scores may result from a few pedigrees with strong linkage signals. Screening gene expressions before linkage analysis using a relatively low heritability (h
2 < 20%) may result in a loss of significant linkage signals, especially for trans-acting expression quantitative trait loci (49%).