bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Integrated Nowcasting through Comprehensive Analysis (INCA) System and Its Validation over the Eastern Alpine Region
Authors: Haiden T. , Kann A. , Wittmann C. , Pistotnik G. , Bica B. , Gruber C. 
Published: November 2010

Abstract
This paper presents the Integrated Nowcasting through Comprehensive Analysis (INCA) system, which has been developed for use in mountainous terrain. Analysis and nowcasting fields include temperature, humidity, wind, precipitation amount, precipitation type, cloudiness, and global radiation. The analysis part of the system combines surface station data with remote sensing data in such a way that the observations at the station locations are reproduced, whereas the remote sensing data provide the spatial structure for the interpolation. The nowcasting part employs classical correlation-based motion vectors derived from previous consecutive analyses. In the case of precipitation the nowcast includes an intensity-dependent elevation effect. After 2–6 h of forecast time the nowcast is merged into an NWP forecast provided by a limited-area model, using a predefined temporal weighting function. Cross validation of the analysis and verification of the nowcast are performed. Analysis quality is high for temperature, but comparatively low for wind and precipitation, because of the limited representativeness of station data in mountainous terrain, which can be only partially compensated by the analysis algorithm. Significant added value of the system compared to the NWP forecast is found in the first few hours of the nowcast. At longer lead times the effects of the latest observations becomes small, but in the case of temperature the downscaling of the NWP forecast within the INCA system continues to provide some improvement compared to the direct NWP output.
Forecasting Tropical Cyclone Formation in the Fiji Region: A Probit Regression Approach Using Bayesian Fitting
Authors: Chand Savin S. , Walsh Kevin J. E. 
Published: November 2010

Abstract
An objective methodology for forecasting the probability of tropical cyclone (TC) formation in the Fiji, Samoa, and Tonga regions (collectively the FST region) using antecedent large-scale environmental conditions is investigated. Three separate probabilistic forecast schemes are developed using a probit regression approach where model parameters are determined via Bayesian fitting. These schemes provide forecasts of TC formation from an existing system (i) within the next 24 h (W24h), (ii) within the next 48 h (W48h), and (iii) within the next 72 h (W72h). To assess the performance of the three forecast schemes in practice, verification methods such as the posterior expected error, Brier skill scores, and relative operating characteristic skill scores are applied. Results suggest that the W24h scheme, which is formulated using large-scale environmental parameters, on average, performs better than that formulated using climatology and persistence (CLIPER) variables. In contrast, the W48h (W72h) scheme formulated using large-scale environmental parameters performs similar to (poorer than) that formulated using CLIPER variables. Therefore, large-scale environmental parameters (CLIPER variables) are preferred as predictors when forecasting TC formation in the FST region within 24 h (at least 48 h) using models formulated in the present investigation.
The internalized stigma experienced by members of a mental health advocacy group in South Africa
Authors: Sorsdahl Katherine R. , Kakuma Ritsuko , Wilson Zane , Stein Dan J. 
Published: November 2010

Background: Although there is a growing literature on internalized stigma from the developed world, very little research has been conducted in developing countries such as South Africa. Therefore, the purpose of this study was to describe the internalized stigma experienced by members of a mental health advocacy group in South Africa and relationships between self-stigma and other constructs, namely, empowerment, perceived devaluation and discrimination. Methods: Self-administered questionnaires measuring respondents reported levels of internalized stigma, empowerment and perceived devaluation and discrimination were distributed to all the members of the South African Depression & Anxiety Group (SADAG) by post and via email. Of the 850 members invited to participate, 142 members of SADAG completed the questionnaire. Pearson correlations were computed and multiple regression analyses were carried out to analyse the data. Results: The highest reports of stigma were for stigma resistance (mean = 2.9), alienation (mean = 2.47) and perceived discrimination (mean = 2.24). Low levels of stereotype endorsement (mean = 1.77) and social withdrawal (mean = 1.22) were reported. Although respondents often felt that the public held negative attitudes towards individuals suffering with a mental illness (perceived devaluation and discrimination scale (PDD), mean = 2.95), a majority of respondents reported high levels of empowerment (mean = 3.0) and self-efficacy (mean = 2.47). After controlling for socio-demographic factors, higher scores on the PDD were associated with social withdrawal and having experienced discrimination. Conclusion: Internalization of stigma, disempowerment and loss of self-esteem are not inevitable consequences for all individuals with a mental illness. Nevertheless, perceived stigma is significantly associated with social withdrawal and experienced discrimination.
Clinical and Radiographic Predictors of Intra-articular Hip Disease in Arthroscopy
Authors: Nepple Jeffrey J. , Carlisle John C. , Nunley Ryan M. , Clohisy John C. 
Published: November 2010

Background: The arthroscopic treatment of intra-articular hip disease and associated structural abnormalities continues to evolve. Nevertheless, contemporary diagnostic tools have significant limitations in predicting severity of disease preoperatively. Hypothesis: Clinical characteristics and radiographic parameters correlate with and predict intra-articular disease patterns in patients undergoing hip arthroscopy. Study Design: Cohort study; Level of evidence, 3. Methods: In sum, 355 hips in 338 patients undergoing hip arthroscopy by a single surgeon were retrospectively reviewed. Clinical characteristics and radiographic findings (on anteroposterior pelvis and frog lateral radiographs) of mild dysplasia, cam, and pincer-type femoroacetabular impingement were compared with intraoperative labral and chondral disease patterns. Results: Labral tears were present in 90.1% of hips, and acetabular cartilage lesions were present in 67.3%, including 41.7% with grade 3 or 4 chondromalacia. Multivariate logistic regression analysis found male sex, older age (<30, 30-50, >50 years old), Tönnis osteoarthritis grade, and alpha angle >50° on frog lateral radiograph to be independently associated with increased risk of grade 3 or 4 acetabular chondromalacia (all P < .001). Insidious onset of pain (in contrast to acute onset) was independently associated with the presence of acetabular chondromalacia ( P = .002). Cam-type femoroacetabular impingement (alpha angle >50°) was strongly associated with more severe labral disease ( P < .001). Findings of acetabular dysplasia and pincer femoroacetabular impingement did not remain significantly associated with acetabular chondral disease in the multivariate analysis. Conclusion: Several clinical and radiographic characteristics—most notably, male sex, older age, Tönnis grade, and elevated alpha angle—are associated with more severe intra-articular hip disease. The recognition of these associations between clinical and radiographic characteristics and hip disease patterns is important for patient selection, surgical planning, and patient counseling.
Return to the Preinjury Level of Competitive Sport After Anterior Cruciate Ligament Reconstruction Surgery
Authors: Ardern Clare L. , Webster Kate E. , Taylor Nicholas F. , Feller Julian A. 
Published: November 2010

Background: An athlete’s desire to return to sport after anterior cruciate ligament (ACL) injury is a major indication for ACL reconstruction surgery. Typical clearance to return is 6 to 12 months postoperatively. Purpose: To investigate the return-to-sport rate and participation level of a large cohort at 12 months after ACL reconstruction surgery. Study Design: Case series; Level of evidence, 4. Methods: Data were analyzed for 503 patients who participated in competitive-level Australian football, basketball, netball, or soccer after ACL reconstruction surgery using a quadruple-strand hamstring autograft. Inclusion criteria included participation in competitive sport before the ACL injury and clearance from the orthopaedic surgeon to return to sport postoperatively. Patients completed a self-report questionnaire regarding preoperative and postoperative sports participation and the Cincinnati Sports Activity Scale. The International Knee Documentation Committee (IKDC) knee evaluation form and hop tests were used to evaluate knee function. Results: Sixty-seven percent of patients attempted some form of sports activity by 12 months postoperatively; 33% attempted competitive sport. Of those who did not attempt any sports activity by 12 months, 47% indicated that they were planning to return. Men were significantly more likely than women to return. Patients who played sports with a seasonal competition, versus a year-round competition, were significantly more likely to return by 12 months. Patients with normal postoperative knee function (IKDC category A), versus those with nearly normal function (IKDC category B), were no more likely to return, but patients with good hop test results (≥85% limb symmetry index) were more likely to return than patients with poor results (<85%). Conclusion: People may require a longer postoperative rehabilitation period than that typically advocated to facilitate a successful return to competitive sport after ACL reconstruction surgery. The relationship between postoperative knee function and return-to-sport outcomes at 12 months after surgery was inconclusive.
SR-A/MARCO–mediated ligand delivery enhances intracellular TLR and NLR function, but ligand scavenging from cell surface limits TLR4 response to pathogens
Authors: Mukhopadhyay Subhankar , Varin Audrey , Chen Yunying , Liu Baoying , Tryggvason Karl , Gordon Siamon 
Published: November 2010

AbstractPhagocytic and pathogen sensing receptors are responsible for particle uptake and inflammation. It is unclear how these receptors' systems influence each other's function to shape an innate response. The class-A scavenger receptors SR-A (scavenger receptor A) and MARCO (macrophage receptor with collagenous structure) are 2 well-characterized phagocytic receptors that are unable to initiate inflammatory responses by themselves, yet are implicated in the pathogenesis of various inflammatory disorders. However, the mechanism for such an apparent discrepancy is still unclear. We utilized SR-A−/−, MARCO−/−, and SR-A−/−-MARCO−/− mice, along with microbe-derived, environmental, and synthetic polyanions to assess the inflammatory responses following combinatorial ligation of SR-A/MARCO and selected Toll-like receptors (TLRs) and nucleotide-binding oligomerization domain (NOD)–like receptors (NLRs) by their shared ligands. In addition to ligating SR-A and MARCO, these agonists also selectively activated the cell-surface sensor TLR4, endosomal TLR3, and the cytosolic NOD2 and NALP3 (NACHT domain–, leucine-rich repeat–, and pyrin domain–containing protein 3). We show that, following recognition of common ligands, SR-A and MARCO attenuate TLR4-mediated responses while enhancing responses by the intracellular TLR3, NOD2, and NALP3. We conclude that SR-A/MARCO-mediated rapid ligand internalization prevented sensing by surface TLRs while increasing ligand availability in intracellular compartments, thus allowing sensing and robust responses by intracellular sensors.
Pregnancy outcomes after maternal exposure to rituximab
Authors: Chakravarty Eliza F. , Murray Elaine R. , Kelman Ariella , Farmer Pamela 
Published: November 2010

Abstract
Rituximab is a chimeric anti-CD20 monoclonal B cell–depleting antibody indicated for certain hematologic malignancies and active rheumatoid arthritis with inadequate response to tumor necrosis factor antagonists. Despite counseling to avoid pregnancy, women may inadvertently become pregnant during or after rituximab treatment. Using the rituximab global drug safety database, we identified 231 pregnancies associated with maternal rituximab exposure. Maternal indications included lymphoma, autoimmune cytopenias, and other autoimmune diseases. Most cases were confounded by concomitant use of potentially teratogenic medications and severe underlying disease. Of 153 pregnancies with known outcomes, 90 resulted in live births. Twenty-two infants were born prematurely; with one neonatal death at 6 weeks. Eleven neonates had hematologic abnormalities; none had corresponding infections. Four neonatal infections were reported (fever, bronchiolitis, cytomegalovirus hepatitis, and chorioamnionitis). Two congenital malformations were identified: clubfoot in one twin, and cardiac malformation in a singleton birth. One maternal death from pre-existing autoimmune thrombocytopenia occurred. Although few congenital malformations or neonatal infections were seen among exposed neonates, women should continue to be counseled to avoid pregnancy for ≤ 12 months after rituximab exposure; however, inadvertent pregnancy does occasionally occur. Practitioners are encouraged to report complete information to regulatory authorities for all pregnancies with suspected or known exposure to rituximab.
Sampling the conformation of protein surface residues for flexible protein docking
Authors: Francis-Lyon Patricia , Gu Shengyin , Hass Joel , Amenta Nina , Koehl Patrice 
Published: November 2010

Abstract

Background
The problem of determining the physical conformation of a protein dimer, given the structures of the two interacting proteins in their unbound state, is a difficult one. The location of the docking interface is determined largely by geometric complementarity, but finding complementary geometry is complicated by the flexibility of the backbone and side-chains of both proteins. We seek to generate candidates for docking that approximate the bound state well, even in cases where there is backbone and/or side-chain difference from unbound to bound states.

Results
We divide the surfaces of each protein into local patches and describe the effect of side-chain flexibility on each patch by sampling the space of conformations of its side-chains. Likely positions of individual side-chains are given by a rotamer library; this library is used to derive a sample of possible mutual conformations within the patch. We enforce broad coverage of torsion space. We control the size of the sample by using energy criteria to eliminate unlikely configurations, and by clustering similar configurations, resulting in 50 candidates for a patch, a manageable number for docking.

Conclusions
Using a database of protein dimers for which the bound and unbound structures of the monomers are known, we show that from the unbound patch we are able to generate candidates for docking that approximate the bound structure. In patches where backbone change is small (within 1 Å RMSD of bound), we are able to account for flexibility and generate candidates that are good approximations of the bound state (82% are within 1 Å and 98% are within 1.4 Å RMSD of the bound conformation). We also find that even in cases of moderate backbone flexibility our candidates are able to capture some of the overall shape change. Overall, in 650 of 700 test patches we produce a candidate that is either within 1 Å RMSD of the bound conformation or is closer to the bound state than the unbound is.
The rapid generation of chimerical genes expanding protein diversity in zebrafish
Authors: Fu Beide , Chen Ming , Zou Ming , Long Manyuan , He Shunping 
Published: November 2010

Abstract

Background
Variation of gene number among species indicates that there is a general process of new gene origination. One of the major mechanism providing raw materials for the origin of new genes is gene duplication. Retroposition, as a special type of gene duplication- the RNA-based duplication, has been found to play an important role in new gene evolution in mammals and plants, but little is known about the process in the teleostei genome.

Results
Here we screened the zebrafish genome for identification of retrocopies and new chimerical retrogenes and investigated their origination and evolution. We identified 652 retrocopies, of which 440 are intact retrogenes and 212 are pseudogenes. Retrocopies have long been considered evolutionary dead ends without functional significance due to the presumption that retrocopies lack the regulatory element needed for expression. However, 437 transcribed retrocopies were identified from all of the retrocopies. This discovery combined with the substitution analysis suggested that the majority of all retrocopies are subject to negative selection, indicating that most of the retrocopies may be functional retrogenes. Moreover, we found that 95 chimerical retrogenes had recruited new sequences from neighboring genomic regions that formed de novo splice sites, thus generating new intron-containing chimeric genes. Based on our analysis of 38 pairs of orthologs between Cyprinus carpio and Danio rerio, we found that the synonymous substitution rate of zebrafish genes is 4.13×10-9 substitution per silent site per year. We also found 10 chimerical retrogenes that were created in the last 10 million years, which is 7.14 times the rate of 0.14 chimerical retrogenes per million years in the primate lineage toward human and 6.25 times the rate of 0.16 chimerical genes per million years in Drosophila. This is among the most rapid rates of generation of chimerical genes, just next to the rice.

Conclusion
There is compelling evidence that much of the extensive transcriptional activity of retrogenes does not represent transcriptional "noise" but indicates the functionality of these retrogenes. Our results indicate that retroposition created a large amount of new genes in the zebrafish genome, which has contributed significantly to the evolution of the fish genome.
Comparative analyses of vertebrate posterior HoxD clusters reveal atypical cluster architecture in the caecilian Typhlonectes natans
Authors: Mannaert An , Amemiya Chris T , Bossuyt Franky 
Published: November 2010

Abstract

Background
The posterior genes of the HoxD cluster play a crucial role in the patterning of the tetrapod limb. This region is under the control of a global, long-range enhancer that is present in all vertebrates. Variation in limb types, as is the case in amphibians, can probably not only be attributed to variation in Hox genes, but is likely to be the product of differences in gene regulation. With a collection of vertebrate genome sequences available today, we used a comparative genomics approach to study the posterior HoxD cluster of amphibians. A frog and a caecilian were included in the study to compare coding sequences as well as to determine the gain and loss of putative regulatory sequences.

Results
We sequenced the posterior end of the HoxD cluster of a caecilian and performed comparative analyses of this region using HoxD clusters of other vertebrates. We determined the presence of conserved non-coding sequences and traced gains and losses of these footprints during vertebrate evolution, with particular focus on amphibians. We found that the caecilian HoxD cluster is almost three times larger than its mammalian counterpart. This enlargement is accompanied with the loss of one gene and the accumulation of repeats in that area. A similar phenomenon was observed in the coelacanth, where a different gene was lost and expansion of the area where the gene was lost has occurred. At least one phylogenetic footprint present in all vertebrates was lost in amphibians. This conserved region is a known regulatory element and functions as a boundary element in neural tissue to prevent expression of Hoxd genes.

Conclusion
The posterior part of the HoxD cluster of Typhlonectes natans is among the largest known today. The loss of Hoxd-12 and the expansion of the intergenic region may exert an influence on the limb enhancer, by having to bypass a distance seven times that of regular HoxD clusters. Whether or not there is a correlation with the loss of limbs remains to be investigated. These results, together with data on other vertebrates show that the tetrapod Hox clusters are more variable than previously thought.
Skeletal muscle gene expression in response to resistance exercise: sex specific regulation
Authors: Liu Dongmei , Sartor Maureen A , Nader Gustavo A , Gutmann Laurie , Treutelaar Mary K , Pistilli Emidio E , IglayReger Heidi B , Burant Charles F , Hoffman Eric P , Gordon Paul M 
Published: November 2010

Abstract
Background
The molecular mechanisms underlying the sex differences in human muscle morphology and function remain to be elucidated. The sex differences in the skeletal muscle transcriptome in both the resting state and following anabolic stimuli, such as resistance exercise (RE), might provide insight to the contributors of sexual dimorphism of muscle phenotypes. We used microarrays to profile the transcriptome of the biceps brachii of young men and women who underwent an acute unilateral RE session following 12 weeks of progressive training. Bilateral muscle biopsies were obtained either at an early (4 h post-exercise) or late recovery (24 h post-exercise) time point. Muscle transcription profiles were compared in the resting state between men (n = 6) and women (n = 8), and in response to acute RE in trained exercised vs. untrained non-exercised control muscle for each sex and time point separately (4 h post-exercise, n = 3 males, n = 4 females; 24 h post-exercise, n = 3 males, n = 4 females). A logistic regression-based method (LRpath), following Bayesian moderated t-statistic (IMBT), was used to test gene functional groups and biological pathways enriched with differentially expressed genes.

Results
This investigation identified extensive sex differences present in the muscle transcriptome at baseline and following acute RE. In the resting state, female muscle had a greater transcript abundance of genes involved in fatty acid oxidation and gene transcription/translation processes. After strenuous RE at the same relative intensity, the time course of the transcriptional modulation was sex-dependent. Males experienced prolonged changes while females exhibited a rapid restoration. Most of the biological processes involved in the RE-induced transcriptional regulation were observed in both males and females, but sex specificity was suggested for several signaling pathways including activation of notch signaling and TGF-beta signaling in females. Sex differences in skeletal muscle transcriptional regulation might implicate a mechanism behind disproportional muscle growth in males as compared with female counterparts after RE training at the same relative intensity.

Conclusions
Sex differences exist in skeletal muscle gene transcription both at rest and following acute RE, suggesting that sex is a significant modifier of the transcriptional regulation in skeletal muscle. The findings from the present study provide insight into the molecular mechanisms for sex differences in muscle phenotypes and for muscle transcriptional regulation associated with training adaptations to resistance exercise.