bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and Validation of an Operational Search and Rescue Modeling System for the Yellow Sea and the East and South China Seas
Authors: Cho Kyoung-Ho , Li Yan , Wang Hui , Park Kwang-Soon , Choi Jin-Yong , Shin Kwang-Il , Kwon Jae-Il 
Published: October 2013

Abstract
An operational search and rescue (SAR) modeling system was developed to forecast the tracks of victims or debris from marine accidents in the marginal seas of the northwestern Pacific Ocean. The system is directly linked to a real-time operational forecasting system that provides wind and surface current forecasts for the Yellow Sea and the East and South China Seas and is thus capable of immediately predicting the tracks and area to be searched for up to 72 h in the future. A stochastic trajectory model using a Monte Carlo ensemble technique is employed within the system to estimate the trajectories of drifting objects. It is able to consider leeway drift and to deal with uncertainties in the forcing fields obtained from the operational forecasting system. A circle assessment method was applied to evaluate the performance of the SAR model using comparisons in buoy and ship trajectories obtained from field drifter experiments. The method effectively analyzed the effects of the forcing fields and diagnosed the model’s performance. Results showed that accurate wind and current forcing fields play a significant role in improving the behavior of the SAR model. Operationally, the SAR modeling system is used to support the Korea Coast Guard during marine emergencies. Additionally, some sensitivity tests for model parameters and wave effect on the SAR model prediction are discussed.
On the Filtering Properties of Ensemble Averaging for Storm-Scale Precipitation Forecasts
Authors: Surcel Madalina , Zawadzki Isztar , Yau M. K. 
Published: October 2013

Abstract
The mean (ENM) of an ensemble of precipitation forecasts is generally more skillful than any of the members as verified against observations. A major reason is that the averaging filters out nonpredictable features on which the members disagree. Previous research showed that the nonpredictable features occur at small scales, in both numerical forecasts and Lagrangian persistence nowcasts. Hence, it is plausible that the unpredictable features filtered through ensemble averaging would also occur at small scales. In this study, the exact range of scales affected by averaging is determined by comparing the statistical properties of precipitation fields between the ENM and the individual members from a Storm-Scale Ensemble Forecasting (SSEF) system run during NOAA’s 2008 Hazardous Weather Testbed (HWT) Spring Experiment. The filtering effect of ensemble averaging results in a low-intensity bias for the ENM forecasts. It has been previously proposed to correct the ENM forecasts by recalibrating the intensities in the ENM using the probability density function (PDF) of rainfall values from the ensemble members. This procedure, probability matching (PM), leads to a new ensemble mean, the probability matched mean (PMM). Past studies have shown that the PMM appears more realistic and yields better skill as evaluated using traditional scores. However, the authors demonstrate here that despite the PMM having the same PDF of rainfall intensities as the ensemble members, the spectral structure and the spatial distribution of the precipitation field differs from that of the members. It is the lesser variability of the PMM fields at small scales that causes the better scores of the PMM relative to the ensemble members.
Desmolaris, a novel factor XIa anticoagulant from the salivary gland of the vampire bat (Desmodus rotundus) inhibits inflammation and thrombosis in vivo
Authors: Ma Dongying , Mizurini Daniella M. , Assumpção Teresa C. F. , Li Yuan , Qi Yanwei , Kotsyfakis Michail , Ribeiro José M. C. , Monteiro Robson Q. , Francischetti Ivo M. B. 
Published: October 2013

Key Points
Desmolaris, a major anticoagulant from vampire bat saliva, has been identified as a novel FXIa inhibitor. Desmolaris inhibits arterial thrombosis at concentrations that does not impair hemostasis.
Association of Genetic polymorphism of PPARγ-2, ACE, MTHFR, FABP-2 and FTO genes in risk prediction of type 2 diabetes mellitus
Authors: Abbas Shania , Raza Syed Tasleem , Ahmed Faisal , Ahmad Absar , Rizvi Saliha , Mahdi Farzana 
Published: October 2013

Abstract
Type 2 diabetes mellitus (T2DM) is a non-autoimmune, complex, heterogeneous and polygenic metabolic disease condition characterized by persistent elevated blood glucose levels (hyperglycemia). India as said to be the diabetic capital of the world is likely to experience the largest increase in T2DM and a greater number of diabetic individuals in the world by the year 2030. Identification of specific genetic variations in a particular ethnic group has a critical role in understanding the risk of developing T2DM in a much efficient way in future. These genetic variations include numerous types of polymorphisms among which single nucleotide polymorphisms (SNPs) is the most frequent. SNPs are basically located within the regulatory elements of several gene sequences. There are scores of genes interacting with various environmental factors affecting various pathways and sometimes even the whole signalling network that cause diseases like T2DM. This review discusses the biomarkers for early risk prediction of T2DM. Such predictions could be used in order to understand the pathogenesis of T2DM and to better diagnostics, treatment, and eventually prevention.
Molecular co-evolution of a protease and its substrate elucidated by analysis of the activity of predicted ancestral hatching enzyme
Authors: Kawaguchi Mari , Inoue Koji , Iuchi Ichiro , Nishida Mutsumi , Yasumasu Shigeki 
Published: October 2013

Abstract

Background
Hatching enzyme is a protease that digests the egg envelope, enabling hatching of the embryo. We have comprehensively studied the molecular mechanisms of the enzyme action to its substrate egg envelope, and determined the gene/protein structure and phylogenetic relationships. Because the hatching enzyme must have evolved while maintaining its ability to digest the egg envelope, the hatching enzyme-egg envelope protein pair is a good model for studying molecular co-evolution of a protease and its substrate.

Results
Hatching enzymes from medaka (Oryzias latipes) and killifish (Fundulus heteroclitus) showed species-specific egg envelope digestion. We found that by introducing four medaka-type residue amino acid substitutions into recombinant killifish hatching enzyme, the mutant killifish hatching enzyme could digest medaka egg envelope. Further, we studied the participation of the cleavage site of the substrate in the species-specificity of hatching enzyme. A P2-site single amino acid substitution was responsible for the species-specificity. Estimation of the activity of the predicted ancestral enzymes towards various types of cleavage sites along with prediction of the evolutionary timing of substitutions allowed prediction of a possible evolutionary pathway, as follows: ancestral hatching enzyme, which had relatively strict substrate specificity, developed broader specificity as a result of four amino acid substitutions in the active site cleft of the enzyme. Subsequently, a single substitution occurred within the cleavage site of the substrate, and the recent feature of species-specificity was established in the hatching enzyme-egg envelope system.

Conclusions
The present study clearly provides an ideal model for protease-substrate co-evolution. The evolutionary process giving rise to species-specific egg envelope digestion of hatching enzyme was initiated by amino acid substitutions in the enzyme, resulting in altered substrate specificity, which later allowed an amino acid substitution in the substrate.
Genome-wide association and prediction of direct genomic breeding values for composition of fatty acids in Angus beef cattlea
Authors: Saatchi Mahdi , Garrick Dorian J , Tait Richard G , Mayes Mary S , Drewnoski Mary , Schoonmaker Jon , Diaz Clara , Beitz Don C , Reecy James M 
Published: October 2013

AbstractBackgroundAs consumers continue to request food products that have health advantages, it will be important for the livestock industry to supply a product that meet these demands. One such nutrient is fatty acids, which have been implicated as playing a role in cardiovascular disease. Therefore, the objective of this study was to determine the extent to which molecular markers could account for variation in fatty acid composition of skeletal muscle and identify genomic regions that harbor genetic variation.ResultsSubsets of markers on the Illumina 54K bovine SNPchip were able to account for up to 57% of the variance observed in fatty acid composition. In addition, these markers could be used to calculate a direct genomic breeding values (DGV) for a given fatty acids with an accuracy (measured as simple correlations between DGV and phenotype) ranging from -0.06 to 0.57. Furthermore, 57 1-Mb regions were identified that were associated with at least one fatty acid with a posterior probability of inclusion greater than 0.90. 1-Mb regions on BTA19, BTA26 and BTA29, which harbored fatty acid synthase, Sterol-CoA desaturase and thyroid hormone responsive candidate genes, respectively, explained a high percentage of genetic variance in more than one fatty acid. It was also observed that the correlation between DGV for different fatty acids at a given 1-Mb window ranged from almost 1 to -1.ConclusionsFurther investigations are needed to identify the causal variants harbored within the identified 1-Mb windows. For the first time, Angus breeders have a tool whereby they could select for altered fatty acid composition. Furthermore, these reported results could improve our understanding of the biology of fatty acid metabolism and deposition.
Potential cancer-related role of circadian gene TIMELESS suggested by expression profiling and in vitro analyses
Authors: Mao Yingying , Fu Alan , Leaderer Derek , Zheng Tongzhang , Chen Kun , Zhu Yong 
Published: October 2013

AbstractBackgroundThe circadian clock and cell cycle are two global regulatory systems that have pervasive behavioral and physiological effects on eukaryotic cells, and both play a role in cancer development. Recent studies have indicated that the circadian and cell cycle regulator, TIMELESS, may serve as a molecular bridge between these two regulatory systems.MethodsTo assess the role of TIMELESS in tumorigenesis, we analyzed TIMELESS expression data from publically accessible online databases. A loss-of-function analysis was then performed using TIMELESS-targeting siRNA oligos followed by a whole-genome expression microarray and network analysis. We further tested the effect of TIMELESS down-regulation on cell proliferation rates of a breast and cervical cancer cell line, as suggested by the results of our network analysis.ResultsTIMELESS was found to be frequently overexpressed in different tumor types compared to normal controls. Elevated expression of TIMELESS was significantly associated with more advanced tumor stage and poorer breast cancer prognosis. We identified a cancer-relevant network of transcripts with altered expression following TIMELESS knockdown which contained many genes with known functions in cancer development and progression. Furthermore, we observed that TIMELESS knockdown significantly decreased cell proliferation rate.ConclusionsOur results suggest a potential role for TIMELESS in tumorigenesis, which warrants further investigation of TIMELESS expression as a potential biomarker of cancer susceptibility and prognostic outcome.
Transient anterior subcapsular vacuolar change of the crystalline lens in patients after posterior chamber phakic intraocular lens implantation
Authors: Chung Jin Kwon , Shin Jin Hee , Lee Sung Jin 
Published: October 2013

Abstract

Background
We present two cases of transient vacuolar changes in the anterior subcapsular space of the crystalline lens in patients after posterior chamber phakic intraocular lens implantation.

Case presentation
Implantable collamer lenses (ICL) were implanted in healthy myopic patients. Vacuolar changes developed just after the irrigating procedure through the narrow space between the ICL and the crystalline lens. Slit-lamp examinations and spectral domain optical coherence tomography showed bleb-like lesions in the anterior subcapsular space of one eye in each case, though the lesions gradually improved without visual deterioration. Consequently, the lesions turned into a few anterior subcapsular small faint opacities.

Conclusion
Direct irrigation of the narrow space confined by the ICL and the crystalline lens is at risk for the development of vacuolar changes in the crystalline lens. The observed spontaneous reversal indicates that surgeons should not rush to surgical intervention but rather opt for close follow over several weeks.
Use of different subjective health indicators to assess health inequalities in an urban immigrant population in north-western Italy: a cross-sectional study
Authors: Domnich Alexander , Amicizia Daniela , Panatto Donatella , Signori Alessio , Perelli Valentina , Adamoli Sergio , Riboli Edoardo Berti , Gasparini Roberto 
Published: October 2013

Abstract

Background
Despite the steady growth of the immigrant population in Italy, data on the health status of immigrants are scarce. Our main goals were to measure Health-Related Quality of Life (HRQoL), Self-Rated Health (SRH) and morbidity among immigrants in Genoa. We aimed to assess the relative contribution of some social, structural and behavioral determinants to “within-group” health disparities.

Methods
We enrolled 502 subjects by means of snowball sampling. The SF-12 questionnaire, integrated with socio-demographic and health-related items, was used. Multivariate logistic and Poisson regression models were applied in order to identify characteristics associated with poor SRH, lower SF-12 scores and prevalence of self-reported morbidities.

Results
Subjects showed relatively moderate levels of HRQoL (median physical and mental scores of 51.6 and 47.3, respectively) and about 15% of them rated their health as fair or poor. Lower scores in the physical dimension of HRQoL were associated with the presence of morbidities and immigration for work and religious reasons, while those who had migrated for religious and family reasons displayed a lower probability of lower scores in the mental dimension of HRQoL. Poor SRH was associated with female gender, overweight/obesity and presence of morbidities. Moreover, compared with immigrants from countries with a low human development index, immigrants from highly developed societies showed significantly lower odds of reporting poor SRH. About one-third of respondents reported at least one medical condition, while the prevalence of multi-morbidity was 10%. Females, over 45-year-olds, overweight and long-term immigrants had a higher prevalence of medical conditions.

Conclusions
Our study confirms the presence of health inequalities within a heterogeneous immigrant population. HRQoL, SRH and morbidity are valid, relatively rapid and cheap tools for measuring health inequalities, though they do so in different ways. These indicators should be used with caution and, if possible, simultaneously, as they could help to identify and to monitor more vulnerable subjects among immigrants.
Meta-analysis confirms association between TNFA- G238A variant and JIA, and between PTPN22-C1858T variant and oligoarticular, RF-polyarticular and RF-positive polyarticular JIA
Authors: Kaalla Merlyn J , Broadaway K Alaine , Rohani-Pichavant Mina , Conneely Karen N , Whiting April , Ponder Lori , Okou David T , Angeles-Han Sheila , Rouster-Stevens Kelly , Brown Milton R , Vogler Larry B , Jorde Lynn B , Bohnsack John F , Epstein Michael P , Prahalad Sampath 
Published: October 2013

Abstract

Background
Although more than 100 non-HLA variants have been tested for associations with juvenile idiopathic arthritis (JIA) in candidate gene studies, only a few have been replicated. We sought to replicate reported associations of single nucleotide polymorphisms (SNPs) in the PTPN22, TNFA and MIF genes in a well-characterized cohort of children with JIA.

Methods
We genotyped and analyzed 4 SNPs in 3 genes: PTPN22 C1858T (rs2476601), TNFA G-308A, G-238A (rs1800629, rs361525) and MIF G-173C (rs755622) in 647 JIA cases and 751 healthy controls. We tested for association between each variant and JIA as well as JIA subtypes. We adjusted for multiple testing using permutation procedures. We also performed a meta-analysis that combined our results with published results from JIA association studies.

Results
While the PTPN22 variant showed only modest association with JIA (OR = 1.29, p = 0.0309), it demonstrated a stronger association with the RF-positive polyarticular JIA subtype (OR = 2.12, p = 0.0041). The MIF variant was not associated with the JIA as a whole or with any subtype. The TNFA-238A variant was associated with JIA as a whole (OR 0.66, p = 0.0265), and demonstrated a stronger association with oligoarticular JIA (OR 0.33, p = 0.0006) that was significant after correction for multiple testing. TNFA-308A was not associated with JIA, but was nominally associated with systemic JIA (OR = 0.33, p = 0.0089) and enthesitis-related JIA (OR = 0.40, p = 0.0144). Meta-analyses confirmed significant associations between JIA and PTPN22 (OR 1.44, p <0.0001) and TNFA-238A (OR 0.69, p < 0.0086) variants. Subtype meta-analyses of the PTPN22 variant revealed associations between RF-positive, RF-negative, and oligoarticular JIA, that remained significant after multiple hypothesis correction (p < 0.0005, p = 0.0007, and p < 0.0005, respectively).

Conclusions
We have confirmed associations between JIA and PTPN22 and TNFA G-308A. By performing subtype analyses, we discovered a statistically-significant association between the TNFA-238A variant and oligoarticular JIA. Our meta-analyses confirm the associations between TNFA-238A and JIA, and show that PTPN22 C1858T is associated with JIA as well as with RF-positive, RF-negative and oligoarticular JIA.
Predictive value of in vitro assays depends on the mechanism of toxicity of metal oxide nanoparticles
Authors: Cho Wan-Seob , Duffin Rodger , Bradley Mark , Megson Ian L , MacNee William , Lee Jong Kwon , Jeong Jayoung , Donaldson Ken 
Published: October 2013

AbstractBackgroundHazard identification for risk assessment of nanoparticles (NPs) is mainly composed ofin vitrocell-based assays andin vivoanimal experimentation. The rapidly increasing number and functionalizations of NPs makesin vivotoxicity tests undesirable on both ethical and financial grounds, creating an urgent need for development ofin vitrocell-based assays that accurately predictin vivotoxicity and facilitate safe nanotechnology.MethodsIn this study, we used 9 different NPs (CeO2, TiO2, carbon black, SiO2, NiO, Co3O4, Cr2O3, CuO, and ZnO). As anin vivotoxicity endpoint, the acute lung inflammogenicity in a rat instillation model was compared with thein vitrotoxicity endpoints comprising cytotoxicity, pro-inflammatory cytokine expression, or haemolytic potential. Forin vitroassays, 8 different cell-based assays were used including epithelial cells, monocytic/macrophage cells, human erythrocytes, and combined culture.ResultsZnO and CuO NPs acting via soluble toxic ions showed positive results in most of assays and were consistent with the lung inflammation data. When compared inin vitroassays at the same surface area dose (30 cm2/mL), NPs that were low solubility and therefore acting via surface reactivity had no convincing activity, except for CeO2NP. Cytotoxicity in differentiated peripheral blood mononuclear cells was the most accurate showing 89% accuracy and 11% false negativity in predicting acute lung inflammogenicity. However, the haemolysis assay showed 100% consistency with the lung inflammation if any dose, having statistical significance was considered positivity. Other cell-basedin vitroassays showed a poorer correlation within vivoinflammogenicity.ConclusionsBased on the toxicity mechanisms of NPs, two different approaches can be applied for prediction ofin vivolung inflammogenicity. Mostin vitroassays were good at detecting NPs that act via soluble ions (i.e., ZnO and CuO NP). However,in vitroassays were limited in detecting NPs acting via surface reactivity as their mechanism of toxicity, except for the haemolysis assay.
The impact of the genome-wide supported variant in the cyclin M2 gene on gray matter morphology in schizophrenia
Authors: Ohi Kazutaka , Hashimoto Ryota , Yamamori Hidenaga , Yasuda Yuka , Fujimoto Michiko , Umeda-Yano Satomi , Fukunaga Masaki , Watanabe Yoshiyuki , Iwase Masao , Kazui Hiroaki , Takeda Masatoshi 
Published: October 2013

Abstract

Background
Genome-wide significant associations of schizophrenia with eight SNPs in the CNNM2, MIR137, PCGEM1, TRIM26, CSMD1, MMP16, NT5C2 and CCDC68 genes have been identified in a recent mega-analysis of genome-wide association studies. To date, the role of these SNPs on gray matter (GM) volumes remains unclear.

Methods
After performing quality control for minor-allele frequency > 5% using a JPT HapMap sample and our sample, a genotyping call rate > 95% and Hardy-Weinberg equilibrium testing (p > 0.01), five of eight SNPs were eligible for analysis. We used a comprehensive voxel-based morphometry (VBM) technique to investigate the effects of these five SNPs on GM volumes between major-allele homozygotes and minor-allele carriers in Japanese patients with schizophrenia (n = 173) and healthy subjects (n = 449).

Results
The rs7914558 risk variant at CNNM2 was associated with voxel-based GM volumes in the bilateral inferior frontal gyri (right T = 4.96, p = 0.0088, left T = 4.66, p = 0.031). These peak voxels, which were affected by the variant, existed in the orbital region of the inferior frontal gyri. Individuals with the risk G/G genotype of rs7914558 had smaller GM volumes in the bilateral inferior frontal gyri than carriers of the non-risk A-allele. Although several effects of the genotype and the genotype-diagnosis interaction of other SNPs on GM volumes were observed in the exploratory VBM analyses, these effects did not remain after the FWE- correction for multiple tests (p > 0.05).

Conclusions
Our findings suggest that the genetic variant in the CNNM2 gene could be implicated in the pathogenesis of schizophrenia through the GM volumetric vulnerability of the orbital regions in the inferior frontal gyri.