bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tractable Analytic Expressions for the Wind Speed Probability Density Functions Using Expansions of Orthogonal Polynomials
Authors: Morrissey Mark L. , Greene J. Scott 
Published: March 2012

AbstractThe use of the two-parameter Weibull function as an estimator of the wind speed probability density function (PDF) is known to be problematic when a high accuracy of fit is required, such as in the computation of the wind power density function. Various types of nonparametric kernels can provide excellent fits to wind speed histograms but cannot provide tractable analytical expressions. Analytic expressions for the wind speed PDF are needed for many applications, particularly in the downscaling of model or satellite wind speed estimates to the regional or point scale. It is demonstrated that the judicious use of an expansion of orthogonal polynomials can produce more accurate estimates of the wind speed PDF than relatively simply parametric functions, such as the commonly used Weibull function. This study examines four such expansions applied to two different surface wind speed datasets in Oklahoma. The results indicate that the accuracy of fit of a given expansion is strongly related to how close the basis weight function in an expansion resembles the wind speed histogram. It is shown that this basis function, which is the first term in the expansion, acts as a first “best guess” to the true wind speed PDF and that the additional terms act to “adjust” the fit to converge on the true density function. The results indicate that appropriately chosen orthogonal polynomials can provide an excellent fit and are quite tractable.
On Recent Trends in Atmospheric and Limnological Variables in Lake Ontario
Authors: Huang Anning , Rao Yerubandi R. , Zhang Weitao 
Published: March 2012

Abstract
The surface air and water temperatures increased at all seasonal and annual time scales during the last 40 yr in Lake Ontario. The annual mean air and surface water temperatures have increased by 1.43° ±0.39° and 1.26° ±0.32°C, respectively, over 1970–2009. The air temperature increased at a faster rate than the surface water temperature in winter and autumn, whereas in spring and summer the surface water temperature warmed faster than the air temperature. The length of summer stratified season has increased by 12 ± 2 days since the early 1970s due to the increase in water temperature. The decline of surface wind speed over Lake Ontario resulted in a shallower surface mixed layer and enhanced the summer thermal stratification, which increased the summer surface water temperature more rapidly than the air temperature.
Realism of Rainfall in a Very High-Resolution Regional Climate Model
Authors: Kendon Elizabeth J. , Roberts Nigel M. , Senior Catherine A. , Roberts Malcolm J. 
Published: March 2012

AbstractThe realistic representation of rainfall on the local scale in climate models remains a key challenge. Realism encompasses the full spatial and temporal structure of rainfall, and is a key indicator of model skill in representing the underlying processes. In particular, if rainfall is more realistic in a climate model, there is greater confidence in its projections of future change.In this study, the realism of rainfall in a very high-resolution (1.5 km) regional climate model (RCM) is compared to a coarser-resolution 12-km RCM. This is the first time a convection-permitting model has been run for an extended period (1989–2008) over a region of the United Kingdom, allowing the characteristics of rainfall to be evaluated in a climatological sense. In particular, the duration and spatial extent of hourly rainfall across the southern United Kingdom is examined, with a key focus on heavy rainfall.Rainfall in the 1.5-km RCM is found to be much more realistic than in the 12-km RCM. In the 12-km RCM, heavy rain events are not heavy enough, and tend to be too persistent and widespread. While the 1.5-km model does have a tendency for heavy rain to be too intense, it still gives a much better representation of its duration and spatial extent. Long-standing problems in climate models, such as the tendency for too much persistent light rain and errors in the diurnal cycle, are also considerably reduced in the 1.5-km RCM. Biases in the 12-km RCM appear to be linked to deficiencies in the representation of convection.
A New Regime of the Agulhas Current Retroflection: Turbulent Choking of Indian–Atlantic leakage
Authors: Le Bars Dewi , De Ruijter Wilhelmus P. M. , Dijkstra Henk A. 
Published: March 2012

Abstract
An analysis of the Indian Ocean circulation and the Agulhas Current retroflection is carried out using a primitive equation model with simplified coastline and flat bottom. Four configurations with 0.25° and 0.1° horizontal resolution and in barotropic and baroclinic cases are considered. The wind stress is taken as control parameter to increase the inertia of the currents. The volume transport of the Indonesian Throughflow, Mozambique Channel, and Agulhas Current are found to increase linearly with the wind stress strength, and three nonlinear retroflection regimes are found. A viscous and an inertial regime had already been documented, but a new turbulent regime appears at large wind stress amplitude. In this turbulent regime, the volume of Agulhas leakage reaches a plateau because of strong mesoscale variability and, in contrast to the other regimes, does not depend on the wind stress magnitude. The physical mechanism causing the plateau is shown to be associated with the cross-jet exchange of Indian Ocean water and water from the Antarctic Circumpolar Current. In the turbulent regime, the permeability of the Agulhas Return Current to material transport increases and the Indian Ocean water available for the Agulhas leakage decreases.
Simulation of a North American Monsoon Gulf Surge Event and Comparison to Observations
Authors: Newman Andrew J. , Johnson Richard H. 
Published: March 2012

Abstract
Gulf surges are transient disturbances that propagate along the Gulf of California (GoC) from south to north, transporting cool moist air toward the deserts of northwest Mexico and the southwest United States during the North American monsoon. They have been shown to modulate precipitation and have been linked to severe weather and flooding in northern Mexico and the southwest United States. The general features and progression of surge events are well studied, but their detailed evolution is still unclear. To address this, several convection-permitting simulations are performed over the core monsoon region for the 12–14 July 2004 gulf surge event. This surge event occurred during the North American Monsoon Experiment, which allows for extensive comparison to field observations.
A 60-h reference simulation is able to reproduce the surge event, capturing its main characteristics: speed and direction of motion, thermodynamic changes during its passage, and strong northward moisture flux. While the timing of the simulated surge is accurate to within 1–3 h, it is weaker and shallower than observed. This deficiency is likely due to a combination of weaker convection and lack of stratiform precipitation along the western slopes of the Sierra Madre Occidental than observed, hence, weaker precipitation evaporation to aid the surge. Sensitivity simulations show that convective outflow does modulate the intensity of the simulated surge, in agreement with past studies. The removal of gap flows from the Pacific Ocean across the Baja Peninsula into the GoC shows they also impact surge intensity.
Antigen-presenting genes and genomic copy number variations in the Tasmanian devil MHC
Authors: Cheng Yuanyuan , Stuart Andrew , Morris Katrina , Taylor Robyn , Siddle Hannah , Deakin Janine , Jones Menna , Amemiya Chris T , Belov Katherine 
Published: March 2012

Abstract

Background
The Tasmanian devil (Sarcophilus harrisii) is currently under threat of extinction due to an unusual fatal contagious cancer called Devil Facial Tumour Disease (DFTD). DFTD is caused by a clonal tumour cell line that is transmitted between unrelated individuals as an allograft without triggering immune rejection due to low levels of Major Histocompatibility Complex (MHC) diversity in Tasmanian devils.

Results
Here we report the characterization of the genomic regions encompassing MHC Class I and Class II genes in the Tasmanian devil. Four genomic regions approximately 960 kb in length were assembled and annotated using BAC contigs and physically mapped to devil Chromosome 4q. 34 genes and pseudogenes were identified, including five Class I and four Class II loci. Interestingly, when two haplotypes from two individuals were compared, three genomic copy number variants with sizes ranging from 1.6 to 17 kb were observed within the classical Class I gene region. One deletion is particularly important as it turns a Class Ia gene into a pseudogene in one of the haplotypes. This deletion explains the previously observed variation in the Class I allelic number between individuals. The frequency of this deletion is highest in the northwestern devil population and lowest in southeastern areas.

Conclusions
The third sequenced marsupial MHC provides insights into the evolution of this dynamic genomic region among the diverse marsupial species. The two sequenced devil MHC haplotypes revealed three copy number variations that are likely to significantly affect immune response and suggest that future work should focus on the role of copy number variations in disease susceptibility in this species.
Genomic variation in Salmonella enterica core genes for epidemiological typing
Authors: Leekitcharoenphon Pimlapas , Lukjancenko Oksana , Friis Carsten , Aarestrup Frank M , Ussery David W 
Published: March 2012

Abstract

Background
Technological advances in high throughput genome sequencing are making whole genome sequencing (WGS) available as a routine tool for bacterial typing. Standardized procedures for identification of relevant genes and of variation are needed to enable comparison between studies and over time. The core genes--the genes that are conserved in all (or most) members of a genus or species--are potentially good candidates for investigating genomic variation in phylogeny and epidemiology.

Results
We identify a set of 2,882 core genes clusters based on 73 publicly available Salmonella enterica genomes and evaluate their value as typing targets, comparing whole genome typing and traditional methods such as 16S and MLST. A consensus tree based on variation of core genes gives much better resolution than 16S and MLST; the pan-genome family tree is similar to the consensus tree, but with higher confidence. The core genes can be divided into two categories: a few highly variable genes and a larger set of conserved core genes, with low variance. For the most variable core genes, the variance in amino acid sequences is higher than for the corresponding nucleotide sequences, suggesting that there is a positive selection towards mutations leading to amino acid changes.

Conclusions
Genomic variation within the core genome is useful for investigating molecular evolution and providing candidate genes for bacterial genome typing. Identification of genes with different degrees of variation is important especially in trend analysis.
The gap in injury mortality rates between urban and rural residents of Hubei province, China
Authors: Liu Qing , Zhang Lan , Li Junlin , Zuo Dan , Kong Deguang , Shen Xingfu , Guo Yi , Zhang Qingjun 
Published: March 2012

Abstract

Background
Injury is a growing public health concern in China. Injury death rates are often higher in rural areas than in urban areas in general. The objective of this study is to compare the injury mortality rates in urban and rural residents in Hubei Province in central China by age, sex and mechanism of injury.

Methods
Using data from the Disease Surveillance Points (DSP) system maintained by the Hubei Province Centers for Disease Control and Prevention (CDC) from 2006 to 2008, injury deaths were classified according to the International Classification of Disease-10th Revision (ICD-10). Crude and age-adjusted annual mortality rates were calculated for rural and urban residents of Hubei Province.

Results
The crude and age-adjusted injury death rates were significantly higher for rural residents than for urban residents (crude rate ratio 1.9, 95% confidence interval 1.8-2.0; adjusted rate ratio 2.4, 95% confidence interval 2.3-2.4). The age-adjusted injury death rate for males was 81.6/100,000 in rural areas compared with 37.0/100 000 in urban areas; for females, the respective rates were 57.9/100,000 and 22.4/100 000. Death rates for suicide (32.4 per 100 000 vs 3.9 per 100 000), traffic-related injuries (15.8 per 100 000 vs 9.5 per 100 000), drowning (6.9 per 100 000 vs 2.3 per 100 000) and crushing injuries (2.0 per 100 000 vs 0.7 per 100 000) were significantly higher in rural areas. Overall injury death rates were much higher in persons over 65 years, with significantly higher rates in rural residents compared with urban residents for suicide (279.8 per 100 000 vs 10.7 per 100 000), traffic-related injuries, and drownings in this age group. Death rates for falls, poisoning, and suffocation were similar in the two geographic groups.

Conclusions
Rates of suicide, traffic-related injury deaths and drownings are demonstrably higher in rural compared with urban locations and should be targeted for injury prevention activity. There is a need for injury prevention policies targeted at elderly residents, especially with regard to suicide prevention in rural areas in Central China.
Evaluation of chemiluminescence, toluidine blue and histopathology for detection of high risk oral precancerous lesions: A cross-sectional study
Authors: Ujaoney Shweta , Motwani Mukta B , Degwekar Shirish , Wadhwan Vijay , Zade Prajakta , Chaudhary Minal , Hazarey Vinay , Thakre Tushar P , Mamtani Manju 
Published: March 2012

Abstract

Background
Early detection holds the key to an effective control of cancers in general and of oral cancers in particular. However, screening procedures for oral cancer are not straightforward due to procedural requirements as well as feasibility issues, especially in resource-limited countries.

Methods
We conducted a cross-sectional study to compare the performance of chemiluminescence, toluidine blue and histopathology for detection of high-risk precancerous oral lesions. We evaluated 99 lesions from 55 patients who underwent chemiluminescence and toluidine blue tests along with biopsy and histopathological examination. We studied inter-as well as intra-rater agreement in the histopathological evaluation and then using latent class modeling, we estimated the operating characteristics of these tests in the absence of a reference standard test.

Results
There was a weak inter-rater agreement (kappa < 0.15) as well as a weak intra-rater reproducibility (Pearson's r = 0.28, intra-class correlation rho = 0.03) in the histopathological evaluation of potentially high-risk precancerous lesions. When compared to histopathology, chemiluminescence and toluidine blue retention had a sensitivity of 1.00 and 0.59, respectively and a specificity of 0.01 and 0.79, respectively. However, latent class analysis indicated a low sensitivity (0.37) and high specificity (0.90) of histopathological evaluation. Toluidine blue had a near perfect high sensitivity and specificity for detection of high-risk lesions.

Conclusion
In our study, there was variability in the histopathological evaluation of oral precancerous lesions. Our results indicate that toluidine blue retention test may be better suited than chemiluminescence to detect high-risk oral precancerous lesions in a high-prevalence and low-resource setting like India.
Ameliorative effects of polyunsaturated fatty acids against palmitic acid-induced insulin resistance in L6 skeletal muscle cells
Authors: Sawada Keisuke , Kawabata Kyuichi , Yamashita Takatoshi , Kawasaki Kengo , Yamamoto Norio , Ashida Hitoshi 
Published: March 2012

Abstract

Background
Fatty acid-induced insulin resistance and impaired glucose uptake activity in muscle cells are fundamental events in the development of type 2 diabetes and hyperglycemia. There is an increasing demand for compounds including drugs and functional foods that can prevent myocellular insulin resistance.

Methods
In this study, we established a high-throughput assay to screen for compounds that can improve myocellular insulin resistance, which was based on a previously reported non-radioisotope 2-deoxyglucose (2DG) uptake assay. Insulin-resistant muscle cells were prepared by treating rat L6 skeletal muscle cells with 750 μM palmitic acid for 14 h. Using the established assay, the impacts of several fatty acids on myocellular insulin resistance were determined.

Results
In normal L6 cells, treatment with saturated palmitic or stearic acid alone decreased 2DG uptake, whereas unsaturated fatty acids did not. Moreover, co-treatment with oleic acid canceled the palmitic acid-induced decrease in 2DG uptake activity. Using the developed assay with palmitic acid-induced insulin-resistant L6 cells, we determined the effects of other unsaturated fatty acids. We found that arachidonic, eicosapentaenoic and docosahexaenoic acids improved palmitic acid-decreased 2DG uptake at lower concentrations than the other unsaturated fatty acids, including oleic acid, as 10 μM arachidonic acid showed similar effects to 750 μM oleic acid.

Conclusions
We have found that polyunsaturated fatty acids, in particular arachidonic and eicosapentaenoic acids prevent palmitic acid-induced myocellular insulin resistance.
TGFBR3 variation is not a common cause of Marfan-like syndrome and Loeys-Dietz-like syndrome
Authors: Singh Krishna K , Schmidtke Joerg , Keyser Britta , Arslan-Kirchner Mine 
Published: March 2012

Abstract
Marfan syndrome (MFS) is caused by mutations in the fibrillin-1 (FBN1) gene, and mutations in FBN1 are known to be responsible for over 90% of all MFS cases. Locus heterogeneity has also been reported and confirmed, with mutations in the receptor genes TGFBR1 and TGFBR2 identified in association with MFS-related phenotypes. It is now known that dysregulation of TGF-ß signaling is involved in MFS pathogenesis. To test the hypothesis that dysregulation of TGFBR3-associated TGF-ß signaling is implicated in MFS or related phenotype pathogenesis, we selected a cohort of 49 patients, fulfilling or nearly fulfilling the diagnostic criteria for MFS. The patients were known not to carry a mutation in the FBN1 gene (including three 5' upstream alternatively spliced exons), the TGFBR1 and TGFBR2 genes. Mutation screening for the TGFBR3 gene in these patients and in controls led to the identification of a total of ten exonic (one novel), four intronic (one novel) and one 3'UTR variant in the TGFBR3 gene. Our data suggest that variations in TGFBR3 gene appear not to be associated with MFS or related phenotype.
SiC surface orientation and Si loss rate effects on epitaxial graphene
Authors: Kim Moonkyung , Hwang Jeonghyun , Shields Virgil B , Tiwari Sandip , Spencer Michael G , Lee Jo-Won 
Published: March 2012

Abstract
We have explored the properties of SiC-based epitaxial graphene grown in a cold wall UHV chamber. The effects of the SiC surface orientation and silicon loss rate were investigated by comparing the characteristics of each formed graphene. Graphene was grown by thermal decomposition on both the silicon (0001) and carbon (000-1) faces of on-axis semi-insulating 6H-SiC with a "face-down" and "face-up" orientations. The thermal gradient, in relation to the silicon flux from the surface, was towards the surface and away from the surface, respectively, in the two configurations. Raman results indicate the disorder characteristics represented by ID/IG down to < 0.02 in Si-face samples and < 0.05 in C-faces over the 1 cm2 wafer surface grown at 1,450°C. AFM examination shows a better morphology in face-down surfaces. This study suggests that the optimum configuration slows the thermal decomposition and allows the graphene to form near the equilibrium. The Si-face-down orientation (in opposition to the temperature gradient) results in a better combination of low disorder ratio, ID/IG, and smooth surface morphology. Mobility of Si-face-down orientation has been measured as high as approximately 1,500 cm2/Vs at room temperature. Additionally, the field effect transistors have been fabricated on both Si-face-down and C-face-down showing an ambipolar behavior with more favorable electron conduction.
Conference highlights of the 5th international workshop on HIV persistence during therapy, 6-9 December 2011, St. Maartin, West Indies
Authors: Stevenson Mario , Chomont Nicolas , Lafeuillade Alain 
Published: March 2012

Abstract
The December 2011 5th International Workshop on HIV Persistence during Therapy addressed the issue of HIV persistence among 210 scientists from 10 countries involved in the study of HIV reservoirs and the search of an HIV cure. High quality abstracts were selected and discussed as oral or poster presentations. The aim of this review is to distribute the scientific highlights of this workshop outside the group as analyzed and represented by experts in retrovirology, immunology and clinical research.
Emergence of HIV‐1 drug resistance mutations among antiretroviral‐naïve HIV‐1‐infected patients after rapid scaling up of antiretroviral therapy in Thailand
Authors: Sungkanuparph Somnuek , Sukasem Chonlaphat , Kiertiburanakul Sasisopin , Pasomsub Ekawat , Chantratita Wasun 
Published: March 2012

BackgroundAfter rapid scaling up of antiretroviral therapy in HIV‐1‐infected patients, the data of primary HIV‐1 drug resistance in Thailand is still limited. This study aims to determine the prevalence and associated factors of primary HIV‐1 drug resistance in Thailand.MethodsA prospective observational study was conducted among antiretroviral‐naïve HIV‐1‐infected Thai patients from 2007 to 2010. HIV‐1 subtypes and mutations were assayed by sequencing a region of HIV‐1 pol gene. Surveillance drug resistance mutations recommended by the World Health Organization for surveillance of transmitted HIV‐1 drug resistance in 2009 were used in all analyses. Primary HIV‐1 drug resistance was defined as the presence of one or more surveillance drug resistance mutations.ResultsOf 466 patients with a mean age of 38.8 years, 58.6% were males. Risks of HIV‐1 infection included heterosexual (77.7%), homosexual (16.7%), and intravenous drug use (5.6%). Median (IQR) CD4 cell count and HIV‐1 RNA were 176 (42‐317) cells/mm3and 68,600 (19,515‐220,330) copies/mL, respectively. HIV‐1 subtypes were CRF01_AE (86.9%), B (8.6) and other recombinants (4.5%). The prevalence of primary HIV‐1 drug resistance was 4.9%; most of these (73.9%) had surveillance drug resistance mutations to only one class of antiretroviral drugs. The prevalence of patients with NRTI, NNRTI, and PI surveillance drug resistance mutations was 1.9%, 2.8% and 1.7%, respectively. From logistic regression analysis, there was no factor significantly associated with primary HIV‐1 drug resistance. There was a trend toward higher prevalence in females [odds ratio 2.18; 95% confidence interval 0.896‐5.304; p = 0.086].ConclusionsThere is a significant emergence of primary HIV‐1 drug resistance in Thailand after rapid scaling up of antiretroviral therapy. Although HIV‐1 genotyping prior to antiretroviral therapy initiation is not routinely recommended in Thailand, our results raise concerns about the risk of early treatment failure in patients with primary HIV‐1 drug resistance. Interventions to prevent the transmission of HIV‐1 drug resistance and continuation of surveillance for primary HIV‐1 drug resistance in Thailand are indicated.