bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uremic Serum and Solutes Increase Post–Vascular Interventional Thrombotic Risk Through Altered Stability of Smooth Muscle Cell Tissue Factor
Authors: Chitalia Vipul C. , Shivanna Sowmya , Martorell Jordi , Balcells Mercedes , Bosch Irene , Kolandaivelu Kumaran , Edelman Elazer R. 
Published: December 2012

Background—
Stent thrombosis (ST), a postinterventional complication with a mortality rate of 50%, has an incidence that rises precipitously in patients at risk. Chronic renal failure and end-stage renal disease have emerged as particularly strong ST risk factors, yet the mechanism remains elusive. Tissue factor (TF) is a crucial mediator of injury-related thrombosis and has been implicated for ST. We posit that uremia modulates TF in the local vessel wall to induce postinterventional thrombosis in patients with end-stage renal disease.

Methods and Results—
As a model of the de-endothelialized, postinterventional state, we exposed primary human vascular smooth muscle cells (vSMCs) pretreated with uremic serum (obtained from ESRD patients on hemodialysis) to coronary-like blood flow. vSMC TF expression, activity, stability, and posttranslational modification were examined after vSMCs were treated with uremic serum or solutes. We found significantly greater clot formation after uremic serum exposure, which was substantially reduced with the prior treatment with anti-TF neutralizing antibody. Uremic sera induced 2- to 3-fold higher TF expression and activity in vSMCs independent of diabetes mellitus. Relevant concentrations of isolated uremic solutes such as indole-3-acetic acid (3.5 μg/mL), indoxyl sulfate (25 μg/mL), and uric acid (80 μg/mL) recapitulated these effects in cell culture and the flow loop model. We show further that TF undergoes ubiquitination at baseline and that uremic serum, indole-3-acetic acid, and indoxyl sulfate significantly prolong TF half-life by inhibiting its ubiquitination.

Conclusions—
The uremic milieu is profoundly thrombogenic and upregulates vSMC TF levels by increasing TF stability and decreasing its ubiquitination. Together, these data demonstrate for the first time that the posttranslational regulation of TF in uremia may have a causative role in the increased ST risk observed in uremic patients. These data suggest that interventions that reduce vSMC TF may help to prevent ST and that uremic solutes should be considered as novel risk factors for ST in patients with chronic renal failure.
A Satellite Study of the Relationship between Sea Surface Temperature and Column Water Vapor over Tropical and Subtropical Oceans
Authors: Kanemaru Kaya , Masunaga Hirohiko 
Published: December 2012

Abstract
The known characteristics of the relationship between sea surface temperature (SST) and column water vapor (CWV) are reevaluated with recent satellite observations over tropical and subtropical oceans. Satellite data acquired by the Aqua Advanced Microwave Scanning Radiometer for Earth Observing System (AMSR-E), Atmospheric Infrared Sounder (AIRS)/Advanced Microwave Sounder Unit (AMSU) suite, the Tropical Rainfall Measuring Mission (TRMM) precipitation radar (PR), and the Quick Scatterometer (QuikSCAT) SeaWinds are analyzed together for 7 years from October 2002 to September 2009. CWV is decomposed into surface humidity, presumably coupled closely to SST, and the water vapor scale height as an index of vertical moisture gradient between the boundary layer and the free troposphere. Surface relative humidity is climatologically homogeneous across tropical and subtropical oceans, while the dependence of CWV on SST varies from one region to another. SST mainly accounts for the variation of CWV with the water vapor scale height, which is virtually invariant over subtropical oceans. On the other hand, over tropical oceans, the variability of CWV is explained not only by SST but also by a systematic change of the water vapor scale height. The regional contrast between tropical and subtropical oceans is discussed in the context of the regional moisture budget including vertical moisture transport through convection.
Feedbacks in Emission-Driven and Concentration-Driven Global Carbon Budgets
Authors: Boer G. J. , Arora V. K. 
Published: December 2012

Abstract
Emissions of CO2 into the atmosphere affect the carbon budgets of the land and ocean as biogeochemical processes react to increased CO2 concentrations. Biogeochemical processes also react to changes in temperature and other climate parameters. This behavior is characterized in terms of carbon–concentration and carbon–climate feedback parameters. The results of this study include 1) the extension of the direct carbon feedback formalism of Boer and Arora to include results from radiatively coupled simulations, as well as those from the biogeochemically coupled and fully coupled simulations used in earlier analyses; 2) a brief analysis of the relationship between this formalism and the integrated feedback formalism of Friedlingstein et al.; 3) the feedback analysis of simulations based on each of the representative concentration pathways (RCPs) RCP2.6, RCP4.5, and RCP8.5; 4) a comparison of the effects of specifying atmospheric CO2 concentrations or CO2 emissions; and 5) the quantification of the relative importance of the two feedback mechanisms in terms of their cumulative contribution to the change in atmospheric CO2.
Feedback results are broadly in agreement with earlier studies in that carbon–concentration feedback is negative for the atmosphere and carbon–climate feedback is positive. However, the magnitude and evolution of feedback behavior depends on the formalism employed, the scenario considered, and the specification of CO2 from emissions or as atmospheric concentrations. Both feedback parameters can differ by factors of two or more, depending on the scenario and on the specification of CO2 emissions or concentrations. While feedback results are qualitatively useful and illustrative of carbon budget behavior, they apply quantitatively to particular scenarios and cases.
A Supplementary Clear-Sky Snow and Ice Recognition Technique for CERES Level 2 Products
Authors: Radkevich Alexander , Khlopenkov Konstantin , Rutan David , Kato Seiji 
Published: December 2012

Abstract
Identification of clear-sky snow and ice is an important step in the production of cryosphere radiation budget products, which are used in the derivation of long-term data series for climate research. In this paper, a new method of clear-sky snow/ice identification for Moderate Resolution Imaging Spectroradiometer (MODIS) is presented. The algorithm’s goal is to enhance the identification of snow and ice within the Clouds and the Earth’s Radiant Energy System (CERES) data after application of the standard CERES scene identification scheme. The input of the algorithm uses spectral radiances from five MODIS bands and surface skin temperature available in the CERES Single Scanner Footprint (SSF) product. The algorithm produces a cryosphere rating from an aggregated test: a higher rating corresponds to a more certain identification of the clear-sky snow/ice-covered scene. Empirical analysis of regions of interest representing distinctive targets such as snow, ice, ice and water clouds, open waters, and snow-free land selected from a number of MODIS images shows that the cryosphere rating of snow/ice targets falls into 95% confidence intervals lying above the same confidence intervals of all other targets. This enables recognition of clear-sky cryosphere by using a single threshold applied to the rating, which makes this technique different from traditional branching techniques based on multiple thresholds. Limited tests show that the established threshold clearly separates the cryosphere rating values computed for the cryosphere from those computed for noncryosphere scenes, whereas individual tests applied consequently cannot reliably identify the cryosphere for complex scenes.
Can a Moderate-Resolution Limited-Area Data Assimilation System Add Value to the Global Analysis of Tropical Cyclones?
Authors: Holt Christina R. , Szunyogh Istvan , Gyarmati Gyorgyi 
Published: December 2012

AbstractThis study investigates the benefits of employing a limited-area data assimilation (DA) system to enhance lower-resolution global analyses in the northwest Pacific tropical cyclone (TC) basin. Numerical experiments are carried out with a global analysis system at horizontal resolution T62 and a limited-area analysis system at resolutions from 200 to 36 km. The global and limited-area DA systems, which are both based on the local ensemble transform Kalman filter algorithm, are implemented using a unique configuration, in which the global DA system provides information about the large-scale analysis and background uncertainty to the limited-area DA system. The limited-area analyses of the storm locations are, on average, more accurate than those from the global analyses, but increasing the resolution of the limited-area system beyond 100 km has little benefit. Two factors contribute to the higher accuracy of the limited-area analyses. First, the limited-area system improves the accuracy of the location estimates for strong storms, which is introduced when the background is updated by the global assimilation. Second, it improves the accuracy of the background estimate of the storm locations for moderate and weak storms. Improvements in the steering flow analysis as a result of increased resolution are modest and short lived in the forecasts. Limited-area track forecasts are more accurate, on average, than global forecasts, independently of the strength of the storms up to five days. This forecast improvement is due to the more accurate analysis of the initial position of storms and the better representation of the interactions between the storms and their immediate environment.
Observing Strategy and Observation Targeting for Tropical Cyclones Using Ensemble-Based Sensitivity Analysis and Data Assimilation
Authors: Xie Baoguo , Zhang Fuqing , Zhang Qinghong , Poterjoy Jonathan , Weng Yonghui 
Published: December 2012

Abstract
An ensemble Kalman filter data assimilation system for the Weather Research and Forecasting Model is used with ensemble-based sensitivity analysis to explore observing strategies and observation targeting for tropical cyclones. The case selected for this study is Typhoon Morakot (2009), a western Pacific storm that brought record-breaking rainfall to Taiwan. Forty-eight hours prior to making landfall, ensemble sensitivity analysis using a 50-member convection-permitting ensemble predicts that dropsonde observations located in the southwest quadrant of the typhoon will have the highest impact on reducing the forecast uncertainty of the track, intensity, and rainfall of Morakot. A series of observing system simulation experiments (OSSEs) demonstrate that assimilating synthetic dropsonde observations located in regions with higher predicted observation impacts will, on average, lead to a better rainfall forecast than in regions with smaller predicted impacts. However, these OSSEs also suggest that the effectiveness of the current-generation ensemble-based tropical cyclone targeting strategies may be limited. The limitations may be due to strong nonlinearity in the governing dynamics of the typhoon (e.g., moist convection), the accuracy of the ensemble background covariance, and the projection of individual dropsonde observations to the complicated targeted sensitivity vectors from the ensemble.
An Intercomparison of UW Cloud-Top Cooling Rates with WSR-88D Radar Data
Authors: Hartung Daniel C. , Sieglaff Justin M. , Cronce Lee M. , Feltz Wayne F. 
Published: December 2012

Abstract
The University of Wisconsin Convective Initiation (UWCI) algorithm utilizes geostationary IR satellite data to compute cloud-top cooling (UW-CTC) rates and assign CI nowcasts to vertically growing clouds. This study is motivated by National Weather Service (NWS) forecaster reviews of the algorithm output, which hypothesized that more intense cloud-top cooling corresponds to more vigorous short-term (0–60 min) convective development. An objective validation of UW-CTC rates using a satellite-based object-tracking methodology is presented, along with a prognostic evaluation of such cloud-top cooling rates for use in forecasting the growth and development of deep convection. In general, both a cloud object’s instantaneous and maximum cooling rate(s) are shown to be useful prognostic tools in predicting future radar intensification. UW-CTC rates are shown to be most skillful in detecting convective clouds that achieved intense radar signatures. The UW-CTC rate lead time ahead of the various radar fields is also shown, along with an illustration of the benefit of UW-CTC rates in operational forecasting. The results of this study suggest that convective clouds with the strongest UW-CTC rates are more likely to achieve significant near-term (0–60 min) radar signatures in such fields as composite reflectivity, vertically integrated liquid (VIL), and maximum estimated size of hail (MESH) compared to clouds that exhibit only weak UW-CTC rates.
Sustaining a Creative Community-Based Diabetes Education Program
Authors: Bielamowicz Mary Kinney , Pope Paul , Rice Carol Ann 
Published: December 2012

Purpose The purpose of the community-based diabetes education project was to evaluate participants’ knowledge and use of healthy cooking practices as they relate to controlling diabetes. In addition, an attempt was made to ascertain whether participants’ self-reported blood glucose levels and hemoglobin A1C changed as a result of the educational intervention. Methods Extension agents were trained statewide on principles of diabetes self-management education (DSME) and nutrition concepts for the programs Do Well, Be Well with Diabetes (DWBW) and Cooking Well with Diabetes (CWWD). Upon returning to their respective counties, trained extension agents established health coalitions for program delivery. In 86 counties, online data were collected on perceived knowledge and behaviors related to healthy cooking practice and were assessed before the start of the program (pretest; time 1), after the third lesson (posttest; time 2), and again after the fourth and final lesson (time 3). Results Most participants trained in DWBW joined cooking classes so the group already had some knowledge of food preparation techniques and had adopted many of the recommended practices, yet the program still had impact. Findings suggest an improvement in participants’ knowledge and self-reported behaviors. Conclusions The CWWD program provided a short-term impact of knowledge gain, and the adoption of healthy cooking practices was observed among program participants. A pattern of healthy eating should lead to a reduction of blood glucose levels and hemoglobin A1C. The relatively short time between pretest and posttest was not sufficient to realize and measure such reductions.
Inclusion of cow records in genomic evaluations and impact on bias due to preferential treatment
Authors: Dassonneville Romain , Baur Aurelia , Fritz Sébastien , Boichard Didier , Ducrocq Vincent 
Published: December 2012

Abstract

Background
Today, genomic evaluations are an essential feature of dairy cattle breeding. Initially, genomic evaluation targeted young bulls but recently, a rapidly increasing number of females (both heifers and cows) are being genotyped. A rising issue is whether and how own performance of genotyped cows should be included in genomic evaluations. The purpose of this study was to assess the impact of including yield deviations, i.e. own performance of cows, in genomic evaluations.

Methods
Two different genomic evaluations were performed: one including only reliable daughter yield deviations of proven bulls based on their non-genotyped daughters, and one including both daughter yield deviations for males and own yield deviations for genotyped females. Milk yield, the trait most prone to preferential treatment, and somatic cell count, for which such a bias is very unlikely, were studied. Data consisted of two groups of animals from the three main dairy breeds in France: 11 884 elite females genotyped by breeding companies and 7032 cows genotyped for a research project (and considered as randomly selected from the commercial population).

Results
For several measures that could be related to preferential treatment bias, the elite group presented a different pattern of estimated breeding values for milk yield compared to the other combinations of trait and group: for instance, for milk yield, the average difference between estimated breeding values with or without own yield deviations was significantly different from 0 for this group. Correlations between estimated breeding values with or without yield deviations were lower for elite females than for randomly selected cows for milk yield but were very similar for somatic cell count.

Conclusions
This study demonstrated that including own milk performance of elite females leads to biased (over-estimated) genomic evaluations. Thus, milk production records of elite cows require specific treatment in genomic evaluation.
Copy number variation signature to predict human ancestry
Authors: Pronold Melissa , Vali Marzieh , Pique-Regi Roger , Asgharzadeh Shahab 
Published: December 2012

Abstract

Background
Copy number variations (CNVs) are genomic structural variants that are found in healthy populations and have been observed to be associated with disease susceptibility. Existing methods for CNV detection are often performed on a sample-by-sample basis, which is not ideal for large datasets where common CNVs must be estimated by comparing the frequency of CNVs in the individual samples. Here we describe a simple and novel approach to locate genome-wide CNVs common to a specific population, using human ancestry as the phenotype.

Results
We utilized our previously published Genome Alteration Detection Analysis (GADA) algorithm to identify common ancestry CNVs (caCNVs) and built a caCNV model to predict population structure. We identified a 73 caCNV signature using a training set of 225 healthy individuals from European, Asian, and African ancestry. The signature was validated on an independent test set of 300 individuals with similar ancestral background. The error rate in predicting ancestry in this test set was 2% using the 73 caCNV signature. Among the caCNVs identified, several were previously confirmed experimentally to vary by ancestry. Our signature also contains a caCNV region with a single microRNA (MIR270), which represents the first reported variation of microRNA by ancestry.

Conclusions
We developed a new methodology to identify common CNVs and demonstrated its performance by building a caCNV signature to predict human ancestry with high accuracy. The utility of our approach could be extended to large case–control studies to identify CNV signatures for other phenotypes such as disease susceptibility and drug response.
Adaptive evolution by recombination is not associated with increased mutation rates in Maize streak virus
Authors: Monjane Adérito L , Pande Daniel , Lakay Francisco , Shepherd Dionne N , van der Walt Eric , Lefeuvre Pierre , Lett Jean-Michel , Varsani Arvind , Rybicki Edward P , Martin Darren P 
Published: December 2012

Abstract

Background
Single-stranded (ss) DNA viruses in the family Geminiviridae are proving to be very useful in real-time evolution studies. The high mutation rate of geminiviruses and other ssDNA viruses is somewhat mysterious in that their DNA genomes are replicated in host nuclei by high fidelity host polymerases. Although strand specific mutation biases observed in virus species from the geminivirus genus Mastrevirus indicate that the high mutation rates in viruses in this genus may be due to mutational processes that operate specifically on ssDNA, it is currently unknown whether viruses from other genera display similar strand specific mutation biases. Also, geminivirus genomes frequently recombine with one another and an alternative cause of their high mutation rates could be that the recombination process is either directly mutagenic or produces a selective environment in which the survival of mutants is favoured. To investigate whether there is an association between recombination and increased basal mutation rates or increased degrees of selection favoring the survival of mutations, we compared the mutation dynamics of the MSV-MatA and MSV-VW field isolates of Maize streak virus (MSV; Mastrevirus), with both a laboratory constructed MSV recombinant, and MSV recombinants closely resembling MSV-MatA. To determine whether strand specific mutation biases are a general characteristic of geminivirus evolution we compared mutation spectra arising during these MSV experiments with those arising during similar experiments involving the geminivirus Tomato yellow leaf curl virus (Begomovirus genus).

Results
Although both the genomic distribution of mutations and the occurrence of various convergent mutations at specific genomic sites indicated that either mutation hotspots or selection for adaptive mutations might elevate observed mutation rates in MSV, we found no association between recombination and mutation rates. Importantly, when comparing the mutation spectra of MSV and TYLCV we observed similar strand specific mutation biases arising predominantly from imbalances in the complementary mutations G → T: C → A.

Conclusions
While our results suggest that recombination does not strongly influence mutation rates in MSV, they indicate that high geminivirus mutation rates are at least partially attributable to increased susceptibility of all geminivirus genomes to oxidative damage while in a single stranded state.
Evolutionary mechanisms driving the evolution of a large polydnavirus gene family coding for protein tyrosine phosphatases
Authors: Serbielle Céline , Dupas Stéphane , Perdereau Elfie , Héricourt François , Dupuy Catherine , Huguet Elisabeth , Drezen Jean-Michel 
Published: December 2012

Abstract

Background
Gene duplications have been proposed to be the main mechanism involved in genome evolution and in acquisition of new functions. Polydnaviruses (PDVs), symbiotic viruses associated with parasitoid wasps, are ideal model systems to study mechanisms of gene duplications given that PDV genomes consist of virulence genes organized into multigene families. In these systems the viral genome is integrated in a wasp chromosome as a provirus and virus particles containing circular double-stranded DNA are injected into the parasitoids’ hosts and are essential for parasitism success. The viral virulence factors, organized in gene families, are required collectively to induce host immune suppression and developmental arrest. The gene family which encodes protein tyrosine phosphatases (PTPs) has undergone spectacular expansion in several PDV genomes with up to 42 genes.

Results
Here, we present strong indications that PTP gene family expansion occurred via classical mechanisms: by duplication of large segments of the chromosomally integrated form of the virus sequences (segmental duplication), by tandem duplications within this form and by dispersed duplications. We also propose a novel duplication mechanism specific to PDVs that involves viral circle reintegration into the wasp genome. The PTP copies produced were shown to undergo conservative evolution along with episodes of adaptive evolution. In particular recently produced copies have undergone positive selection in sites most likely involved in defining substrate selectivity.

Conclusion
The results provide evidence about the dynamic nature of polydnavirus proviral genomes. Classical and PDV-specific duplication mechanisms have been involved in the production of new gene copies. Selection pressures associated with antagonistic interactions with parasitized hosts have shaped these genes used to manipulate lepidopteran physiology with evidence for positive selection involved in adaptation to host targets.