bluuebunny/crossref_metadata_2025_split huggingface dataset:
Burden of smoking on cause-specific mortality: application to the Nurses' Health Study
Authors: Kenfield Stacey A , Wei Esther K , Rosner Bernard A , Glynn Robert J , Stampfer Meir J , Colditz Graham A 
Published: May 2010

ObjectiveThe burden of smoking on six causes of death in women was evaluated using various novel modelling approaches.DesignA prospective US-based nationwide cohort study.Participants102 635 women in the Nurses' Health Study followed biennially from 1980 to 2004.MethodsThe relation between cigarette smoking and cause-specific death was compared using baseline versus biennially updated smoking status. The authors used competing risk survival analysis to formally compare associations of smoking-related variables on risk of death as a result of coronary heart disease (CHD), cerebrovascular diseases, lung cancer, other respiratory diseases, other smoking-caused cancers and other causes.ResultsThe associations of current and former smoking were stronger with most cause-specific mortality when using updated information. The effect of each smoking-related variable differed significantly (ph<0.0001) across some causes of death. For example, risks increased by 5% for death due to other causes up to 37% for lung cancer death for a 5-year earlier age at initiation. Compared with continuing to smoke, former smokers with 5–10 years of cessation had a 25% reduction in risk of dying from other causes of death up to a 61% reduction in risk of dying from CHD and cerebrovascular diseases.ConclusionsThe risks of smoking and the benefits from quitting are greater than previously reported, when utilising repeated measures of smoking data collected during follow-up, and vary by cause of death. Focused efforts to communicate the benefits of quitting to smokers and to prevent smoking initiation among children and youths should remain top public health priorities to reduce the worldwide mortality burden caused by smoking.
Verifying safety properties of concurrent heap-manipulating programs
Authors: Yahav Eran , Sagiv Mooly 
Published: May 2010

We provide a parametric framework for verifying safety properties of concurrent heap-manipulating programs. The framework combines thread-scheduling information with information about the shape of the heap. This leads to verification algorithms that are more precise than existing techniques. The framework also provides a precise shape-analysis algorithm for concurrent programs. In contrast to most existing verification techniques, we do not put a bound on the number of allocated objects. The framework produces interesting results even when analyzing programs with an unbounded number of threads. The framework is applied to successfully verify the following properties of a concurrent program:
—Concurrent manipulation of linked-list based ADT preserves the ADT datatype invariant.
—The program does not perform inconsistent updates due to interference.
—The program does not reach a deadlock.
—The program does not produce runtime errors due to illegal thread interactions.
We also found bugs in erroneous programs violating such properties. A prototype of our framework has been implemented and applied to small, but interesting, example programs.
Reducing Consumption of Sugar-Sweetened Beverages Is Associated With Reduced Blood Pressure
Authors: Chen Liwei , Caballero Benjamin , Mitchell Diane C. , Loria Catherine , Lin Pao-Hwa , Champagne Catherine M. , Elmer Patricia J. , Ard Jamy D. , Batch Bryan C. , Anderson Cheryl A.M. , Appel Lawrence J. 
Published: May 2010

Background—Increased consumption of sugar-sweetened beverages (SSBs) has been associated with an elevated risk of obesity, metabolic syndrome, and type II diabetes mellitus. However, the effects of SSB consumption on blood pressure (BP) are uncertain. The objective of this study was to determine the relationship between changes in SSB consumption and changes in BP among adults.Methods and Results—This was a prospective analysis of 810 adults who participated in the PREMIER Study (an 18-month behavioral intervention trial). BP and dietary intake (by two 24-hour recalls) were measured at baseline and at 6 and 18 months. Mixed-effects models were applied to estimate the changes in BP in responding to changes in SSB consumption. At baseline, mean SSB intake was 0.9±1.0 servings per day (10.5±11.9 fl oz/d), and mean systolic BP/diastolic BP was 134.9±9.6/84.8±4.2 mm Hg. After potential confounders were controlled for, a reduction in SSB of 1 serving per day was associated with a 1.8-mm Hg (95% confidence interval, 1.2 to 2.4) reduction in systolic BP and 1.1-mm Hg (95% confidence interval, 0.7 to 1.4) reduction in diastolic BP over 18 months. After additional adjustment for weight change over the same period, a reduction in SSB intake was still significantly associated with reductions in systolic and diastolic BPs (P<0.05). Reduced intake of sugars was also significantly associated with reduced BP. No association was found for diet beverage consumption or caffeine intake and BP. These findings suggest that sugars may be the nutrients that contribute to the observed association between SSB and BP.Conclusions—Reduced consumption of SSB and sugars was significantly associated with reduced BP. Reducing SSB and sugar consumption may be an important dietary strategy to lower BP.Clinical Trial Registration—URL: http://clinicaltrials.gov. Unique identifier: NCT00000616.
Endothelial Cell–Derived Endothelin-1 Promotes Cardiac Fibrosis in Diabetic Hearts Through Stimulation of Endothelial-to-Mesenchymal Transition
Authors: Widyantoro Bambang , Emoto Noriaki , Nakayama Kazuhiko , Anggrahini Dyah W. , Adiarto Suko , Iwasa Naoko , Yagi Keiko , Miyagawa Kazuya , Rikitake Yoshiyuki , Suzuki Takashi , Kisanuki Yaz Y. , Yanagisawa Masashi , Hirata Ken-ichi 
Published: May 2010

Background—Persistently high plasma endothelin-1 (ET-1) levels in diabetic patients have been associated with the development of cardiac fibrosis, which results from the deposition of extracellular matrix and fibroblast recruitment from an as-yet unknown source. The underlying mechanism, however, remains elusive. Here, we hypothesize that ET-1 might contribute to the accumulation of cardiac fibroblasts through an endothelial-to-mesenchymal transition in diabetic hearts.Methods and Results—We induced diabetes mellitus in vascular endothelial cell–specific ET-1 knockout [ET-1f/f;Tie2-Cre (+)] mice and their wild-type littermates using the toxin streptozotocin. Gene expression and histological and functional parameters were examined at 8, 24, and 36 weeks after the induction of diabetes mellitus. Diabetes mellitus increased cardiac ET-1 expression in wild-type mice, leading to mitochondrial disruption and myofibril disarray through the generation of superoxide. Diabetic mice also showed impairment of cardiac microvascularization and a decrease in cardiac vascular endothelial growth factor expression. ET-1 further promotes cardiac fibrosis and heart failure through the accumulation of fibroblasts via endothelial-to-mesenchymal transition. All of these features were abolished in ET-1f/f;Tie2-Cre (+) hearts. Targeted ET-1 gene silencing by small interfering RNA in cultured human endothelial cells ameliorated high glucose–induced phenotypic transition and acquisition of a fibroblast marker through the inhibition of transforming growth factor-β signaling activation and preservation of the endothelial cell-to-cell contact regulator VE-cadherin.Conclusions—These results provide new insights suggesting that diabetes mellitus–induced cardiac fibrosis is associated with the emergence of fibroblasts from endothelial cells and that this endothelial-to-mesenchymal transition process is stimulated by ET-1. Targeting endothelial cell–derived ET-1 might be beneficial in the prevention of diabetic cardiomyopathy.
Improved Estimates of the European Winter Windstorm Climate and the Risk of Reinsurance Loss Using Climate Model Data
Authors: Della-Marta Paul M. , Liniger Mark A. , Appenzeller Christof , Bresch David N. , Köllner-Heck Pamela , Muccione Veruska 
Published: May 2010

AbstractCurrent estimates of the European windstorm climate and their associated losses are often hampered by either relatively short, coarse resolution or inhomogeneous datasets. This study tries to overcome some of these shortcomings by estimating the European windstorm climate using dynamical seasonal-to-decadal (s2d) climate forecasts from the European Centre for Medium-Range Weather Forecasts (ECMWF). The current s2d models have limited predictive skill of European storminess, making the ensemble forecasts ergodic samples on which to build pseudoclimates of 310–396 yr in length. Extended winter (October–April) windstorm climatologies are created using scalar extreme wind indices considering only data above a high threshold. The method identifies up to 2363 windstorms in s2d data and up to 380 windstorms in the 40-yr ECMWF Re-Analysis (ERA-40). Classical extreme value analysis (EVA) techniques are used to determine the windstorm climatologies. Differences between the ERA-40 and s2d windstorm climatologies require the application of calibration techniques to result in meaningful comparisons. Using a combined dynamical–statistical sampling technique, the largest influence on ERA-40 return period (RP) uncertainties is the sampling variability associated with only 45 seasons of storms. However, both maximum likelihood (ML) and L-moments (LM) methods of fitting a generalized Pareto distribution result in biased parameters and biased RP at sample sizes typically obtained from 45 seasons of reanalysis data. The authors correct the bias in the ML and LM methods and find that the ML-based ERA-40 climatology overestimates the RP of windstorms with RPs between 10 and 300 yr and underestimates the RP of windstorms with RPs greater than 300 yr. A 50-yr event in ERA-40 is approximately a 40-yr event after bias correction. Biases in the LM method result in higher RPs after bias correction although they are small when compared with those of the ML method. The climatologies are linked to the Swiss Reinsurance Company (Swiss Re) European windstorm loss model. New estimates of the risk of loss are compared with those from historical and stochastically generated windstorm fields used by Swiss Re. The resulting loss-frequency relationship matches well with the two independently modeled estimates and clearly demonstrates the added value by using alternative data and methods, as proposed in this study, to estimate the RP of high RP losses.
Climatology of Thunderstorms for North Dakota, 2002–06
Authors: Mohee Faizul M. , Miller Craig 
Published: May 2010

Abstract
Radar and surface thunderstorm data in North Dakota were investigated to obtain the climatology of thunderstorms in the state. A life cycle analysis for the individual storm cells between 2002 and 2006 was carried out, and it was found that June and July were the peak months, late afternoon to early morning was the peak time for thunderstorms, the average lifetime of storm cells was 23.6 min, the average gust wind speed was 16.5 m s−1, the average track length was 21.8 km, and the average movement speed was 16.4 m s−1. The average movement of storm cells varied with months, and the storms moved toward the north, the northeast, and the east. It was also demonstrated that there were 19–35 thunderstorm days each year in North Dakota and that, of these, 9–14 thunderstorm days each year were associated with high speed winds. Severe thunderstorms composed 1.7% of all the thunderstorms in 2002–06. The most intense thunderstorm in North Dakota between 2002 and 2006 was associated with a 5-yr-high wind speed of 31.4 m s−1. It was also found that the longer-lasting storms were the stronger storms.
Mechanisms of Meridional Teleconnection Observed between a Summer Monsoon System and a Subtropical Anticyclone. Part II: A Global Survey
Authors: Kosaka Yu , Nakamura Hisashi 
Published: May 2010

Abstract
A global survey is conducted for atmospheric anomaly patterns of meridional teleconnection over the summer hemisphere associated with anomalous tropical convection. The patterns may be akin to the Pacific–Japan (PJ) teleconnection pattern analyzed in detail in the companion paper. From the survey, meridional teleconnections are identified over five regions, namely, the western North Pacific and Central/North America in boreal summer, as well as the western South Indian Ocean, central South Pacific, and western South Atlantic in austral summer. All of the patterns are observed in the western peripheries of the summertime surface subtropical anticyclones over the individual ocean basins. Although all of the patterns can convert available potential energy (APE) efficiently from the vertically sheared subtropical westerly jets, the efficiencies of barotropic energy conversion from the mean flow and diabatic APE generation differ from one pattern to another. Still, all of the patterns gain energy as the net, to maintain themselves against dissipative processes. Both the anomalous moisture convergence near the surface and the midtropospheric anomalous ascent required for the vorticity and thermal balance act to sustain the anomalous tropical convection, while the wind-evaporation feedback contributes positively only to the PJ pattern over the western North Pacific. Examination of common features and discrepancies among the five teleconnection patterns with respect to their structures and energetics reveals that climatological background features, including the largest horizontal extent of the Asian monsoon system and the North Pacific subtropical anticyclone, in addition to particularly high SST over the Pacific warm pool, render the PJ pattern an outstanding mode of variability.
Last Glacial Maximum East Asian Monsoon: Results of PMIP Simulations
Authors: Jiang Dabang , Lang Xianmei 
Published: May 2010

AbstractDuring glacial periods, the East Asian monsoon is typically thought to have been stronger in boreal winters and weaker in boreal summers. It is unclear, however, whether this view is true at larger scales and to what extent the East Asian monsoon responds to glacial conditions as a whole. Using all experiments conducted as part of the Paleoclimate Modeling Intercomparison Project (PMIP), this paper examines East Asian monsoon climatology during the Last Glacial Maximum (LGM), around 21 000 calendar years ago. In contrast to conclusions drawn from sparse proxy data, the intensity of the East Asian winter (December–February) monsoon (EAWM) during the LGM, as measured by regionally averaged meridional wind speed at 850 hPa, was found to vary both in sign and magnitude, with reference to baseline climate, across the PMIP simulations. It strengthened in 10 out of the 21 models but weakened in the remaining 11 models, with an average weakening of 4% for the 21-model ensemble mean (15% for the ensemble mean of the 14 models with computed sea surface temperatures). At the subregional scale, the LGM EAWM strengthened north of about 30°N but weakened south of this region in East Asia, which can be explained by changes in surface temperature. On the other hand, all of the 14 models chosen in this study consistently simulated a weaker than baseline East Asian summer (June–August) monsoon during the LGM, with an average weakening of 25%.
Alternating Dual-Pulse, Dual-Frequency Techniques for Range and Velocity Ambiguity Mitigation on Weather Radars
Authors: Torres Sebastián , Passarelli Richard , Siggia Alan , Karhunen Pentti 
Published: May 2010

Abstract
This paper introduces a family of alternating dual-pulse, dual-frequency (ADPDF) techniques. These are based on frequency diversity and are proposed as a means to mitigate range and velocity ambiguities on Doppler weather radars. ADPDF techniques are analyzed theoretically and through simulated and real weather data collected with a prototype C-band radar. Analogous to single-frequency, multiple-pulse-repetition-time (mPRT) techniques, such as staggered or triple PRT, it is demonstrated that ADPDF techniques can extend the maximum unambiguous velocity beyond what is achievable with uniform sampling. However, unlike mPRT techniques, ADPDF techniques exhibit better statistical performance and, more importantly, may be designed to preserve uniform sampling on one of the frequency channels, thus avoiding some of the difficulties associated with processing nonuniformly sampled data.
Characterization of the GXXXG motif in the first transmembrane segment of Japanese encephalitis virus precursor membrane (prM) protein
Authors: Lin Ying-Ju , Peng Jia-Guan , Wu Suh-Chin 
Published: May 2010

Abstract
The interaction between prM and E proteins in flavivirus-infected cells is a major driving force for the assembly of flavivirus particles. We used site-directed mutagenesis to study the potential role of the transmembrane domains of the prM proteins of Japanese encephalitis virus (JEV) in prM-E heterodimerization as well as subviral particle formation. Alanine insertion scanning mutagenesis within the GXXXG motif in the first transmembrane segment of JEV prM protein affected the prM-E heterodimerization; its specificity was confirmed by replacing the two glycines of the GXXXG motif with alanine, leucine and valine. The GXXXG motif was found to be conserved in the JEV serocomplex viruses but not other flavivirus groups. These mutants with alanine inserted in the two prM transmembrane segments all impaired subviral particle formation in cell cultures. The prM transmembrane domains of JEV may play importation roles in prM-E heterodimerization and viral particle assembly.
Human parvovirus B19 nonstructural protein NS1 enhanced the expression of cleavage of 70 kDa U1-snRNP autoantigen
Authors: Tzang Bor-Show , Chen Der-Yuan , Tsai Chun-Chou , Chiang Szu-Yi , Lin Tsung-Ming , Hsu Tsai-Ching 
Published: May 2010

Abstract

Background
Human parvovirus B19 (B19) is known to induce apoptosis that has been associated with a variety of autoimmune disorders. Although we have previously reported that B19 non-structural protein (NS1) induces mitochondrial-dependent apoptosis in COS-7 cells, the precise mechanism of B19-NS1 in developing autoimmunity is still obscure.

Methods
To further examine the effect of B19-NS1 in presence of autoantigens, COS-7 cells were transfected with pEGFP, pEGFP-B19-NS1 and pEGFP-NS1K334E, a mutant form of B19-NS1, and detected the expressions of autoantigens by various autoantibodies against Sm, U1 small nuclear ribonucleoprotein (U1-snRNP), SSA/Ro, SSB/La, Scl-70, Jo-1, Ku, and centromere protein (CENP) A/B by using Immunoblotting.

Results
Significantly increased apoptosis was detected in COS-7 cells transfected with pEGFP-B19-NS1 compared to those transfected with pEGFP. Meanwhile, the apoptotic 70 kDa U1-snRNP protein in COS-7 cells transfected with pEGFP-B19-NS1 is cleaved by caspase-3 and converted into a specific 40 kDa product, which were recognized by anti-U1-snRNP autoantibody. In contrast, significantly decreased apoptosis and cleaved 40 kDa product were observed in COS-7 cells transfected with pEGFP-NS1K334E compared to those transfected with pEGFP-B19-NS1.

Conclusions
These findings suggested crucial association of B19-NS1 in development of autoimmunity by inducing apoptosis and specific cleavage of 70 kDa U1-snRNP.
APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility
Authors: Xia Jun-Feng , Zhao Xing-Ming , Song Jiangning , Huang De-Shuang 
Published: May 2010

Abstract

Background
It is well known that most of the binding free energy of protein interaction is contributed by a few key hot spot residues. These residues are crucial for understanding the function of proteins and studying their interactions. Experimental hot spots detection methods such as alanine scanning mutagenesis are not applicable on a large scale since they are time consuming and expensive. Therefore, reliable and efficient computational methods for identifying hot spots are greatly desired and urgently required.

Results
In this work, we introduce an efficient approach that uses support vector machine (SVM) to predict hot spot residues in protein interfaces. We systematically investigate a wide variety of 62 features from a combination of protein sequence and structure information. Then, to remove redundant and irrelevant features and improve the prediction performance, feature selection is employed using the F-score method. Based on the selected features, nine individual-feature based predictors are developed to identify hot spots using SVMs. Furthermore, a new ensemble classifier, namely APIS (A combined model based on Protrusion Index and Solvent accessibility), is developed to further improve the prediction accuracy. The results on two benchmark datasets, ASEdb and BID, show that this proposed method yields significantly better prediction accuracy than those previously published in the literature. In addition, we also demonstrate the predictive power of our proposed method by modelling two protein complexes: the calmodulin/myosin light chain kinase complex and the heat shock locus gene products U and V complex, which indicate that our method can identify more hot spots in these two complexes compared with other state-of-the-art methods.

Conclusion
We have developed an accurate prediction model for hot spot residues, given the structure of a protein complex. A major contribution of this study is to propose several new features based on the protrusion index of amino acid residues, which has been shown to significantly improve the prediction performance of hot spots. Moreover, we identify a compact and useful feature subset that has an important implication for identifying hot spot residues. Our results indicate that these features are more effective than the conventional evolutionary conservation, pairwise residue potentials and other traditional features considered previously, and that the combination of our and traditional features may support the creation of a discriminative feature set for efficient prediction of hot spot residues. The data and source code are available on web site http://home.ustc.edu.cn/~jfxia/hotspot.html.
Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context
Authors: Abraham Gad , Kowalczyk Adam , Loi Sherene , Haviv Izhak , Zobel Justin 
Published: May 2010

Abstract

Background
Different microarray studies have compiled gene lists for predicting outcomes of a range of treatments and diseases. These have produced gene lists that have little overlap, indicating that the results from any one study are unstable. It has been suggested that the underlying pathways are essentially identical, and that the expression of gene sets, rather than that of individual genes, may be more informative with respect to prognosis and understanding of the underlying biological process.

Results
We sought to examine the stability of prognostic signatures based on gene sets rather than individual genes. We classified breast cancer cases from five microarray studies according to the risk of metastasis, using features derived from predefined gene sets. The expression levels of genes in the sets are aggregated, using what we call a set statistic. The resulting prognostic gene sets were as predictive as the lists of individual genes, but displayed more consistent rankings via bootstrap replications within datasets, produced more stable classifiers across different datasets, and are potentially more interpretable in the biological context since they examine gene expression in the context of their neighbouring genes in the pathway. In addition, we performed this analysis in each breast cancer molecular subtype, based on ER/HER2 status. The prognostic gene sets found in each subtype were consistent with the biology based on previous analysis of individual genes.

Conclusions
To date, most analyses of gene expression data have focused at the level of the individual genes. We show that a complementary approach of examining the data using predefined gene sets can reduce the noise and could provide increased insight into the underlying biological pathways.