bluuebunny/crossref_metadata_2025_split huggingface dataset:
S
cala
E
xtrap
Authors: Wu Xing , Mueller Frank 
Published: May 2012

Performance modeling for scientific applications is important for assessing potential application performance and systems procurement in high-performance computing (HPC). Recent progress on communication tracing opens up novel opportunities for communication modeling due to its lossless yet scalable trace collection. Estimating the impact of scaling on communication efficiency still remains nontrivial due to execution-time variations and exposure to hardware and software artifacts.
This work contributes a fundamentally novel modeling scheme. We synthetically generate the application trace for large numbers of nodes via extrapolation from a set of smaller traces. We devise an innovative approach for topology extrapolation of single program, multiple data (SPMD) codes with stencil or mesh communication. Experimental results show that the extrapolated traces precisely reflect the communication behavior and the performance characteristics at the target scale for both strong and weak scaling applications. The extrapolated trace can subsequently be (a) replayed to assess communication requirements before porting an application, (b) transformed to autogenerate communication benchmarks for various target platforms, and (c) analyzed to detect communication inefficiencies and scalability limitations.
To the best of our knowledge, rapidly obtaining the communication behavior of parallel applications at arbitrary scale with the availability of timed replay, yet without actual execution of the application, at this scale, is without precedence and has the potential to enable otherwise infeasible system simulation at the exascale level.
Expression of the p53 Target CDIP Correlates with Sensitivity to TNFα-Induced Apoptosis in Cancer Cells
Authors: Brown-Endres Lauren , Schoenfeld David , Tian Fang , Kim Hyung-Gu , Namba Takushi , Muñoz-Fontela César , Mandinova Anna , Aaronson Stuart A. , Lee Sam W. 
Published: May 2012

Abstract
TNFα is a pleiotropic cytokine that signals for both survival and apoptotic cell fates. It is still unclear that the dual role of TNFα can be regulated in cancer cells. We previously described an apoptotic pathway involving p53→CDIP→TNFα that was activated in response to genotoxic stress. This pathway operated in the presence of JNK activation; therefore, we postulated that CDIP itself could sensitize cells to a TNFα apoptotic cell fate, survival, or death. We show that CDIP mediates sensitivity to TNFα-induced apoptosis and that cancer cells with endogenous CDIP expression are inherently sensitive to the growth-suppressive effects of TNFα in vitro and in vivo. Thus, CDIP expression correlates with sensitivity of cancer cells with TNFα, and CDIP seems to be a regulator of the p53-mediated death versus survival response of cells to TNFα. This CDIP-mediated sensitivity to TNFα-induced apoptosis favors pro- over antiapoptotic program in cancer cells, and CDIP may serve as a predictive biomarker for such sensitivity. Cancer Res; 72(9); 2373–82. ©2012 AACR.
Cardiovascular Health Behavior and Health Factor Changes (1988–2008) and Projections to 2020
Authors: Huffman Mark D. , Capewell Simon , Ning Hongyan , Shay Christina M. , Ford Earl S. , Lloyd-Jones Donald M. 
Published: May 2012

Background—
The American Heart Association's 2020 Strategic Impact Goals target a 20% relative improvement in overall cardiovascular health with the use of 4 health behavior (smoking, diet, physical activity, body mass) and 3 health factor (plasma glucose, cholesterol, blood pressure) metrics. We sought to define current trends and forward projections to 2020 in cardiovascular health.

Methods and Results—
We included 35 059 cardiovascular disease–free adults (aged ≥20 years) from the National Health and Nutrition Examination Survey 1988–1994 and subsequent 2-year cycles during 1999–2008. We calculated population prevalence of poor, intermediate, and ideal health behaviors and factors and also computed a composite, individual-level Cardiovascular Health Score for all 7 metrics (poor=0 points; intermediate=1 point; ideal=2 points; total range, 0–14 points). Prevalence of current and former smoking, hypercholesterolemia, and hypertension declined, whereas prevalence of obesity and dysglycemia increased through 2008. Physical activity levels and low diet quality scores changed minimally. Projections to 2020 suggest that obesity and impaired fasting glucose/diabetes mellitus could increase to affect 43% and 77% of US men and 42% and 53% of US women, respectively. Overall, population-level cardiovascular health is projected to improve by 6% overall by 2020 if current trends continue. Individual-level Cardiovascular Health Score projections to 2020 (men=7.4 [95% confidence interval, 5.7–9.1]; women=8.8 [95% confidence interval, 7.6–9.9]) fall well below the level needed to achieve a 20% improvement (men=9.4; women=10.1).

Conclusions—
The American Heart Association 2020 target of improving cardiovascular health by 20% by 2020 will not be reached if current trends continue.
U.K. Rainfall Data: A Long-Term Persistence Approach
Authors: Gil-Alana Luis A. 
Published: May 2012

AbstractThis paper looks at the analysis of U.K. monthly rainfall data from a long-term persistence viewpoint. Different modeling approaches are considered, taking into account the strong dependence and the seasonality in the data. The results indicate that the most appropriate model is the one that presents cyclical long-run dependence with the order of integration being positive though small, and the cycles having a periodicity of about a year.
A Particle-Surface-Area-Based Parameterization of Immersion Freezing on Desert Dust Particles
Authors: Niemand Monika , Möhler Ottmar , Vogel Bernhard , Vogel Heike , Hoose Corinna , Connolly Paul , Klein Holger , Bingemer Heinz , DeMott Paul , Skrotzki Julian , Leisner Thomas 
Published: May 2012

Abstract
In climate and weather models, the quantitative description of aerosol and cloud processes relies on simplified assumptions. This contributes major uncertainties to the prediction of global and regional climate change. Therefore, models need good parameterizations for heterogeneous ice nucleation by atmospheric aerosols. Here the authors present a new parameterization of immersion freezing on desert dust particles derived from a large number of experiments carried out at the Aerosol Interaction and Dynamics in the Atmosphere (AIDA) cloud chamber facility. The parameterization is valid in the temperature range between −12° and −36°C at or above water saturation and can be used in atmospheric models that include information about the dust surface area. The new parameterization was applied to calculate distribution maps of ice nuclei during a Saharan dust event based on model results from the regional-scale model Consortium for Small-Scale Modelling–Aerosols and Reactive Trace Gases (COSMO-ART). The results were then compared to measurements at the Taunus Observatory on Mount Kleiner Feldberg, Germany, and to three other parameterizations applied to the dust outbreak. The aerosol number concentration and surface area from the COSMO-ART model simulation were taken as input to different parameterizations. Although the surface area from the model agreed well with aerosol measurements during the dust event at Kleiner Feldberg, the ice nuclei (IN) number concentration calculated from the new surface-area-based parameterization was about a factor of 13 less than IN measurements during the same event. Systematic differences of more than a factor of 10 in the IN number concentration were also found among the different parameterizations. Uncertainties in the modeled and measured parameters probably both contribute to this discrepancy and should be addressed in future studies.
A multicentre, randomized study of telmisartan versus carvedilol for prevention of atrial fibrillation recurrence in hypertensive patients
Authors: Galzerano Domenico , Di Michele Sara , Paolisso Giuseppe , Tuccillo Bernardino , Lama Diana , Carbotta Sabino , Cittadini Antonio , Tedesco Michele Adolfo , Gaudio Carlo 
Published: May 2012

Introduction: Atrial remodelling, leading to atrial fibrillation (AF), is mediated by the renin–angiotensin–aldosterone system. Methods: Mild hypertensive outpatients (systolic/diastolic blood pressure 140–159/90–99 mmHg) in sinus rhythm who had experienced ≥ 1 electrocardiogram (ECG)-documented AF episode in the previous six months received randomly telmisartan 80 mg/day or carvedilol 25 mg/day. Blood pressure and 24-hour ECG were monitored monthly for one year; patients were asked to report symptomatic AF episodes and to undergo an ECG as early as possible. Results: One hundred and thirty-two patients completed the study (telmisartan, n=70; carvedilol, n=62). Significantly fewer AF episodes were reported with telmisartan versus carvedilol (14.3% vs. 37.1%; p<0.003). Left atrial diameter, assessed by echocardiography, was similar with telmisartan and carvedilol (3.4±2.3 cm vs. 3.6±2.4 cm). At study end, both regimes significantly reduced mean left ventricular mass index, but the reduction obtained with telmisartan was significantly greater than with carvedilol (117.8±10.7 vs. 124.7±14.5; p<0.0001). Mean blood pressure values were not significantly different between the groups (telmisartan 154/97 to 123/75 mmHg; p<0.001; carvedilol 153/94 to 125/78 mmHg; p<0.001). Conclusions: Telmisartan was significantly more effective than carvedilol in preventing recurrent AF episodes in hypertensive AF patients, despite a similar lowering of blood pressure.
Tumor-derived tissue factor activates coagulation and enhances thrombosis in a mouse xenograft model of human pancreatic cancer
Authors: Wang Jian-Guo , Geddings Julia E. , Aleman Maria M. , Cardenas Jessica C. , Chantrathammachart Pichika , Williams Julie C. , Kirchhofer Daniel , Bogdanov Vladimir Y. , Bach Ronald R. , Rak Janusz , Church Frank C. , Wolberg Alisa S. , Pawlinski Rafal , Key Nigel S. , Yeh Jen Jen , Mackman Nigel 
Published: May 2012

Abstract
Cancer patients often have an activated clotting system and are at increased risk for venous thrombosis. In the present study, we analyzed tissue factor (TF) expression in 4 different human pancreatic tumor cell lines for the purpose of producing derivative tumors in vivo. We found that 2 of the lines expressed TF and released TF-positive microparticles (MPs) into the culture medium. The majority of TF protein in the culture medium was associated with MPs. Only TF-positive cell lines activated coagulation in nude mice, and this activation was abolished by an anti–human TF Ab. Of the 2 TF-positive lines, only one produced detectable levels of human MP TF activity in the plasma when grown orthotopically in nude mice. Surprisingly, < 5% of human TF protein in plasma from tumor-bearing mice was associated with MPs. Mice with TF-positive tumors and elevated levels of circulating TF-positive MPs had increased thrombosis in a saphenous vein model. In contrast, we observed no difference in thrombus weight between tumor-bearing and control mice in an inferior vena cava stenosis model. The results of the present study using a xenograft mouse model suggest that tumor TF activates coagulation, whereas TF on circulating MPs may trigger venous thrombosis.
Multiple inhibitory ligands induce impaired T-cell immunologic synapse function in chronic lymphocytic leukemia that can be blocked with lenalidomide: establishing a reversible immune evasion mechanism in human cancer
Authors: Ramsay Alan G. , Clear Andrew J. , Fatah Rewas , Gribben John G. 
Published: May 2012

Abstract
Cancer immune evasion is an emerging hallmark of disease progression. We have demonstrated previously that impaired actin polymerization at the T-cell immunologic synapse is a global immune dysfunction in chronic lymphocytic leukemia (CLL). Direct contact with tumor cells induces defective actin polarization at the synapse in previously healthy T cells, but the molecules mediating this dysfunction were not known. In the present study, we show via functional screening assays that CD200, CD270, CD274, and CD276 are coopted by CLL cells to induce impaired actin synapse formation in both allogeneic and autologous T cells. We also show that inhibitory ligand–induced impairment of T-cell actin dynamics is a common immunosuppressive strategy used by both hematologic (including lymphoma) and solid carcinoma cells. This immunosuppressive signaling targets T-cell Rho-GTPase activation. Of clinical relevance, the immunomodulatory drug lenalidomide prevented the induction of these defects by down-regulating tumor cell–inhibitory molecule expression. These results using human CLL as a model cancer establish a novel evasion mechanism whereby malignant cells exploit multiple inhibitory ligand signaling to down-regulate small GTPases and lytic synapse function in global T-cell populations. These findings should contribute to the design of immunotherapeutic strategies to reverse T-cell tolerance in cancer.
How I treat POEMS syndrome
Authors: Dispenzieri Angela 
Published: May 2012

AbstractPOEMS syndrome is a paraneoplastic syndrome whose acronym stands for less than half of the defining features of the disease, that is, polyradiculoneuropathy, organomegaly, potentially including coexisting Castleman disease, endocrinopathy, monoclonal plasma cell neoplasm, and skin changes. The other important features include papilledema, extravascular volume overload, sclerotic bone lesions, thrombocytosis, elevated VEGF, and abnormal pulmonary function. The diagnosis is based on having both the polyradiculoneuropathy and the monoclonal plasma cell disorder, and at least 1 of the other 3 major criteria (Castleman disease, sclerotic bone lesions, or elevated VEGF) and at least one minor criterion. The diagnosis is often delayed with intervening incorrect diagnoses of chronic inflammatory demyelinating polyradiculoneuropathy, myeloproliferative disorder, and monoclonal gammopathy of undetermined significance. Prompt treatment directed at the underlying plasma cell clone produces dramatic responses in the majority of patients. Although there are no randomized clinical trial data to direct best therapy, for patients with disseminated disease, high-dose chemotherapy with peripheral blood transplantation has yielded durable benefit, whereas radiation therapy is typically effective for patients with a more localized presentation. More universal recognition of and more scientific inquiry into the underpinnings of the disease will provide direction toward the best treatment strategies in the future.
Mayday - integrative analytics for expression data
Authors: Battke Florian , Symons Stephan , Nieselt Kay 
Published: May 2012

Abstract

Background
DNA Microarrays have become the standard method for large scale analyses of gene expression and epigenomics. The increasing complexity and inherent noisiness of the generated data makes visual data exploration ever more important. Fast deployment of new methods as well as a combination of predefined, easy to apply methods with programmer's access to the data are important requirements for any analysis framework. Mayday is an open source platform with emphasis on visual data exploration and analysis. Many built-in methods for clustering, machine learning and classification are provided for dissecting complex datasets. Plugins can easily be written to extend Mayday's functionality in a large number of ways. As Java program, Mayday is platform-independent and can be used as Java WebStart application without any installation. Mayday can import data from several file formats, database connectivity is included for efficient data organization. Numerous interactive visualization tools, including box plots, profile plots, principal component plots and a heatmap are available, can be enhanced with metadata and exported as publication quality vector files.

Results
We have rewritten large parts of Mayday's core to make it more efficient and ready for future developments. Among the large number of new plugins are an automated processing framework, dynamic filtering, new and efficient clustering methods, a machine learning module and database connectivity. Extensive manual data analysis can be done using an inbuilt R terminal and an integrated SQL querying interface. Our visualization framework has become more powerful, new plot types have been added and existing plots improved.

Conclusions
We present a major extension of Mayday, a very versatile open-source framework for efficient micro array data analysis designed for biologists and bioinformaticians. Most everyday tasks are already covered. The large number of available plugins as well as the extension possibilities using compiled plugins and ad-hoc scripting allow for the rapid adaption of Mayday also to very specialized data exploration. Mayday is available at http://microarray-analysis.org.
Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals
Authors: Takane Kahori , Fujishima Kosuke , Watanabe Yuka , Sato Asako , Saito Nobuto , Tomita Masaru , Kanai Akio 
Published: May 2012

Abstract

Background
In many eukaryotes, microRNAs (miRNAs) bind to complementary sites in the 3'-untranslated regions (3'-UTRs) of target messenger RNAs (mRNAs) and regulate their expression at the stage of translation. Recent studies have revealed that many miRNAs are evolutionarily conserved; however, the evolution of their target genes has yet to be systematically characterized. We sought to elucidate a set of conserved miRNA/target-gene pairs and to analyse the mechanism underlying miRNA-mediated gene regulation in the early stage of bilaterian evolution.

Results
Initially, we extracted five evolutionarily conserved miRNAs (let-7, miR-1, miR-124, miR-125/lin-4, and miR-34) among five diverse bilaterian animals. Subsequently, we designed a procedure to predict evolutionarily conserved miRNA/target-gene pairs by introducing orthologous gene information. As a result, we extracted 31 orthologous miRNA/target-gene pairs that were conserved among at least four diverse bilaterian animals; the prediction set showed prominent enrichment of orthologous miRNA/target-gene pairs that were verified experimentally. Approximately 84% of the target genes were regulated by three miRNAs (let-7, miR-1, and miR-124) and their function was classified mainly into the following categories: development, muscle formation, cell adhesion, and gene regulation. We used a reporter gene assay to experimentally verify the downregulation of six candidate pairs (out of six tested pairs) in HeLa cells.

Conclusions
The application of our new method enables the identification of 31 miRNA/target-gene pairs that were expected to have been regulated from the era of the common bilaterian ancestor. The downregulation of all six candidate pairs suggests that orthologous information contributed to the elucidation of the primordial set of genes that has been regulated by miRNAs; it was also an efficient tool for the elimination of false positives from the predicted candidates. In conclusion, our study identified potentially important miRNA-target pairs that were evolutionarily conserved throughout diverse bilaterian animals and that may provide new insights into early-stage miRNA functions.
Functional and evolutionary correlates of gene constellations in the Drosophila melanogaster genome that deviate from the stereotypical gene architecture
Authors: Li Shuwei , Shih Ching-Hua , Kohn Michael H 
Published: May 2012

Abstract

Background
The biological dimensions of genes are manifold. These include genomic properties, (e.g., X/autosomal linkage, recombination) and functional properties (e.g., expression level, tissue specificity). Multiple properties, each generally of subtle influence individually, may affect the evolution of genes or merely be (auto-)correlates. Results of multidimensional analyses may reveal the relative importance of these properties on the evolution of genes, and therefore help evaluate whether these properties should be considered during analyses. While numerous properties are now considered during studies, most work still assumes the stereotypical solitary gene as commonly depicted in textbooks. Here, we investigate the Drosophila melanogaster genome to determine whether deviations from the stereotypical gene architecture correlate with other properties of genes.

Results
Deviations from the stereotypical gene architecture were classified as the following gene constellations: Overlapping genes were defined as those that overlap in the 5-prime, exonic, or intronic regions. Chromatin co-clustering genes were defined as genes that co-clustered within 20 kb of transcriptional territories. If this scheme is applied the stereotypical gene emerges as a rare occurrence (7.5%), slightly varied schemes yielded between ~1%-50%. Moreover, when following our scheme, paired-overlapping genes and chromatin co-clustering genes accounted for 50.1 and 42.4% of the genes analyzed, respectively. Gene constellation was a correlate of a number of functional and evolutionary properties of genes, but its statistical effect was ~1-2 orders of magnitude lower than the effects of recombination, chromosome linkage and protein function. Analysis of datasets on male reproductive proteins showed these were biased in their representation of gene constellations and evolutionary rate Ka/Ks estimates, but these biases did not overwhelm the biologically meaningful observation of high evolutionary rates of male reproductive genes.

Conclusion
Given the rarity of the solitary stereotypical gene, and the abundance of gene constellations that deviate from it, the presence of gene constellations, while once thought to be exceptional in large Eukaryote genomes, might have broader relevance to the understanding and study of the genome. However, according to our definition, while gene constellations can be significant correlates of functional properties of genes, they generally are weak correlates of the evolution of genes. Thus, the need for their consideration would depend on the context of studies.
Gene expression profile of the skin in the 'hairpoor' (HrHp) mice by microarray analysis
Authors: Kim Bong-Kyu , Baek In-Cheol , Lee Hwa-Young , Kim Jeong-Ki , Song Hae-Hiang , Yoon Sungjoo K 
Published: May 2012

Abstract

Background
The transcriptional cofactor, Hairless (HR), acts as one of the key regulators of hair follicle cycling; the loss of function mutations is the cause of the expression of the hairless phenotype in humans and mice. Recently, we reported a new Hr mutant mouse called 'Hairpoor' (Hr

Hp
). These mutants harbor a gain of the function mutation, T403A, in the Hr gene. This confers the overexpression of HR and Hr

Hp
is an animal model of Marie Unna hereditary hypotrichosis in humans. In the present study, the expression profile of Hr

Hp

/Hr

Hp
skin was investigated using microarray analysis to identify genes whose expression was affected by the overexpression of HR.

Results
From 45,282 mouse probes, differential expressions in 43 (>2-fold), 306 (>1.5-fold), and 1861 genes (>1.2-fold) in skin from Hr

Hp

/Hr

Hp
mice were discovered and compared with skin from wild-type mice. Among the 1861 genes with a > 1.2-fold increase in expression, further analysis showed that the expression of eight genes known to have a close relationship with hair follicle development, ascertained by conducting real-time PCR on skin RNA produced during hair follicle morphogenesis (P0-P14), indicated that four genes, Wif1, Casp14, Krt71, and Sfrp1, showed a consistent expression pattern with respect to HR overexpression in vivo.

Conclusion

Wif1 and Casp14 were found to be upregulated, whereas Krt71 and Sfrp1 were downregulated in cells overexpressing HR in transient transfection experiments on keratinocytes, suggesting that HR may transcriptionally regulate these genes. Further studies are required to understand the mechanism of this regulation by the HR cofactor.