bluuebunny/crossref_metadata_2025_split huggingface dataset:
A GEFA Assessment of Observed Global Ocean Influence on U.S. Precipitation Variability: Attribution to Regional SST Variability Modes
Authors: Zhong Yafang , Liu Zhengyu , Notaro Michael 
Published: October 2010

Abstract
This paper presents a comprehensive assessment of the observed influence of the global ocean on U.S. precipitation variability using the method of Generalized Equilibrium Feedback Assessment (GEFA), which enables an unambiguous attribution of the influence from multiple ocean basins within a unified framework. The GEFA assessment based on observations for 1950–99 suggests that the tropical Pacific SST variability has the greatest consequence for U.S. precipitation, as both ENSO and meridional modes are associated with notable responses in seasonal mean precipitation. The anomalously cold tropical Indian Ocean is a good indicator for U.S. dry conditions during spring and late winter. The impact of North Pacific SST variability is detected in springtime precipitation, yet it is overshadowed by that of the tropical Indo-Pacific on seasonal-to-interannual time scales. Tropical Atlantic forcing of U.S. precipitation appears to be most effective in winter, whereas the northern Atlantic forcing is likely more important during spring and summer.
Global ocean influence on U.S. precipitation is found to be most significant in winter, explaining over 20% of the precipitation variability in the Southwest and southern Great Plains throughout the cold seasons and in the northern Great Plains and northeast United States during late winter. The Southwest and southern Great Plains is likely the region that is most susceptible to oceanic influence, primarily to the forcing of the tropical Indo-Pacific. The Pacific Northwest is among the regions that may experience the least oceanic influence as far as precipitation variability is concerned.
A New Approach to Homogenize Daily Radiosonde Humidity Data
Authors: Dai Aiguo , Wang Junhong , Thorne Peter W. , Parker David E. , Haimberger Leopold , Wang Xiaolan L. 
Published: October 2010

Abstract
Radiosonde humidity records represent the only in situ observations of tropospheric water vapor content with multidecadal length and quasi-global coverage. However, their use has been hampered by ubiquitous and large discontinuities resulting from changes to instrumentation and observing practices. Here a new approach is developed to homogenize historical records of tropospheric (up to 100 hPa) dewpoint depression (DPD), the archived radiosonde humidity parameter. Two statistical tests are used to detect changepoints, which are most apparent in histograms and occurrence frequencies of the daily DPD: a variant of the Kolmogorov–Smirnov (K–S) test for changes in distributions and the penalized maximal F test (PMFred) for mean shifts in the occurrence frequency for different bins of DPD. These tests capture most of the apparent discontinuities in the daily DPD data, with an average of 8.6 changepoints (∼1 changepoint per 5 yr) in each of the analyzed radiosonde records, which begin as early as the 1950s and ended in March 2009. Before applying breakpoint adjustments, artificial sampling effects are first adjusted by estimating missing DPD reports for cold (T &lt; −30°C) and dry (DPD artificially set to 30°C) conditions using empirical relationships at each station between the anomalies of air temperature and vapor pressure derived from recent observations when DPD reports are available under these conditions. Next, the sampling-adjusted DPD is detrended separately for each of the 4–10 quantile categories and then adjusted using a quantile-matching algorithm so that the earlier segments have histograms comparable to that of the latest segment. Neither the changepoint detection nor the adjustment uses a reference series given the stability of the DPD series.
Using this new approach, a homogenized global, twice-daily DPD dataset (available online at www.cgd.ucar.edu/cas/catalog/) is created for climate and other applications based on the Integrated Global Radiosonde Archive (IGRA) and two other data sources. The adjusted-daily DPD has much smaller and spatially more coherent trends during 1973–2008 than the raw data. It implies only small changes in relative humidity in the lower and middle troposphere. When combined with homogenized radiosonde temperature, other atmospheric humidity variables can be calculated, and these exhibit spatially more coherent trends than without the DPD homogenization. The DPD adjustment yields a different pattern of change in humidity parameters compared to the apparent trends from the raw data. The adjusted estimates show an increase in tropospheric water vapor globally.
Observational Error Estimation of FORMOSAT-3/COSMIC GPS Radio Occultation Data
Authors: Chen Shu-Ya , Huang Ching-Yuang , Kuo Ying-Hwa , Sokolovskiy Sergey 
Published: October 2010

Abstract
The Global Positioning System (GPS) radio occultation (RO) technique is becoming a robust global observing system. GPS RO refractivity is typically modeled at the ray perigee point by a “local refractivity operator” in a data assimilation system. Such modeling does not take into account the horizontal gradients that affect the GPS RO refractivity. A new observable (linear excess phase), defined as an integral of the refractivity along some fixed ray path within the model domain, has been developed in earlier studies to account for the effect of horizontal gradients.
In this study, the error statistics of both observables (refractivity and linear excess phase) are estimated using the GPS RO data from the Formosa Satellite 3–Constellation Observing System for Meteorology, Ionosphere and Climate (FORMOSAT-3/COSMIC) mission. The National Meteorological Center (NMC) method, which is based on lagged forecast differences, is applied for evaluation of the model forecast errors that are used for estimation of the GPS RO observational errors. Also used are Weather Research and Forecasting (WRF) model forecasts in the East Asia region at 45-km resolution for one winter month (mid-January to mid-February) and one summer month (mid-August to mid-September) in 2007.
Fractional standard deviations of the observational errors of refractivity and linear excess phase both show an approximately linear decrease with height in the troposphere and a slight increase above the tropopause; their maximum magnitude is about 2.2% (2.5%) for refractivity and 1.1% (1.3%) for linear excess phase in the lowest 2 km for the winter (summer) month. An increase of both fractional observational errors near the surface in the summer month is attributed mainly to a larger amount of water vapor. The results indicate that the fractional observational error of refractivity is about twice as large as that of linear excess phase, regardless of season. The observational errors of both linear excess phase and refractivity are much less latitude dependent for summer than for winter. This difference is attributed to larger latitudinal variations of the specific humidity in winter.
Objective Bias Correction for Improved Skill in Forecasting Diurnal Cycles of Temperature over Multiple Locations: The Summer Case
Authors: Goswami P. , Mallick S. 
Published: October 2010

Abstract
One factor that limits skill of the numerical models is the bias in the model forecasts with respect to observations. Similarly, while the mesoscale models today can support horizontal grid spacing down to a few kilometers or fewer, downscaling of model forecasts to arrive at station-scale values will remain a necessary step for many applications. While generic improvement in model skill requires parallel and comprehensive development in model and other forecast methodology, one way of achieving skill in station-scale forecasts without (intensive effort) calibration of the model is to implement an objective bias correction (referred to as debiasing). This study shows that a nonlinear objective debiasing can transform zero-skill forecasts from a mesoscale model [fifth-generation Pennsylvania State University–National Center for Atmospheric Research Mesoscale Model (MM5)] to forecasts with significant skill. Twelve locations over India, representing urban sites in different geographical conditions, during May–August 2009 were considered. The model MM5 was integrated for 24 h with initial conditions from the National Centers for Environmental Prediction Global Forecast System (final) global gridded analysis (FNL) for each of the days of May–August 2009 in a completely operational setting (without assuming any observed information on dynamics beyond the time of the initial condition). It is shown that for all the locations and the four months, the skill of the debiased forecast is significant against essentially zero skill of raw forecasts. The procedure provides an applicable forecast strategy to attain realizable significant skill in station-scale forecasts. Potential skill, derived using in-sample data for calibrating the debiasing parameters, shows promise of further improvement with large samples.
Routine screening for eosinophilic esophagitis in patients presenting with dysphagia
Authors: Ricker Jonathan , McNear Scott , Cassidy Timothy , Plott Eric , Arnold Hays , Kendall Brian , Franklin Kevin 
Published: October 2010

Background: Eosinophilic esophagitis (EoE) is a clinicopathologic disorder first described in 1978 which has gained significant recognition over the past 10 years. Numerous prevalence studies have been performed around the globe, both in pediatric and adult populations documenting a prevalence between 0.002% and 6.5%. The aim of this study is to assess the utility of routinely screening for EoE in patients with dysphagia. Methods: A prospective, observational study in which adult patients with a complaint of esophageal dysphagia were enrolled. Results: Of the 135 patients enrolled, 122 completed the study; 100 patients had nonobstructive dysphagia, while 22 patients had a luminal finding which could explain their dysphagia. The prevalence of EoE in the nonobstructive dysphagia group was 22% (95% CI: 13.9–30.1%); 32.7% of male patients with nonobstructive dysphagia were found to have EoE compared with 8.9% of females ( p = 0.004). The mean age of nonobstructive patients found to have EoE was 37.8 years. White patients with nonobstructive dysphagia were found to have a 25.9% prevalence of EoE, compared with 0% of African Americans, 0% of Asians, and 14.3% of Hispanics. When comparing Whites with non-Whites, the prevalence of EoE was noted to be 25.9% versus 5.3%, respectively ( p = 0.050). Conclusions: EoE is a common cause of nonobstructive dysphagia. We believe that the high prevalence of EoE in patients with nonobstructive dysphagia supports the practice of routine biopsies to screen for the presence of abnormally high numbers of eosinophils in this subgroup.
Cellular context-dependent effects of H2ax and p53 deletion on the development of thymic lymphoma
Authors: Yin Bu , Yang-Iott Katherine S. , Chao Linda H. , Bassing Craig H. 
Published: October 2010

AbstractH2AX and Artemis each cooperate with p53 to suppress lymphoma. Germline H2ax−/−p53−/− mice die of T-cell receptor-β− (TCR-β−) thymic lymphomas with translocations and other lesions characteristic of human T-cell acute lymphoblastic leukemia. Here, we demonstrate that mice with inactivation of H2ax and p53 in thymocytes die at later ages to TCR-β− or TCR-β+ thymic lymphomas containing a similar pattern of translocations as H2ax−/−p53−/− tumors. Germline Artemis−/−p53−/− mice die of lymphomas with antigen receptor locus translocations, whereas Artemis−/−H2ax−/−p53−/− mice die at earlier ages from multiple malignancies. We show here that Artemis−/− mice with p53 deletion in thymocytes die of TCR-β− tumors containing Tcrα/δ translocations, other clonal translocations, or aneuploidy, as well as Notch1 mutations. Strikingly, Artemis−/− mice with H2ax and p53 deletion in thymocytes exhibited a lower rate of mortality from TCR-β− tumors, which harbored significantly elevated levels of genomic instability. Our data reveal that the cellular origin of H2ax and p53 loss impacts the rate of mortality from and developmental stage of thymic lymphomas, and suggest that conditional deletion of tumor suppressor genes may provide more physiologic models for human lymphoid malignancies than germline inactivation.
Spontaneous pneumothorax and tuberculosis: long-term follow-up
Authors: Freixinet J.L. , Caminero J.A. , Marchena J. , Rodríguez P.M. , Casimiro J.A. , Hussein M. 
Published: October 2010

Though spontaneous pneumothorax (SP) is a well-known complication of pulmonary tuberculosis (TB), there are very few reports addressing this topic. For this reason, we retrospectively analysed the experience of SP in patients diagnosed with TB in our hospital between 1989 and 2010.Out of 872 patients treated for SP during this period, 47 (5.4%) had TB antecedents, 21 with active TB (0.95% of the 2,089 TB cases diagnosed during this period) and 26 with residual inactive TB. 46 cases were treated with pleural drainage (PD): 40 (85%) with only one PD, two with two, and four with three. The mean±sdlength of PD treatment was 12.9±11.3 days. In 11 (23%) cases, a relapse of SP occurred, with no statistical relationship between the different studied variables. In 13 (28%) cases, it became necessary to carry out a resection (atypical segmentectomy in all cases) for persistent air leaks with PD. Survival statistics were unfavourable only in elderly patients and those infected with HIV.We conclude that the treatment of SP secondary to TB with PD is usually a sound response, with a good general prognosis and a low percentage of cases that require another PD and surgical treatment.
Data structures and compression algorithms for high-throughput sequencing technologies
Authors: Daily Kenny , Rigor Paul , Christley Scott , Xie Xiaohui , Baldi Pierre 
Published: October 2010

Abstract

Background
High-throughput sequencing (HTS) technologies play important roles in the life sciences by allowing the rapid parallel sequencing of very large numbers of relatively short nucleotide sequences, in applications ranging from genome sequencing and resequencing to digital microarrays and ChIP-Seq experiments. As experiments scale up, HTS technologies create new bioinformatics challenges for the storage and sharing of HTS data.

Results
We develop data structures and compression algorithms for HTS data. A processing stage maps short sequences to a reference genome or a large table of sequences. Then the integers representing the short sequence absolute or relative addresses, their length, and the substitutions they may contain are compressed and stored using various entropy coding algorithms, including both old and new fixed codes (e.g Golomb, Elias Gamma, MOV) and variable codes (e.g. Huffman). The general methodology is illustrated and applied to several HTS data sets. Results show that the information contained in HTS files can be compressed by a factor of 10 or more, depending on the statistical properties of the data sets and various other choices and constraints. Our algorithms fair well against general purpose compression programs such as gzip, bzip2 and 7zip; timing results show that our algorithms are consistently faster than the best general purpose compression programs.

Conclusions
It is not likely that exactly one encoding strategy will be optimal for all types of HTS data. Different experimental conditions are going to generate various data distributions whereby one encoding strategy can be more effective than another. We have implemented some of our encoding algorithms into the software package GenCompress which is available upon request from the authors. With the advent of HTS technology and increasingly new experimental protocols for using the technology, sequence databases are expected to continue rising in size. The methodology we have proposed is general, and these advanced compression techniques should allow researchers to manage and share their HTS data in a more timely fashion.
Comparative analysis of acute and chronic corticosteroid pharmacogenomic effects in rat liver: Transcriptional dynamics and regulatory structures
Authors: Nguyen Tung T , Almon Richard R , DuBois Debra C , Jusko William J , Androulakis Ioannis P 
Published: October 2010

Abstract

Background
Comprehensively understanding corticosteroid pharmacogenomic effects is an essential step towards an insight into the underlying molecular mechanisms for both beneficial and detrimental clinical effects. Nevertheless, even in a single tissue different methods of corticosteroid administration can induce different patterns of expression and regulatory control structures. Therefore, rich in vivo datasets of pharmacological time-series with two dosing regimens sampled from rat liver are examined for temporal patterns of changes in gene expression and their regulatory commonalities.

Results
The study addresses two issues, including (1) identifying significant transcriptional modules coupled with dynamic expression patterns and (2) predicting relevant common transcriptional controls to better understand the underlying mechanisms of corticosteroid adverse effects. Following the orientation of meta-analysis, an extended computational approach that explores the concept of agreement matrix from consensus clustering has been proposed with the aims of identifying gene clusters that share common expression patterns across multiple dosing regimens as well as handling challenges in the analysis of microarray data from heterogeneous sources, e.g. different platforms and time-grids in this study. Six significant transcriptional modules coupled with typical patterns of expression have been identified. Functional analysis reveals that virtually all enriched functions (gene ontologies, pathways) in these modules are shown to be related to metabolic processes, implying the importance of these modules in adverse effects under the administration of corticosteroids. Relevant putative transcriptional regulators (e.g. RXRF, FKHD, SP1F) are also predicted to provide another source of information towards better understanding the complexities of expression patterns and the underlying regulatory mechanisms of those modules.

Conclusions
We have proposed a framework to identify significant coexpressed clusters of genes across multiple conditions experimented from different microarray platforms, time-grids, and also tissues if applicable. Analysis on rich in vivo datasets of corticosteroid time-series yielded significant insights into the pharmacogenomic effects of corticosteroids, especially the relevance to metabolic side-effects. This has been illustrated through enriched metabolic functions in those transcriptional modules and the presence of GRE binding motifs in those enriched pathways, providing significant modules for further analysis on pharmacogenomic corticosteroid effects.
Transcriptomic and functional analysis of the Anopheles gambiae salivary gland in relation to blood feeding
Authors: Das Suchismita , Radtke Andrea , Choi Young-Jun , Mendes Antonio M , Valenzuela Jesus G , Dimopoulos George 
Published: October 2010

Abstract
Background
The Anopheles gambiae salivary glands play a major role in malaria transmission and express a variety of bioactive components that facilitate blood-feeding by preventing platelet aggregation, blood clotting, vasodilatation, and inflammatory and other reactions at the probing site on the vertebrate host.

Results
We have performed a global transcriptome analysis of the A. gambiae salivary gland response to blood-feeding, to identify candidate genes that are involved in hematophagy. A total of 4,978 genes were found to be transcribed in this tissue. A comparison of salivary gland transcriptomes prior to and after blood-feeding identified 52 and 41 transcripts that were significantly up-regulated and down-regulated, respectively. Ten genes were further selected to assess their role in the blood-feeding process using RNAi-mediated gene silencing methodology. Depletion of the salivary gland genes encoding D7L2, anophelin, peroxidase, the SG2 precursor, and a 5'nucleotidase gene significantly increased probing time of A. gambiae mosquitoes and thereby their capacity to blood-feed.

Conclusions
The salivary gland transcriptome comprises approximately 38% of the total mosquito transcriptome and a small proportion of it is dynamically changing already at two hours in response to blood feeding. A better understanding of the salivary gland transcriptome and its function can contribute to the development of pathogen transmission control strategies and the identification of medically relevant bioactive compounds.
Systematic identification of conserved motif modules in the human genome
Authors: Cai Xiaohui , Hou Lin , Su Naifang , Hu Haiyan , Deng Minghua , Li Xiaoman 
Published: October 2010

Abstract

Background
The identification of motif modules, groups of multiple motifs frequently occurring in DNA sequences, is one of the most important tasks necessary for annotating the human genome. Current approaches to identifying motif modules are often restricted to searches within promoter regions or rely on multiple genome alignments. However, the promoter regions only account for a limited number of locations where transcription factor binding sites can occur, and multiple genome alignments often cannot align binding sites with their true counterparts because of the short and degenerative nature of these transcription factor binding sites.

Results
To identify motif modules systematically, we developed a computational method for the entire non-coding regions around human genes that does not rely upon the use of multiple genome alignments. First, we selected orthologous DNA blocks approximately 1-kilobase in length based on discontiguous sequence similarity. Next, we scanned the conserved segments in these blocks using known motifs in the TRANSFAC database. Finally, a frequent pattern mining technique was applied to identify motif modules within these blocks. In total, with a false discovery rate cutoff of 0.05, we predicted 3,161,839 motif modules, 90.8% of which are supported by various forms of functional evidence. Compared with experimental data from 14 ChIP-seq experiments, on average, our methods predicted 69.6% of the ChIP-seq peaks with TFBSs of multiple TFs. Our findings also show that many motif modules have distance preference and order preference among the motifs, which further supports the functionality of these predictions.

Conclusions
Our work provides a large-scale prediction of motif modules in mammals, which will facilitate the understanding of gene regulation in a systematic way.