bluuebunny/crossref_metadata_2025_split huggingface dataset:
Verification of TIGGE Multimodel and ECMWF Reforecast-Calibrated Probabilistic Precipitation Forecasts over the Contiguous United States*
Authors: Hamill Thomas M. 
Published: February 2012

Abstract
Probabilistic quantitative precipitation forecasts (PQPFs) were generated from The Observing System Research and Predictability Experiment (THORPEX) Interactive Grand Global Ensemble (TIGGE) database from July to October 2010 using data from Europe (ECMWF), the United Kingdom [Met Office (UKMO)], the United States (NCEP), and Canada [Canadian Meteorological Centre (CMC)]. Forecasts of 24-h accumulated precipitation were evaluated at 1° grid spacing within the contiguous United States against analysis data based on gauges and bias-corrected radar data.
PQPFs from ECMWF’s ensembles generally had the highest skill of the raw ensemble forecasts, followed by CMC. Those of UKMO and NCEP were less skillful. PQPFs from CMC forecasts were the most reliable but the least sharp, and PQPFs from NCEP and UKMO ensembles were the least reliable but sharper.
Multimodel PQPFs were more reliable and skillful than individual ensemble prediction system forecasts. The improvement was larger for heavier precipitation events [e.g., >10 mm (24 h)−1] than for smaller events [e.g., >1 mm (24 h)−1].
ECMWF ensembles were statistically postprocessed using extended logistic regression and the five-member weekly reforecasts for the June–November period of 2002–09, the period where precipitation analyses were also available. Multimodel ensembles were also postprocessed using logistic regression and the last 30 days of prior forecasts and analyses. The reforecast-calibrated ECMWF PQPFs were much more skillful and reliable for the heavier precipitation events than ECMWF raw forecasts but much less sharp. Raw multimodel PQPFs were generally more skillful than reforecast-calibrated ECMWF PQPFs for the light precipitation events but had about the same skill for the higher-precipitation events; also, they were sharper but somewhat less reliable than ECMWF reforecast-based PQPFs. Postprocessed multimodel PQPFs did not provide as much improvement to the raw multimodel PQPF as the reforecast-based processing did to the ECMWF forecast.
The evidence presented here suggests that all operational centers, even ECMWF, would benefit from the open, real-time sharing of precipitation forecast data and the use of reforecasts.
Predictors of proteinuria reduction by monotherapy with an angiotensin receptor blocker, olmesartan
Authors: Ono Minamo , Fukuda Michio , Miura Toshiyuki , Mizuno Masashi , Kato Yoko , Sato Ryo , Naito Takehiro , Togawa Hiroyuki , Sasakawa Yuji , Tomonari Tatsuya , Ichikawa Tadashi , Shirasawa Yuichi , Ito Akinori , Yoshida Atsuhiro , Kimura Genjiro 
Published: February 2012

Introduction: It is known that reduced glomerular filtration rate (GFR) is a crucial factor to limit the blood pressure lowering effect of antihypertensives. In the present study, we tested whether the effects of monotherapy with an angiotensin receptor blocker (ARB) to lower proteinuria could be restricted by reduced GFR. Materials and methods: Thirty-five renal patients who had albuminuria more than 30 mg/day, but did not have diabetic nephropathy or nephrotic syndrome, were studied before and during eight weeks of monotherapy with ARB, olmesartan. Results: Blood pressure was lowered from 129 ± 18/79 ± 12 to 116 ± 18/72 ± 12 mmHg ( p < 0.0001), while albuminuria was reduced from 614±630 to 343±472 mg/day ( p < 0.0001). Albuminuria was inversely correlated with GFR both before and during treatment. Albuminuria reduction was enhanced as plasma renin activity ( p = 0.047) and dose of olmesartan were increased ( p = 0.04). Although the absolute reduction in proteinuria was not correlated with GFR ( p = 0.56), the % reduction was significantly proportional with GFR ( p = 0.027). Multiple regression analysis demonstrated that 64% of proteinuria reduction could be explained by baseline levels of albuminuria, GFR and renin activity. Conclusions: The reduction in proteinuria by olmesartan may be roughly predicted using baseline GFR and other parameters. These findings clarify that the effect of ARB on proteinuria reduction is restricted by reduced GFR.
The matri-cellular proteins ‘cysteine-rich, angiogenic-inducer, 61’ and ‘connective tissue growth factor’ are regulated in experimentally-induced sepsis with multiple organ dysfunction
Authors: Hviid Claus VB , Erdem Johanna Samulin , Kunke David , Ahmed Shakil M , Kjeldsen Signe F , Wang Yun Yong , Attramadal Håvard , Aasen Ansgar O 
Published: February 2012

Organ failure is a severe complication in sepsis for which the pathophysiology remains incompletely understood. Recently, the matri-cellular cysteine-rich, angiogenic induced, 61 ( Cyr61/CCN1); connective tissue growth factor ( Ctgf/CCN2); and nephroblastoma overexpressed gene ( Nov/CCN3) (CCN)-protein family have been attributed organ-protective properties. Their expression is sensitive to mediators of sepsis pathophysiology but a potential role in sepsis remains elusive. To provide an initial assessment, 50 rats were subjected to 18 h of cecal-ligation and puncture or sham operation. Hepatic and pulmonary CCN1 mRNA displayed an average 7.4- and 3.3-fold induction, while its cardiac expression was unchanged. The changes coincided with excessive hepatic and pulmonary inflammatory gene activation and a restricted cardiac inflammation. Furthermore, hepatocytes displayed a dosage-dependent CCN1 mRNA response in vitro, supporting a cytokine-mediated CCN1 regulation in sepsis. CCN2 mRNA was 2.2-fold induced in the liver, while 2.0-fold and 1.4-fold repressed in the heart and lung. Meanwhile, it did not respond to TNF-α exposure in vitro, which indicates different means of regulation than for CCN1. Taken together, this study provides the first evidence for multi-organ regulation of CCN1 and CCN2 in early stages of sepsis, and implies the eruption of inflammatory mediators as a potential mechanism behind the observed CCN1 regulation.
Imatinib mesylate directly impairs class switch recombination through down-regulation of AID: its potential efficacy as an AID suppressor
Authors: Kawamata Toyotaka , Lu Jun , Sato Tadayuki , Tanaka Masafumi , Nagaoka Hitoshi , Agata Yasutoshi , Toyoshima Takae , Yokoyama Kazuaki , Oyaizu Naoki , Nakamura Naoya , Ando Kiyoshi , Tojo Arinobu , Kotani Ai 
Published: February 2012

Abstract
Activation-induced cytidine deaminase (AID) is essential for class switch recombination and somatic hypermutation. Its deregulated expression acts as a genomic mutator that can contribute to the development of various malignancies. During treatment with imatinib mesylate (IM), patients with chronic myeloid leukemia often develop hypogammaglobulinemia, the mechanism of which has not yet been clarified. Here, we provide evidence that class switch recombination on B-cell activation is apparently inhibited by IM through down-regulation of AID. Furthermore, expression of E2A, a key transcription factor for AID induction, was markedly suppressed by IM. These results elucidate not only the underlying mechanism of IM-induced hypogammaglobulinemia but also its potential efficacy as an AID suppressor.
High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade
Authors: Christie-Oleza Joseph A , Miotello Guylaine , Armengaud Jean 
Published: February 2012

Abstract

Background
The structural and functional annotation of genomes is now heavily based on data obtained using automated pipeline systems. The key for an accurate structural annotation consists of blending similarities between closely related genomes with biochemical evidence of the genome interpretation. In this work we applied high-throughput proteogenomics to Ruegeria pomeroyi, a member of the Roseobacter clade, an abundant group of marine bacteria, as a seed for the annotation of the whole clade.

Results
A large dataset of peptides from R. pomeroyi was obtained after searching over 1.1 million MS/MS spectra against a six-frame translated genome database. We identified 2006 polypeptides, of which thirty-four were encoded by open reading frames (ORFs) that had not previously been annotated. From the pool of 'one-hit-wonders', i.e. those ORFs specified by only one peptide detected by tandem mass spectrometry, we could confirm the probable existence of five additional new genes after proving that the corresponding RNAs were transcribed. We also identified the most-N-terminal peptide of 486 polypeptides, of which sixty-four had originally been wrongly annotated.

Conclusions
By extending these re-annotations to the other thirty-six Roseobacter isolates sequenced to date (twenty different genera), we propose the correction of the assigned start codons of 1082 homologous genes in the clade. In addition, we also report the presence of novel genes within operons encoding determinants of the important tricarboxylic acid cycle, a feature that seems to be characteristic of some Roseobacter genomes. The detection of their corresponding products in large amounts raises the question of their function. Their discoveries point to a possible theory for protein evolution that will rely on high expression of orphans in bacteria: their putative poor efficiency could be counterbalanced by a higher level of expression. Our proteogenomic analysis will increase the reliability of the future annotation of marine bacterial genomes.
Identification and localisation of the NB-LRR gene family within the potato genome
Authors: Jupe Florian , Pritchard Leighton , Etherington Graham J , MacKenzie Katrin , Cock Peter JA , Wright Frank , Sharma Sanjeev Kumar , Bolser Dan , Bryan Glenn J , Jones Jonathan DG , Hein Ingo 
Published: February 2012

Abstract

Background
The potato genome sequence derived from the Solanum tuberosum Group Phureja clone DM1-3 516 R44 provides unparalleled insight into the genome composition and organisation of this important crop. A key class of genes that comprises the vast majority of plant resistance (R) genes contains a nucleotide-binding and leucine-rich repeat domain, and is collectively known as NB-LRRs.

Results
As part of an effort to accelerate the process of functional R gene isolation, we performed an amino acid motif based search of the annotated potato genome and identified 438 NB-LRR type genes among the ~39,000 potato gene models. Of the predicted genes, 77 contain an N-terminal toll/interleukin 1 receptor (TIR)-like domain, and 107 of the remaining 361 non-TIR genes contain an N-terminal coiled-coil (CC) domain. Physical map positions were established for 370 predicted NB-LRR genes across all 12 potato chromosomes. The majority of NB-LRRs are physically organised within 63 identified clusters, of which 50 are homogeneous in that they contain NB-LRRs derived from a recent common ancestor.

Conclusions
By establishing the phylogenetic and positional relationship of potato NB-LRRs, our analysis offers significant insight into the evolution of potato R genes. Furthermore, the data provide a blueprint for future efforts to identify and more rapidly clone functional NB-LRR genes from Solanum species.
A point mutation in the DNA-binding domain of HPV-2 E2 protein increases its DNA-binding capacity and reverses its transcriptional regulatory activity on the viral early promoter
Authors: Gao Chen , Pan Ming-Ming , Lei Yan-Jun , Tian Li-Qing , Jiang Hui-Ying , Li Xiao-Li , Shi Qi , Tian Chan , Yuan Yu-Kang , Fan Gui-Xiang , Dong Xiao-Ping 
Published: February 2012

Abstract

Background
The human papillomavirus (HPV) E2 protein is a multifunctional DNA-binding protein. The transcriptional activity of HPV E2 is mediated by binding to its specific binding sites in the upstream regulatory region of the HPV genomes. Previously we reported a HPV-2 variant from a verrucae vulgaris patient with huge extensive clustered cutaneous, which have five point mutations in its E2 ORF, L118S, S235P, Y287H, S293R and A338V. Under the control of HPV-2 LCR, co-expression of the mutated HPV E2 induced an increased activity on the viral early promoter. In the present study, a series of mammalian expression plasmids encoding E2 proteins with one to five amino acid (aa) substitutions for these mutations were constructed and transfected into HeLa, C33A and SiHa cells.

Results
CAT expression assays indicated that the enhanced promoter activity was due to the co-expressions of the E2 constructs containing A338V mutation within the DNA-binding domain. Western blots analysis demonstrated that the transiently transfected E2 expressing plasmids, regardless of prototype or the A338V mutant, were continuously expressed in the cells. To study the effect of E2 mutations on its DNA-binding activity, a serial of recombinant E2 proteins with various lengths were expressed and purified. Electrophoresis mobility shift assays (EMSA) showed that the binding affinity of E2 protein with A338V mutation to both an artificial probe with two E2 binding sites or HPV-2 and HPV-16 promoter-proximal LCR sequences were significantly stronger than that of the HPV-2 prototype E2. Furthermore, co-expression of the construct containing A338V mutant exhibited increased activities on heterologous HPV-16 early promoter P97 than that of prototype E2.

Conclusions
These results suggest that the mutation from Ala to Val at aa 338 is critical for E2 DNA-binding and its transcriptional regulation.
Promising treatment outcomes of intensity-modulated radiation therapy for nasopharyngeal carcinoma patients with N0 disease according to the seventh edition of the AJCC staging system
Authors: Sun Ying , Tang Ling-Long , Chen Lei , Li Wen-Fei , Mao Yan-Ping , Liu Li-Zhi , Lin Ai-Hua , Li Li , Ma Jun 
Published: February 2012

AbstractBackgroundIntensity-modulated radiation therapy (IMRT) provides excellent locoregional control for nasopharyngeal carcinoma (NPC), and has gradually replaced two-dimensional conventional radiotherapy as the first-line radiotherapy technique. Furthermore, in the new seventh edition of the American Joint Committee on Cancer (AJCC) staging system, retropharyngeal lymph nodes were upgraded from N0 to N1 disease as a result of their negative impact on the distant metastasis-free survival (DMFS) rates of NPC. This retrospective study was conducted in order to review the treatment outcomes and patterns of failure in NPC patients with N0 disease after IMRT in order to effectively guide treatment in the future.MethodsWe retrospectively reviewed data from 506 biopsy-proven nonmetastatic NPC patients. There were 191 patients with negative cervical lymph node involvement. According to the seventh edition of the American Joint Committee on Cancer (AJCC) staging system, 110 patients (21.7%) were staged with N0 disease, and 81 patients (16.0%) were reclassified with N1 disease due to the presence of RLN metastasis. All patients received IMRT as the primary treatment.ResultsIn patients with negative cervical lymph node involvement, distant metastasis-free survival (DMFS) was significantly higher in patients without retropharyngeal lymph node (RLN) metastasis than those with RLN metastasis (95.9% vs. 88.1% respectively, P = 0.04). For N0 disease, the 5-year overall survival (OS), local relapse-free survival (LRFS), nodal relapse-free survival (NRFS) and DMFS rates were 93.8%, 97.1%, 99.1% and 95.9%, respectively. For T1N0, T2N0, T3N0 and T4N0, OS was 97.8%, 100%, 93.8% and 76.9%, LRFS was 100%, 92.9%, 100% and 88.9% and DMFS was 96.6%, 90.9%, 100% and 93.3%, respectively. OS and LRFS were higher in T1-3 N0 patients than T4N0 patients (P< 0.01 andP= 0.01, respectively).ConclusionsThe seventh edition of the AJCC N-staging system improves prognostic accuracy by upgrading RLN metastasis to N1 disease. IMRT produces excellent survival rates in T1-3 N0 disease; however, T4N0 disease remains a challenge and additional improvements are required to achieve a favorable prognosis for these NPC patients.
Cholesteryl ester transfer protein Taq IB polymorphism and its association with serum lipid levels and longevity in Chinese Bama Zhuang population
Authors: Pan Shang-Ling , Wang Fei , Lu Ze-Ping , Liu Cheng-Wu , Hu Cai-You , Luo Huan , Peng Jun-Hua , Luo Xiao-Qiu , Pang Guo-Fang , Lu Shao-Hua , Wu Hua-Yu , Huang Ling-Jin , Yin Rui-Xing 
Published: February 2012

Abstract

Background

Taq IB polymorphism in the cholesteryl ester transfer protein (CETP) gene has been reported to be associated with serum high-density lipoprotein cholesterol (HDL-C) levels and longevity in several populations, but controversial results also arose probably due to racial/ethnic diversity. Bama is a remote and mountainous county located in the northwest of Guangxi, People's Republic of China, which has been well known for its longevity for centuries. The current study was to investigate the possible association of CETP Taq IB polymorphism with serum lipid levels and longevity in the Bama Zhuang population.

Methods
The CETP Taq IB genotypes were determined by polymerase chain reaction and restriction fragment length polymorphism in 523 long-lived inhabitants (long-lived group, LG; aged 90-107 years) and 498 healthy controls without longevity family history (non-long-lived group, non-LG; aged 40-69 years) residing in Bama County.

Results
The levels of total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C) were higher but TG, HDL-C/LDL-C ratio and the prevalence of dyslipidemia were lower in LG than in non-LG (P < 0.001 for all). There were no differences in the allelic and genotypic frequencies between the two groups (P > 0.05). Serum HDL-C levels and HDL-C/LDL-C ratio in LG were different among the genotypes (P < 0.01 for each), the subjects with B2B2 and B1B2 genotyes had higher HDL-C levels and HDL-C/LDL-C ratio than the subjects with B1B1genotye, whereas the levels of TC and HDL-C in non-LG were different among/between the genotypes (P < 0.01 for each), the B2 allele carriers had lower TC and higher HDL-C levels than the B2 allele noncarriers. Serum TG and HDL-C levels and HDL-C/LDL-C ratio were correlated with genotypes in LG, whereas serum TC and HDL-C levels were associated with genotypes in non-LG (P < 0.05-0.001).

Conclusions
The association of CETP Taq IB polymorphism and serum lipid profiles is different between LG and non-LG in the Chinese Bama Zhuang population. CETP Taq IB polymorphism might be one of the longevity-related genetic factors in this population.
One-pot synthesis of Bi-Ni nanowire and nanocable arrays by coelectrodeposition approach
Authors: Jia Yuying , Yang Dachi , Luo Bin , Liu Shaomin , Tade Moses O , Zhi Linjie 
Published: February 2012

Abstract
A novel and convenient one-pot electrodeposition approach has been developed for precisely controlled fabrication of large-scale Bi-Ni nanowire and nanocable arrays. Using porous anodic aluminum oxide as a shape-directing template, by simply changing the electrochemical deposition mode, desired Bi-Ni hybrid nanowires and Bi-Ni core-shell nanocables have been obtained in the CV and CC modes, respectively. The structure, morphology, and composition of the as-prepared samples were characterized using X-ray powder diffraction, transmission electron microscopy, elemental mapping, and energy-dispersive X-ray spectrometry.
Partial vanishing viscosity limit for the 2D Boussinesq system with a slip boundary condition
Authors: Jin Liangbing , Fan Jishan , Nakamura Gen , Zhou Yong 
Published: February 2012

Abstract
This article studies the partial vanishing viscosity limit of the 2D Boussinesq system in a bounded domain with a slip boundary condition. The result is proved globally in time by a logarithmic Sobolev inequality.

2010 MSC: 35Q30; 76D03; 76D05; 76D07.
Yabi: An online research environment for grid, high performance and cloud computing
Authors: Hunter Adam A , Macgregor Andrew B , Szabo Tamas O , Wellington Crispin A , Bellgard Matthew I 
Published: February 2012

Abstract

Background
There is a significant demand for creating pipelines or workflows in the life science discipline that chain a number of discrete compute and data intensive analysis tasks into sophisticated analysis procedures. This need has led to the development of general as well as domain-specific workflow environments that are either complex desktop applications or Internet-based applications. Complexities can arise when configuring these applications in heterogeneous compute and storage environments if the execution and data access models are not designed appropriately. These complexities manifest themselves through limited access to available HPC resources, significant overhead required to configure tools and inability for users to simply manage files across heterogenous HPC storage infrastructure.

Results
In this paper, we describe the architecture of a software system that is adaptable to a range of both pluggable execution and data backends in an open source implementation called Yabi. Enabling seamless and transparent access to heterogenous HPC environments at its core, Yabi then provides an analysis workflow environment that can create and reuse workflows as well as manage large amounts of both raw and processed data in a secure and flexible way across geographically distributed compute resources. Yabi can be used via a web-based environment to drag-and-drop tools to create sophisticated workflows. Yabi can also be accessed through the Yabi command line which is designed for users that are more comfortable with writing scripts or for enabling external workflow environments to leverage the features in Yabi. Configuring tools can be a significant overhead in workflow environments. Yabi greatly simplifies this task by enabling system administrators to configure as well as manage running tools via a web-based environment and without the need to write or edit software programs or scripts. In this paper, we highlight Yabi's capabilities through a range of bioinformatics use cases that arise from large-scale biomedical data analysis.

Conclusion
The Yabi system encapsulates considered design of both execution and data models, while abstracting technical details away from users who are not skilled in HPC and providing an intuitive drag-and-drop scalable web-based workflow environment where the same tools can also be accessed via a command line. Yabi is currently in use and deployed at multiple institutions and is available at http://ccg.murdoch.edu.au/yabi.