bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diagnosing the Origin of Extended-Range Forecast Errors
Authors: Jung T. , Miller M. J. , Palmer T. N. 
Published: February 2010

Abstract
Experiments with the ECMWF model are carried out to study the influence that a correct representation of the lower boundary conditions, the tropical atmosphere, and the Northern Hemisphere stratosphere would have on extended-range forecast skill of the extratropical Northern Hemisphere troposphere during boreal winter. Generation of forecast errors during the course of the integration is artificially reduced by relaxing the ECMWF model toward the 40-yr ECMWF Re-Analysis (ERA-40) in certain regions. Prescribing rather than persisting sea surface temperature and sea ice fields leads to a modest forecast error reduction in the extended range, especially over the North Pacific and North America; no beneficial influence is found in the medium range. Relaxation of the tropical troposphere leads to reduced extended-range forecast errors especially over the North Pacific, North America, and the North Atlantic. It is shown that a better representation of the Madden–Julian oscillation is of secondary importance for explaining the results of the tropical relaxation experiments. The influence from the tropical stratosphere is negligible. Relaxation of the Northern Hemisphere stratosphere leads to forecast error reduction primarily in high latitudes and over Europe. However, given the strong influence from the troposphere onto the Northern Hemisphere stratosphere it is argued that stratospherically forced experiments are very difficult to interpret in terms of their implications for extended-range predictability of the tropospheric flow. The results are discussed in the context of future forecasting system development.
Numerical Investigations on the Formation of Tropical Storm Debby during NAMMA-06
Authors: Chiao Sen , Jenkins Gregory S. 
Published: February 2010

Abstract
Mesoscale model forecasts were carried out beginning at 0000 UTC 19 August for simulating Tropical Disturbance 4, which was named Tropical Storm Debby on 22 August 2006. The Weather Research and Forecasting model, with 25-km grid spacing and an inner nested domain of 5-km grid spacing, was used. The development of a small closed vortex at approximately 0600 UTC 20 August 2006 at 850 hPa was found off the coast of Guinea in agreement with satellite images in the 5-km simulation. Intense convection offshore and over the Guinea Highlands during the morning of 20 August 2006 led to the production of a vortex formation by 1400 UTC at 700 hPa. Sensitivity tests show that the Guinea Highlands play an important role in modulating the impinging westerly flow, in which low-level flow deflections (i.e., northward turning) enhance the cyclonic circulation of the vortex formation. Yet, the moist air can be transported by the northward deflection flow from lower latitudes to support the development of mesoscale convective systems (MCSs). Although the model forecast is not perfect, it demonstrates the predictability of the formation and development of the tropical disturbance associated with the Guinea Highlands.
The Association of the Elevated Mixed Layer with Significant Severe Weather Events in the Northeastern United States*
Authors: Banacos Peter C. , Ekster Michael L. 
Published: February 2010

AbstractThe occurrence of rare but significant severe weather events associated with elevated mixed-layer (EML) air in the northeastern United States is investigated herein. A total of 447 convective event days with one or more significant severe weather report [where significant is defined as hail 2 in. (5.1 cm) in diameter or greater, a convective gust of 65 kt (33 m s−1) or greater, and/or a tornado of F2 or greater intensity] were identified from 1970 through 2006 during the warm season (1 May–30 September). Of these, 34 event days (7.6%) were associated with identifiable EML air in regional rawinsondes preceding the event. Taken with two other noteworthy events in 1953 and 1969, a total of 36 significant severe weather events associated with EML air were studied via composite and trajectory analysis. Though a small percentage of the total, these 36 events compose a noteworthy list of historically significant derechos and tornadic events to affect the northeastern United States. It is demonstrated that plumes of EML air emanating from the Intermountain West in subsiding, anticyclonically curved flows can reinforce the capping inversion and maintain the integrity of the EML across the central United States over a few days. The EML plume can ultimately become entrained into a moderately fast westerly to northwesterly midtropospheric flow allowing for the plume’s advection into the northeastern United States. Resultant thermodynamic conditions in the convective storm environment are similar to those more typically observed closer to the EML source region in the Great Plains of the United States. In addition to composite and trajectory analysis, two case studies are employed to demonstrate salient and evolutionary aspects of the EML in such events. A lapse rate tendency equation is explored to put EML advection in context with other processes affecting lapse rate.
Epidemiology of Ankle Sprain at the United States Military Academy
Authors: Waterman Brian R. , Belmont Philip J. , Cameron Kenneth L. , DeBerardino Thomas M. , Owens Brett D. 
Published: February 2010

Background Ankle sprain is a common injury in athletic populations that results in significant time lost to injury. Hypothesis The incidence rates (IRs) of ankle ligament sprains are influenced by gender, height, weight, body mass index (BMI), physical conditioning, level of competition, type of sport, and athlete exposure to sport. Study Design Cohort study; Level of evidence, 2. Methods A longitudinal cohort study was performed to determine the effect of risk factors for ankle sprain at the United States Military Academy between 2005 and 2007. Results A total 614 cadets sustained new ankle sprains during 10 511 person-years at risk, resulting in an overall IR of 58.4 per 1000 person-years. Women (96.4), compared with men (52.7), had a significantly increased rate ratio (IRR) for ankle sprain of 1.83 (95% confidence interval [CI], 1.52-2.20). Men with ankle sprains had higher mean height, weight, and BMI than uninjured men (P < .001). Men with ankle sprains had higher average scores in push-ups, sit-ups, and run time than uninjured men (P < .001). Ankle sprain occurred most commonly during athletics (64.1%). Ankle sprain IR did not significantly differ between intercollegiate and intramural athletic competition after controlling for athlete-exposure (IRR, 1.05; 95% CI, 0.81-1.37). The ankle sprain IRR of female compared with male intercollegiate athletes was 0.93 (95% CI, 0.67-1.32) per 1000 person-years and 1.04 (95% CI, 0.74-1.47) per 1000 athlete-exposures. The intercollegiate sports of men's rugby, women's cheerleading, and men's/women's basketball, soccer, and lacrosse had the highest ankle sprain IR. Conclusion Higher mean height and weight in men, increased BMI in men, greater physical conditioning in men, and athlete exposure to selected sports were all risk factors for ankle sprain.
Distinct, ecotype-specific genome and proteome signatures in the marine cyanobacteria Prochlorococcus
Authors: Paul Sandip , Dutta Anirban , Bag Sumit K , Das Sabyasachi , Dutta Chitra 
Published: February 2010

AbstractBackgroundThe marine cyanobacteriumProchlorococcus marinus, having multiple ecotypes of distinct genotypic/phenotypic traits and being the first documented example of genome shrinkage in free-living organisms, offers an ideal system for studying niche-driven molecular micro-diversity in closely related microbes. The present study, through an extensive comparative analysis of various genomic/proteomic features of 6 high light (HL) and 6 low light (LL) adapted strains, makes an attempt to identify molecular determinants associated with their vertical niche partitioning.ResultsPronounced strand-specific asymmetry in synonymous codon usage is observed exclusively in LL strains. Distinct dinucleotide abundance profiles are exhibited by 2 LL strains with larger genomes and G+C-content ≈ 50% (group LLa), 4 LL strains having reduced genomes and G+C-content ≈ 35-37% (group LLb), and 6 HL strains. Taking into account the emergence of LLa, LLb and HL strains (based on 16S rRNA phylogeny), a gradual increase in average aromaticity, pI values and beta- & coil-forming propensities and a decrease in mean hydrophobicity, instability indices and helix-forming propensities of core proteins are observed. Greater variations in orthologous gene repertoire are found between LLa and LLb strains, while higher number of positively selected genes exist between LL and HL strains.ConclusionStrains of differentProchlorococcusgroups are characterized by distinct compositional, physicochemical and structural traits that are not mere remnants of a continuous genetic drift, but are potential outcomes of a grand scheme of niche-oriented stepwise diversification, that might have driven them chronologically towards greater stability/fidelity and invoked upon them a special ability to inhabit diverse oceanic environments.
Reducing the haystack to find the needle: improved protein identification after fast elimination of non-interpretable peptide MS/MS spectra and noise reduction
Authors: Mujezinovic Nedim , Schneider Georg , Wildpaner Michael , Mechtler Karl , Eisenhaber Frank 
Published: February 2010

Abstract

Background
Tandem mass spectrometry (MS/MS) has become a standard method for identification of proteins extracted from biological samples but the huge number and the noise contamination of MS/MS spectra obstruct swift and reliable computer-aided interpretation. Typically, a minor fraction of the spectra per sample (most often, only a few %) and about 10% of the peaks per spectrum contribute to the final result if protein identification is not prevented by the noise at all.

Results
Two fast preprocessing screens can substantially reduce the haystack of MS/MS data. (1) Simple sequence ladder rules remove spectra non-interpretable in peptide sequences. (2) Modified Fourier-transform-based criteria clear background in the remaining data. In average, only a remainder of 35% of the MS/MS spectra (each reduced in size by about one quarter) has to be handed over to the interpretation software for reliable protein identification essentially without loss of information, with a trend to improved sequence coverage and with proportional decrease of computer resource consumption.

Conclusions
The search for sequence ladders in tandem MS/MS spectra with subsequent noise suppression is a promising strategy to reduce the number of MS/MS spectra from electro-spray instruments and to enhance the reliability of protein matches. Supplementary material and the software are available from an accompanying WWW-site with the URL http://mendel.bii.a-star.edu.sg/mass-spectrometry/MSCleaner-2.0/.
Bioinformatic search of plant microtubule-and cell cycle related serine-threonine protein kinases
Authors: Karpov Pavel A , Nadezhdina Elena S , Yemets Alla I , Matusov Vadym G , Nyporko Alexey Yu , Shashina Nadezhda Yu , Blume Yaroslav B 
Published: February 2010

AbstractA bioinformatic search was carried for plant homologues of human serine-threonine protein kinases involved in regulation of cell division and microtubule protein phosphorylation (SLK, PAK6, PAK7, MARK1, MAST2, TTBK1, TTBK2, AURKA, PLK1, PLK4 and PASK). A number of SLK, MAST2 and AURKA plant homologues were identified. The closest identified homologue of human AURKA kinase was a protein of unknown function, A7PY12/GSVIVT00026259001 fromVitis vinifera(herein named as "STALK", Serine-Threonine Aurora-Like Kinase). Analysis of STALK's three-dimensional structure confirmed its relationship to the subgroup of AURKA-like protein kinases.
Data integration and exploration for the identification of molecular mechanisms in tumor-immune cells interaction
Authors: Mlecnik Bernhard , Sanchez-Cabo Fatima , Charoentong Pornpimol , Bindea Gabriela , Pagès Franck , Berger Anne , Galon Jerome , Trajanoski Zlatko 
Published: February 2010

Abstract
Cancer progression is a complex process involving host-tumor interactions by multiple molecular and cellular factors of the tumor microenvironment. Tumor cells that challenge immune activity may be vulnerable to immune destruction. To address this question we have directed major efforts towards data integration and developed and installed a database for cancer immunology with more than 1700 patients and associated clinical data and biomolecular data. Mining of the database revealed novel insights into the molecular mechanisms of tumor-immune cell interaction. In this paper we present the computational tools used to analyze integrated clinical and biomolecular data. Specifically, we describe a database for heterogenous data types, the interfacing bioinformatics and statistical tools including clustering methods, survival analysis, as well as visualization methods. Additionally, we discuss generic issues relevant to the integration of clinical and biomolecular data, as well as recent developments in integrative data analyses including biomolecular network reconstruction and mathematical modeling.
Bimodal gene expression patterns in breast cancer
Authors: Bessarabova Marina , Kirillov Eugene , Shi Weiwei , Bugrim Andrej , Nikolsky Yuri , Nikolskaya Tatiana 
Published: February 2010

Abstract
We identified a set of genes with an unexpected bimodal distribution among breast cancer patients in multiple studies. The property of bimodality seems to be common, as these genes were found on multiple microarray platforms and in studies with different end-points and patient cohorts. Bimodal genes tend to cluster into small groups of four to six genes with synchronised expression within the group (but not between the groups), which makes them good candidates for robust conditional descriptors. The groups tend to form concise network modules underlying their function in cancerogenesis of breast neoplasms.
Complex sense-antisense architecture of TNFAIP1/POLDIP2 on 17q11.2 represents a novel transcriptional structural-functional gene module involved in breast cancer progression
Authors: Grinchuk Oleg V , Motakis Efthimios , Kuznetsov Vladimir A 
Published: February 2010

Abstract

Background
A sense-antisense gene pair (SAGP) is a gene pair where two oppositely transcribed genes share a common nucleotide sequence region. In eukaryotic genomes, SAGPs can be organized in complex sense-antisense architectures (CSAGAs) in which at least one sense gene shares loci with two or more antisense partners. As shown in several case studies, SAGPs may be involved in cancers, neurological diseases and complex syndromes. However, CSAGAs have not yet been characterized in the context of human disease or cancer.

Results
We characterize five genes (TMEM97, IFT20, TNFAIP1, POLDIP2 and TMEM199) organized in a CSAGA on 17q11.2 (we term this the TNFAIP1/POLDIP2 CSAGA) and demonstrate their strong and reproducible co-regulatory transcription pattern in breast cancer tumours. Genes of the TNFAIP1/POLDIP2 CSAGA are located inside the smallest region of recurrent amplification on 17q11.2 and their expression profile correlates with the DNA copy number of the region. Survival analysis of a group of 410 breast cancer patients revealed significant survival-associated individual genes and gene pairs in the TNFAIP1/POLDIP2 CSAGA. Moreover, several of the gene pairs associated with survival, demonstrated synergistic effects. Expression of genes-members of the TNFAIP1/POLDIP2 CSAGA also strongly correlated with expression of genes of ERBB2 core region of recurrent amplification on 17q12. We clearly demonstrate that the observed co-regulatory transcription profile of the TNFAIP1/POLDIP2 CSAGA is maintained not only by a DNA amplification mechanism, but also by chromatin remodelling and local transcription activation.

Conclusion
We have identified a novel TNFAIP1/POLDIP2 CSAGA and characterized its co-regulatory transcription profile in cancerous breast tissues. We suggest that the TNFAIP1/POLDIP2 CSAGA represents a clinically significant transcriptional structural-functional gene module associated with amplification of the genomic region on 17q11.2 and correlated with expression ERBB2 amplicon core genes in breast cancer. Co-expression pattern of this module correlates with histological grades and a poor prognosis in breast cancer when over-expressed. TNFAIP1/POLDIP2 CSAGA maps the risks of breast cancer relapse onto the complex genomic locus on 17q11.2.
The cell envelope subtilisin-like proteinase is a virulence determinant for Streptococcus suis
Authors: Bonifait Laetitia , de la Cruz Dominguez-Punaro Maria , Vaillancourt Katy , Bart Christian , Slater Josh , Frenette Michel , Gottschalk Marcelo , Grenier Daniel 
Published: February 2010

AbstractBackgroundStreptococcus suisis a major swine pathogen and zoonotic agent that mainly causes septicemia, meningitis, and endocarditis. It has recently been suggested that proteinases produced byS. suis(serotype 2) are potential virulence determinants. In the present study, we screened aS. suismutant library created by the insertion of Tn917transposon in order to isolate a mutant deficient in a cell surface proteinase. We characterized the gene and assessed the proteinase for its potential as a virulence factor.ResultsTwo mutants (G6G and M3G) possessing a single Tn917insertion were isolated. The affected gene coded for a protein (SSU0757) that shared a high degree of identity withStreptococccus thermophilusPrtS (95.9%) and, to a lesser extent, withStreptococcus agalactiaeCspA (49.5%), which are cell surface serine proteinases. The SSU0757 protein had a calculated molecular mass of 169.6 kDa and contained the catalytic triad characteristic of subtilisin family proteinases: motif I (Asp200), motif II (His239), and motif III (Ser568). SSU0757 also had the Gram-positive cell wall anchoring motif (Leu-Pro-X-Thr-Gly) at the carboxy-terminus, which was followed by a hydrophobic domain. All theS. suisisolates tested, which belonged to different serotypes, possessed the gene encoding the SSU0757 protein. The two mutants devoid of subtilisin-like proteinase activity had longer generation times and were more susceptible to killing by whole blood than the wild-type parent strain P1/7. The virulence of the G6G and M3G mutants was compared to the wild-type strain in the CD1 mouse model. Significant differences in mortality rates were noted between the P1/7 group and the M3G and G6G groups (p< 0.001).ConclusionIn summary, we identified a gene coding for a cell surface subtilisin-like serine proteinase that is widely distributed inS. suis. Evidences were brought for the involvement of this proteinase inS. suisvirulence.
Cellular processes of v-Src transformation revealed by gene profiling of primary cells - Implications for human cancer
Authors: Maślikowski Bart M , Néel Benjamin D , Wu Ying , Wang Lizhen , Rodrigues Natalie A , Gillet Germain , Bédard Pierre-André 
Published: February 2010

AbstractBackgroundCell transformation by the Src tyrosine kinase is characterized by extensive changes in gene expression. In this study, we took advantage of several strains of the Rous sarcoma virus (RSV) to characterize the patterns of v-Src-dependent gene expression in two different primary cell types, namely chicken embryo fibroblasts (CEF) and chicken neuroretinal (CNR) cells. We identified a common set of v-Src regulated genes and assessed if their expression is associated with disease-free survival using several independent human tumor data sets.MethodsCEF and CNR cells were infected with transforming, non-transforming, and temperature sensitive mutants of RSV to identify the patterns of gene expression in response to v-Src-transformation. Microarray analysis was used to measure changes in gene expression and to define a common set of v-Src regulated genes (CSR genes) in CEF and CNR cells. A clustering enrichment regime using the CSR genes and two independent breast tumor data-sets was used to identify a 42-gene aggressive tumor gene signature. The aggressive gene signature was tested for its prognostic value by conducting survival analyses on six additional tumor data sets.ResultsThe analysis of CEF and CNR cells revealed that cell transformation by v-Src alters the expression of 6% of the protein coding genes of the genome. A common set of 175 v-Src regulated genes (CSR genes) was regulated in both CEF and CNR cells. Within the CSR gene set, a group of 42 v-Src inducible genes was associated with reduced disease- and metastasis-free survival in several independent patient cohorts with breast or lung cancer. Gene classes represented within this group include DNA replication, cell cycle, the DNA damage and stress responses, and blood vessel morphogenesis.ConclusionBy studying the v-Src-dependent changes in gene expression in two types of primary cells, we identified a set of 42 inducible genes associated with poor prognosis in breast and lung cancer. The identification of these genes provides a set of biomarkers of aggressive tumor behavior and a framework for the study of cancer cells characterized by elevated Src kinase activity.
Incidence of oral cancer in relation to nickel and arsenic concentrations in farm soils of patients' residential areas in Taiwan
Authors: Su Che-Chun , Lin Yo-Yu , Chang Tsun-Kuo , Chiang Chi-Ting , Chung Jian-An , Hsu Yun-Ying , Lian Ie-Bin 
Published: February 2010

Abstract

Background
To explore if exposures to specific heavy metals in the environment is a new risk factor of oral cancer, one of the fastest growing malignancies in Taiwan, in addition to the two established risk factors, cigarette smoking and betel quid chewing.

Methods
This is an observational study utilized the age-standardized incidence rates of oral cancer in the 316 townships and precincts of Taiwan, local prevalence rates of cigarette smoking and betel quid chewing, demographic factors, socio-economic conditions, and concentrations in farm soils of the eight kinds of heavy metal. Spatial regression and GIS (Geographic Information System) were used. The registration contained 22,083 patients, who were diagnosed with oral cancer between 1982 and 2002. The concentrations of metal in the soils were retrieved from a nation-wide survey in the 1980s.

Results
The incidence rate of oral cancer is geographically related to the concentrations of arsenic and nickel in the patients' residential areas, with the prevalence of cigarette smoking and betel quid chewing as controlled variables.

Conclusions
Beside the two established risk factors, cigarette smoking and betel quid chewing, arsenic and nickel in farm soils may be new risk factors for oral cancer. These two kinds of metal may involve in the development of oral cancer. Further studies are required to understand the pathways via which metal in the farm soils exerts its effects on human health.