bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of Hydrologic Landscape Classification to Diagnose Streamflow Predictability in Oregon
Authors: Patil Sopan D. , Wigington Parker J. , Leibowitz Scott G. , Comeleo Randy L. 
Published: November 2013

AbstractWe implement a spatially lumped hydrologic model to predict daily streamflow at 88 catchments within the state of Oregon and analyze its performance using the Oregon Hydrologic Landscape (OHL) classification. OHL is used to identify the physio‐climatic conditions that favor high (or low) streamflow predictability. High prediction catchments (Nash‐Sutcliffe efficiency of (NS) > 0.75) are mainly classified as rain dominated with very wet climate, low aquifer permeability, and low to medium soil permeability. Most of them are located west of the Cascade Mountain Range. Conversely, most low prediction catchments (NS < 0.6) are classified as snow‐dominated with high aquifer permeability and medium to high soil permeability. They are mainly located in the volcano‐influenced High Cascades region. Using a subset of 36 catchments, we further test if class‐specific model parameters can be developed to predict at ungauged catchments. In most catchments, OHL class‐specific parameters provide predictions that are on par with individually calibrated parameters (NS decline < 10%). However, large NS declines are observed in OHL classes where predictability is not high enough. Results suggest higher uncertainty in rain‐to‐snow transition of precipitation phase and external gains/losses of deep groundwater are major factors for low prediction in Oregon. Moreover, regionalized estimation of model parameters is more useful in regions where conditions favor good streamflow predictability.
Party Campaign Contributions Come with a Support Network
Authors: Baker Anne E. 
Published: November 2013

ObjectivesContributions to candidates from the parties’ congressional campaign committees are thought to have a “multiplier effect” in terms of generating contributions from political action committees.MethodUsing structural equation modeling and timed direct contribution data from the 1992 to 2012 general election cycles, I uncover a complex system of relationships within each party network.ResultsAfter controlling for the competitiveness of the race, I find party contributions to challengers and open‐seat contestants early in the election cycle positively and significantly predict political action committee contributions to those candidates in the period after Labor Day, both in the era preceding the Bipartisan Campaign Finance Reform Act and the era after reform; however, the strength of the relationship declines in the postreform era and differences between the party networks also arise.ConclusionsI attribute these developments to changes in campaign finance law that created new hurdles for parties and increased the influence of interest groups.
A systems biology approach using metabolomic data reveals genes and pathways interacting to modulate divergent growth in cattle
Authors: Widmann Philipp , Reverter Antonio , Fortes Marina R S , Weikard Rosemarie , Suhre Karsten , Hammon Harald , Albrecht Elke , Kuehn Christa 
Published: November 2013

Abstract

Background
Systems biology enables the identification of gene networks that modulate complex traits. Comprehensive metabolomic analyses provide innovative phenotypes that are intermediate between the initiator of genetic variability, the genome, and raw phenotypes that are influenced by a large number of environmental effects. The present study combines two concepts, systems biology and metabolic analyses, in an approach without prior functional hypothesis in order to dissect genes and molecular pathways that modulate differential growth at the onset of puberty in male cattle. Furthermore, this integrative strategy was applied to specifically explore distinctive gene interactions of non-SMC condensin I complex, subunit G (NCAPG) and myostatin (GDF8), known modulators of pre- and postnatal growth that are only partially understood for their molecular pathways affecting differential body weight.

Results
Our study successfully established gene networks and interacting partners affecting growth at the onset of puberty in cattle. We demonstrated the biological relevance of the created networks by comparison to randomly created networks. Our data showed that GnRH (Gonadotropin-releasing hormone) signaling is associated with divergent growth at the onset of puberty and revealed two highly connected hubs, BTC and DGKH, within the network. Both genes are known to directly interact with the GnRH signaling pathway. Furthermore, a gene interaction network for NCAPG containing 14 densely connected genes revealed novel information concerning the functional role of NCAPG in divergent growth.

Conclusions
Merging both concepts, systems biology and metabolomic analyses, successfully yielded new insights into gene networks and interacting partners affecting growth at the onset of puberty in cattle. Genetic modulation in GnRH signaling was identified as key modifier of differential cattle growth at the onset of puberty. In addition, the benefit of our innovative concept without prior functional hypothesis was demonstrated by data suggesting that NCAPG might contribute to vascular smooth muscle contraction by indirect effects on the NO pathway via modulation of arginine metabolism. Our study shows for the first time in cattle that integration of genetic, physiological and metabolomics data in a systems biology approach will enable (or contribute to) an improved understanding of metabolic and gene networks and genotype-phenotype relationships.
Evidence of microevolution of Salmonella Typhimurium during a series of egg-associated outbreaks linked to a single chicken farm
Authors: Hawkey Jane , Edwards David J , Dimovski Karolina , Hiley Lester , Billman-Jacobe Helen , Hogg Geoff , Holt Kathryn E 
Published: November 2013

Abstract

Background
The bacterium Salmonella enterica serovar Typhimurium (S. Typhimurium) is one of the most frequent causes of foodborne outbreaks of gastroenteritis. Between 2005–2008 a series of S. Typhimurium outbreaks occurred in Tasmania, Australia, that were all traced to eggs originating from a single chicken farm. We sequenced the genomes of 12 isolates linked to these outbreaks, in order to investigate the microevolution of a pathogenic S. Typhimurium clone in a natural, spatiotemporally restricted population.

Results
The isolates, which shared a phage type similar to DT135 known locally as 135@ or 135a, formed a clade within the S. Typhimurium population with close similarity to the reference genome SL1334 (160 single nucleotide polymorphisms, or SNPs). Ten of the isolates belonged to a single clone (<23 SNPs between isolate pairs) which likely represents the population of S. Typhimurium circulating at the chicken farm; the other two were from sporadic cases and were genetically distinct from this clone. Divergence dating indicated that all 12 isolates diverged from a common ancestor in the mid 1990s, and the clone began to diversify in 2003–2004. This clone spilled out into the human population several times between 2005–2008, during which time it continued to accumulate SNPs at a constant rate of 3–5 SNPs per year or 1x10-6 substitutions site-1 year-1, faster than the longer-term (~50 year) rates estimated previously for S. Typhimurium. Our data suggest that roughly half of non-synonymous substitutions are rapidly removed from the S. Typhimurium population, after which purifying selection is no longer important and the remaining substitutions become fixed in the population. The S. Typhimurium 135@ isolates were nearly identical to SL1344 in terms of gene content and virulence plasmids. Their phage contents were close to SL1344, except that they carried a different variant of Gifsy-1, lacked the P2 remnant found in SL1344 and carried a novel P2 phage, P2-Hawk, in place SL1344’s P2 phage SopEϕ. DT135 lacks P2 prophage. Two additional plasmids were identified in the S. Typhimurium 135@ isolates, pSTM2 and pSTM7. Both plasmids were IncI1, but phylogenetic analysis of the plasmids and their bacterial hosts shows these plasmids are genetically distinct and result from independent plasmid acquisition events.

Conclusions
This study provides a high-resolution insight into short-term microevolution of the important human pathogen S. Typhimurium. It indicates that purifying selection occurs rapidly in this population (≤6 years) and then declines, and provides an estimate for the short-term substitution rate. The latter is likely to be more relevant for foodborne outbreak investigation than previous estimates based on longer time scales.
Identification of late assembly domains of the human endogenous retrovirus-K(HML-2)
Authors: Chudak Claudia , Beimforde Nadine , George Maja , Zimmermann Anja , Lausch Veronika , Hanke Kirsten , Bannert Norbert 
Published: November 2013

Abstract

Background
Late assembly (L)-domains are protein interaction motifs, whose dysfunction causes characteristic budding defects in enveloped viruses. Three different amino acid motifs, namely PT/SAP, PPXY and YPXnL have been shown to play a major role in the release of exogenous retroviruses. Although the L-domains of exogenous retroviruses have been studied comprehensively, little is known about these motifs in endogenous human retroviruses.

Results
Using a molecular clone of the human endogenous retrovirus K113 that had been engineered to reverse the presumed non-synonymous postinsertional mutations in the major genes, we identified three functional L-domains of the virus, all located in the Gag p15 protein. A consensus PTAP tetrapeptide serves as the core of a main L-domain for the virus and its inactivation reduces virus release in HEK 293T cells by over 80%. Electron microscopy of cells expressing the PTAP mutant revealed predominantly late budding structures and budding chains at the plasma membrane. The fact that this motif determines subcellular colocalization with Tsg101, an ESCRT-I complex protein known to bind to the core tetrapeptide, supports its role as an L-domain. Moreover, two YPXnL motifs providing additional L-domain function were identified in the p15 protein. One is adjacent to the PTAP sequence and the other is in the p15 N-terminus. Mutations in either motif diminishes virus release and induces an L-domain phenotype while inactivation of all three L-domains results in a complete loss of particle release in HEK 293T cells. The flexibility of the virus in the use of L-domains for gaining access to the ESCRT machinery is demonstrated by overexpression of Tsg101 which rescues the release of the YPXnL mutants. Similarly, overexpression of Alix not only enhances release of the PTAP mutant by a factor of four but also the release of a triple mutant, indicating that additional cryptic YPXnL domains with a low affinity for Alix may be present. No L-domain activity is provided by the proline-rich peptides at the Gag C-terminus.

Conclusions
Our data demonstrate that HERV-K(HML-2) release is predominantly mediated through a consensus PTAP motif and two auxiliary YPXnL motifs in the p15 protein of the Gag precursor.
Clinicopathologic significance of claudin-6, occludin, and matrix metalloproteinases −2 expression in ovarian carcinoma
Authors: Wang Liping , Jin Xiangshu , Lin Dongjing , Liu Zhijing , Zhang Xiaowei , Lu Yan , Liu Yuanyuan , Wang Min , Yang Minlan , Li Jiuxia , Quan Chengshi 
Published: November 2013

Abstract

Background
Tight junctions (TJs) are mainly composed of claudins, occludin, and tight junction adhesion molecules (JAM). The invasive and metastatic phenotype of highly invasive cancer cells has been related to abnormal structure and function of TJs, and with expression of activated matrix metalloproteinases (MMPs). The relevance of these mechanisms responsible for the invasion and metastasis of ovarian carcinoma is unclear. Similarly, it is not known if the expression of claudin-6, occludin and MMP2 is related with the clinical properties of these tumors.

Methods
Expression of claudin-6, occludin, and MMP2 was detected in samples of human ovarian cancer tissues by immunohistochemistry and correlated with the clinical properties of the tumors.

Results
The positive expression rates of claudin-6 and MMP-2 were higher in ovarian papillary serous carcinomas than n ovarian serous adenomas (P < 0.05). There were no differences in the expression of occludin (P > 0.05). The expression of claudin-6 and occludin in ovarian cancer was not correlated with patient age, pathological grade, clinical stage, and metastasis (P > 0.05). MMP-2 expression was enhanced with increased clinical stage and metastasis (P < 0.05), but was unrelated to patient age or tumor grade (P > 0.05). There were no apparent correlations between expression of claudin-6, occludin and MMP-2 in ovarian cancer tissue (P > 0.05).

Conclusions
Our data suggest, for the first time, that the claudin-6 and MMP-2 are up-regulated in ovarian papillary serous carcinomas, MMP-2 expression was enhanced with increased clinical stage and metastasis. Claudin-6 and MMP-2 may play a positive role in the invasion and metastasis of ovarian cancer.

Virtual slides
The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1775628454106511.
Prognostic factors in nasopharyngeal carcinoma with synchronous liver metastasis: a retrospective study for the management of treatment
Authors: Tian Yun-Ming , Zeng Lei , Wang Feng-Hua , Liu Shuai , Guan Ying , Lu Tai-Xiang , Han Fei 
Published: November 2013

Abstract

Purpose
To retrospectively analyze the prognosis of patients with nasopharyngeal carcinoma (NPC) initially presenting with liver metastasis, in order to identify independent prognostic factors to facilitate management of treatment.

Methods
Eighty-five patients with untreated NPC and synchronous liver metastasis, initially diagnosed between January 2000 and December 2009, were selected for this retrospective study. Seventy-eight received systemic chemotherapy, 32 underwent subsequent radiotherapy of the primary tumor, and 18 received local therapy for metastatic lesions. Clinical features, laboratory parameters and treatment modalities were compared by univariate and multivariate analyses.

Results
The median survival time was 19.0 months and the 3-year overall survival rate was 14.1%. The overall response and disease control rates were 70.4% and 86.4%, respectively. Significant predictors of short survival were KPS ≤ 70 (P = 0.03), serum lactate dehydrogenase levels >245 IU/l (P = 0.01) and poor response to chemotherapy (P < 0.01). In contrast, significantly longer survival rates were achieved by patients having at least six chemotherapy cycles compared to those receiving <6 cycles (3-year OS: 18.3% vs. 7.1%; P < 0.01), and patients receiving radiotherapy of the primary tumor following complete or partial response to chemotherapy (3-year OS: 30.8% vs. 3.8%, P < 0.01).

Conclusions
Five key independent factors were identified and sub-classified as potential prognostic indicators for NPC with liver metastases. Progressive treatments of systemic chemotherapy and radiotherapy at the primary tumor could prolong survival in the subset of patients having fewer negative prognosticators.
A reliable and effective method of DNA isolation from old human blood paper cards
Authors: Song Yang , Fahs Abrahim , Feldman Charles , Shah Suraj , Gu Yali , Wang Yifan , Machado Roberto F , Wunderink Richard G , Chen Jiwang 
Published: November 2013

Abstract
Blood paper cards provide an effective DNA storage method. In this study, we used three DNA dissolving reagents (Tris-EDTA [TE] buffer, Tris–HCl buffer, and water) and one common commercially available kit (DN131 from MRC Inc) to elute DNA from 105 human blood paper cards collected up to 10 years ago. These DNA samples were used as templates for amplification of a single nucleotide polymorphism (SNP, C125T) region of human caspase-12 by PCR and a specific Taqman genotyping assay using the same amount of DNA. We show that DNA isolated by Tris–HCl buffer has higher yield and quality in comparison to DN131 solution. PCR success rate to amplify caspase-12 C125T SNP using Tris–HCl is comparable to the method using DN131 (89.5% vs 87.6%). The Taqman genotyping success rate using Tris–HCl is higher than using DN131 (81.9% vs 70.5%). Using TE or water, PCR success rates are lower than using DN131 (73.3% [TE]; 72.4% [H2O]), but Taqman genotyping success rates are comparable to the method using DN131 (70.5% [TE]; 79.1% [H2O]). We concluded that using Tris–HCl is a reliable and effective method to elute DNA from old human blood paper cards. The crude DNA isolated by Tris–HCl can be used to study genetic polymorphisms in human populations.
Bruton's tyrosine kinase—an integral protein of B cell development that also has an essential role in the innate immune system
Authors: López-Herrera Gabriela , Vargas-Hernández Alexander , González-Serrano Maria Edith , Berrón-Ruiz Laura , Rodríguez-Alba Juan Carlos , Espinosa-Rosales Francisco , Santos-Argumedo Leopoldo 
Published: November 2013

ABSTRACTBtk is the protein affected in XLA, a disease identified as a B cell differentiation defect. Btk is crucial for B cell differentiation and activation, but its role in other cells is not fully understood. This review focuses on the function of Btk in monocytes, neutrophils, and platelets and the receptors and signaling cascades in such cells with which Btk is associated.
High-fertility phenotypes: two outbred mouse models exhibit substantially different molecular and physiological strategies warranting improved fertility
Authors: Langhammer Martina , Michaelis Marten , Hoeflich Andreas , Sobczak Alexander , Schoen Jennifer , Weitzel Joachim M 
Published: November 2013

Animal models are valuable tools in fertility research. Worldwide, there are more than 400 transgenic or knockout mouse models available showing a reproductive phenotype; almost all of them exhibit an infertile or at least subfertile phenotype. By contrast, animal models revealing an improved fertility phenotype are barely described. This article summarizes data on two outbred mouse models exhibiting a ‘high-fertility’ phenotype. These mouse lines were generated via selection over a time period of more than 40 years and 161 generations. During this selection period, the number of offspring per litter and the total birth weight of the entire litter nearly doubled. Concomitantly with the increased fertility phenotype, several endocrine parameters (e.g. serum testosterone concentrations in male animals), physiological parameters (e.g. body weight, accelerated puberty, and life expectancy), and behavioral parameters (e.g. behavior in an open field and endurance fitness on a treadmill) were altered. We demonstrate that the two independently bred high-fertility mouse lines warranted their improved fertility phenotype using different molecular and physiological strategies. The fertility lines display female- as well as male-specific characteristics. These genetically heterogeneous mouse models provide new insights into molecular and cellular mechanisms that enhance fertility. In view of decreasing fertility in men, these models will therefore be a precious information source for human reproductive medicine.Translated abstractA German translation of abstract is freely available athttp://www.reproduction-online.org/content/147/4/427/suppl/DC1.
Changes in snowfall/precipitation-day ratio in Slovakia and their linkages with air temperature and precipitation
Authors: Nikolova Nina , Faško Pavol , Lapin Milan , Švec Marek 
Published: November 2013

Abstract
Knowledge on snowfall and precipitation variability is one of the most important information about climate changes. The presented study is based on daily data for precipitation totals and new snow cover depths and monthly air temperature from 29 meteorological stations in Slovakia. The aim is to determine to what extent the change of monthly air temperature mean affects the snowfall in the mountainous area of Slovakia. In order to achieve the aim of the research work, the snow days and precipitation days (SD/PD) ratio is calculated for the months from October to April and the trend is investigated. On the basis of correlation analysis it is determined that the main factor for changes in the SD/PD ratio is the mean monthly air temperature while precipitation plays an important role only for the stations with the altitude above 1300 m. Spatial distribution of the changes in the SD/PD ratio for the winter time (December - January - February) during the period 1981-2011 was investigated by cluster analyses. The results show that the stations are grouped according to their geographical location and relief of the territory.
Brief Report: Lysyl Oxidase Is a Potential Biomarker of Fibrosis in Systemic Sclerosis
Authors: Rimar Doron , Rosner Itzhak , Nov Yuval , Slobodin Gleb , Rozenbaum Michael , Halasz Katy , Haj Tharwat , Jiries Nizar , Kaly Lisa , Boulman Nina , Daood Rula , Vadasz Zahava 
Published: November 2013

ObjectiveFibrosis is a major cause of morbidity and mortality in systemic sclerosis (SSc). Levels of lysyl oxidase (LOX), an extracellular enzyme that stabilizes collagen fibrils, have been found to be elevated in the skin of SSc patients, but have not been evaluated in the serum or correlated with the clinical parameters. We undertook this study to evaluate serum LOX levels in SSc patients and to correlate these levels with clinical parameters of SSc.MethodsSSc patients were evaluated for demographic features, clinical manifestations, routine laboratory tests, serum autoantibodies, serum LOX concentrations, and nailfold capillaroscopy patterns. They underwent pulmonary function testing, echocardiography, and high‐resolution computed tomography scans of the lung, assessment of skin fibrosis by the modified Rodnan skin thickness score (MRSS), and assessment of disease severity and activity by the Medsger severity scale and the Valentini activity index.ResultsTwenty‐six SSc patients were evaluated and compared with 25 healthy controls and with 9 disease control patients with primary myelofibrosis. Almost 62% of the SSc patients (16 of 26) had limited cutaneous SSc (lcSSc), while 38% had diffuse cutaneous SSc (dcSSc) (10 of 26); 31% of the patients (8 of 26) had lung involvement. The LOX concentration in SSc patients was higher than that in healthy controls and similar to that in disease controls (P < 0.0001), and it was significantly higher in patients with dcSSc than in those with lcSSc (P = 0.006). The LOX concentration correlated with the MRSS in patients without lung fibrosis.ConclusionThis study is the first to demonstrate high serum LOX levels in SSc patients that correlate specifically with skin fibrosis. These correlations suggest that LOX levels may serve as a novel biomarker of fibrosis. Future studies are warranted to determine whether LOX is a potential therapeutic target in SSc.