bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Parameters and Breeding Values for Semen Characteristics in Hanoverian Stallions
Authors: Labitzke D , Sieme H , Martinsson G , Distl O 
Published: May 2014

ContentsThe objectives of this study were to show whether semen traits of 30 Hanoverian stallions regularly used in AI may be useful for breeding purposes. Semen characteristics were studied using 15 149 ejaculates from 30 Hanoverian stallions of the State Stud Celle of Lower Saxony. Semen samples were collected between 2005 and 2009. Traits analysed were gel‐free volume, sperm concentration, total and motile sperm number and progressive motility. A linear multivariate animal model was employed to estimate heritabilities and permanent environmental variances for stallions. The same model was used to predict breeding values for all traits simultaneously. Heritabilities were high for gel‐free volume (h2 = 0.43) and moderate for total number of sperm (h2 = 0.29) and progressive motility (h2 = 0.20). Gel‐free volume, sperm concentration and total number of sperm were genetically negatively correlated with progressive motility. The effect of the permanent environment for stallions accounted for 9–55% of the trait variance. The total variance among stallions explained 37–69% of the trait variance. The average reliabilities of the breeding values were 0.43–0.76 for the 30 Hanoverian stallions. In conclusion, the study could demonstrate large effects of stallions, routinely employed in a breeding programme, on semen characteristics analysed here. We could demonstrate that estimated breeding values (EBV) with sufficient high reliabilities can be predicted using data from these stallions and these EBV are useful in horse breeding programmes to achieve genetic improvement in semen quality.
Induction of Ram Bone Marrow Mesenchymal Stem Cells into Germ Cell Lineage using Transforming Growth Factor‐β Superfamily Growth Factors
Authors: Ghasemzadeh‐Hasankolaei M , Sedighi‐Gilani MA , Eslaminejad MB 
Published: May 2014

ContentsSeveral studies have proposed thatin vitrogeneration of germ cells (GCs) from stem cells can be considered a future option for infertility treatment. Mesenchymal stem cells (MSCs) have the capability to differentiate into maleGCs with the use of inducers such as retinoic acid. Transforming growth factor‐beta 1 (TGFb1) has been shown to play important roles in male fertility and spermatogenesis. Bone morphogenic protein 4 (BMP4) andBMP8b are also involved in the derivation of primordialGCs (PGCs) from epiblast cells. Therefore, this study aims to determine whetherTGFb1,BMP4 andBMP8b can initiate transdifferentiation ofMSCs intoGCsin vitroand to determine the type of changes that occur in the expression ofGC‐specific markers. In this study, we have divided passage‐3 ram bone marrow (BM)‐MSCs into three main groups (BMP4,BMP8b andTGFb1) which were separately treated with 10 ng/mlTGFb1, 100 ng/mlBMP4 and 100 ng/mlBMP8b for a period of 21 days. We have evaluated the ability of these groups to differentiate intoGCs by assessing expressions of GC‐specific markers with reverse transcriptionPCR(RT‐PCR), quantitativeRT‐PCR(qRT‐PCR), immunocytochemistry, morphological changes and alkaline phosphatase (ALP) activity. Our results showed thatBMP4 andBMP8b inducedPGCs properties in someBM‐MSCs andTGFb1 formed spermatogonial stem cells (SSCs) and spermatogonia‐like cells inBM‐MSCs culture. The important results of this study provide the basis for additional studies to determine the exact mechanism ofGCs differentiation and possibly solve the problem of infertility.
Does Coxiella burnetii Affect Reproduction in Cattle? A Clinical Update
Authors: Garcia‐Ispierto I , Tutusaus J , López‐Gatius F 
Published: May 2014

ContentsQ fever is a zoonosis produced by Coxiella burnetii, a bacterium that is widely distributed worldwide. Domestic ruminants are the most important source of C. burnetii for human infection. In sheep and goats, abortion is the main clinical consequence of infection, yet the symptoms described in cattle have so far been inconsistent. Q fever has been also scarcely reported in cattle, most likely because of its difficult diagnosis at the farm level and because of the many existing responsible C. burnetii strains. In this report, the effects of C. burnetii infection or Q fever disease on the reproductive behaviour of dairy cattle are reviewed, with special emphasis placed on the scarcity of data available and possible control actions discussed.
Bronchoalveolar lavage fluid and blood natural killer and natural killer T‐like cells in cryptogenic organizing pneumonia
Authors: Papakosta Despina , Manika Katerina , Gounari Evdoxia , Kyriazis George , Kontakiotis Theodore , Spyropoulos George , Kontakioti Eirini , Zarogoulidis Konstantinos 
Published: May 2014

AbstractBackground and objectiveNatural killer (NK) cells appear to be involved in the development of interstitial lung diseases (ILD). The purpose of this study was to investigate the involvement of NK and natural killer T (NKT)‐like cells in two recognized cytotoxic ILD with systemic character, hypersensitivity pneumonitis (HP) and cryptogenic organizing pneumonia (COP), compared with idiopathic pulmonary fibrosis (IPF) and controls.MethodsBronchoalveolar lavage fluid (BALF) and peripheral blood (PBL) cells and lymphocyte subsets of 83 patients (26 with COP, 19 with HP and 38 with IPF) and 10 controls were prospectively studied by flow cytometry.ResultsThe percentage of NK and NKT‐like cells was lower in BALF than in PBL in all patient groups and controls. Patients with COP presented with statistically significantly higher NK and NKT‐like cell counts in BALF compared with controls (P = 0.044 and P = 0.05 respectively) and IPF (P = 0.049 and P = 0.045 respectively). BALF NKT‐like cell count correlated with PBL NKT‐like cell count only in COP (r = 0.627, P = 0.002). In addition, a significant positive correlation between BALF NKT‐like cell and PBL cytotoxic T CD8+ cell count was observed in COP (r = 0.562, P = 0.006) but not in HP, IPF or controls.ConclusionsOur study provides for the first time evidence for the implication of NKT‐like cells in the pathogenesis of COP, as part of both localized and systemic cytotoxicity.
Introduction to propensity scores
Authors: Williamson Elizabeth J. , Forbes Andrew 
Published: May 2014

AbstractAlthough randomization provides a gold‐standard method of assessing causal relationships, it is not always possible to randomly allocate exposures. Where exposures are not randomized, estimating exposure effects is complicated by confounding. The traditional approach to dealing with confounding is to adjust for measured confounding variables within a regression model for the outcome variable. An alternative approach—propensity scoring—instead fits a regression model to the exposure variable. For a binary exposure, the propensity score is the probability of being exposed, given the measured confounders. These scores can be estimated from the data, for example by fitting a logistic regression model for the exposure including the confounders as explanatory variables and obtaining the estimated propensity scores from the predicted exposure probabilities from this model. These estimated propensity scores can then be used in various ways—matching, stratification, covariate‐adjustment or inverse‐probability weighting—to obtain estimates of the exposure effect.In this paper, we provide an introduction to propensity score methodology and review its use within respiratory health research. We illustrate propensity score methods by investigating the research question: ‘Does personal smoking affect the risk of subsequent asthma?’ using data taken from the Tasmanian Longitudinal Health Study.
Jointly Interventional and Observational Data: Estimation of Interventional Markov Equivalence Classes of Directed Acyclic Graphs
Authors: Hauser Alain , Bühlmann Peter 
Published: May 2014

SummaryIn many applications we have both observational and (randomized) interventional data. We propose a Gaussian likelihood framework for joint modelling of such different data types, based on global parameters consisting of a directed acyclic graph and corresponding edge weights and error variances. Thanks to the global nature of the parameters, maximum likelihood estimation is reasonable with only one or few data points per intervention. We prove consistency of the Bayesian information criterion for estimating the interventional Markov equivalence class of directed acyclic graphs which is smaller than the observational analogue owing to increased partial identifiability from interventional data. Such an improvement in identifiability has immediate implications for tighter bounds for inferring causal effects. Besides methodology and theoretical derivations, we present empirical results from real and simulated data.
Estimation of Hüsler–Reiss Distributions and Brown–Resnick Processes
Authors: Engelke Sebastian , Malinowski Alexander , Kabluchko Zakhar , Schlather Martin 
Published: May 2014

SummaryEstimation of extreme value parameters from observations in the max-domain of attraction of a multivariate max-stable distribution commonly uses aggregated data such as block maxima. Multivariate peaks-over-threshold methods, in contrast, exploit additional information from the non-aggregated ‘large’ observations. We introduce an approach based on peaks over thresholds that provides several new estimators for processes η in the max-domain of attraction of the frequently used Hüsler–Reiss model and its spatial extension: Brown–Resnick processes. The method relies on increments η(·) − η(t 0) conditional on η(t 0) exceeding a high threshold, where t 0 is a fixed location. When the marginals are standardized to the Gumbel distribution, these increments asymptotically form a Gaussian process resulting in computationally simple estimates of the Hüsler–Reiss parameter matrix and particularly enables parametric inference for Brown–Resnick processes based on (high dimensional) multivariate densities. This is a major advantage over composite likelihood methods that are commonly used in spatial extreme value statistics since they rely only on bivariate densities. A simulation study compares the performance of the new estimators with other commonly used methods. As an application, we fit a non-isotropic Brown–Resnick process to the extremes of 12-year data of daily wind speed measurements.
How to more effectively lobby the legislative branch of government: report the extent of intellectual disability amongst a politician's constituents
Authors: Waldman H. Barry , Perlman Steven P. 
Published: May 2014

ABSTRACTThe use of national numbers and percentages to describe the millions of people with intellectual disabilities is beyond the comprehension of most people. The challenge is to personalize these numbers if we are to bring increased attention to these individuals. Examples of Census Bureau report data for the States, Congressional Districts, Counties, and High School districts are suggested as a format to lobby legislators with the realities of the numbers of their constituents who are affected by intellectual disabilities.
Regulation of Dynamin Oligomerization in Cells: The Role of Dynamin–Actin Interactions and Its GTPase Activity
Authors: Gu Changkyu , Chang Joann , Shchedrina Valentina A. , Pham Vincent A. , Hartwig John H. , Suphamungmee Worawit , Lehman William , Hyman Bradley T. , Bacskai Brian J. , Sever Sanja 
Published: May 2014

AbstractDynamin is a 96‐kDa protein that has multiple oligomerization states that influence its GTPase activity. A number of different dynamin effectors, including lipids, actin filaments, and SH3‐domain‐containing proteins, have been implicated in the regulation of dynamin oligomerization, though their roles in influencing dynamin oligomerization have been studied predominantly in vitro using recombinant proteins. Here, we identify higher order dynamin oligomers such as rings and helices in vitro and in live cells using fluorescence lifetime imaging microscopy (FLIM). FLIM detected GTP‐ and actin‐dependent dynamin oligomerization at distinct cellular sites, including the cell membrane and transition zones where cortical actin transitions into stress fibers. Our study identifies a major role for direct dynamin–actin interactions and dynamin's GTPase activity in the regulation of dynamin oligomerization in cells.
Complete Genome Sequences of Nine Mycobacteriophages
Authors: Franceschelli Jorgelina Judith , Suarez Cristian Alejandro , Terán Lucrecia , Raya Raúl Ricardo , Morbidoni Héctor Ricardo 
Published: May 2014

ABSTRACT

Genome analyses of a large number of mycobacteriophages, bacterial viruses that infect members of the genus
Mycobacterium
, yielded novel enzymes and tools for the genetic manipulation of mycobacteria. We report here the complete genome sequences of nine mycobacteriophages, including a new singleton, isolated using
Mycobacterium smegmatis
mc
2
155 as a host strain.
Genome Sequencing of Ralstonia solanacearum Biovar 3, Phylotype I, Strains Rs-09-161 and Rs-10-244, Isolated from Eggplant and Chili in India
Authors: Ramesh Raman , Gaitonde Sapna , Achari Gauri , Asolkar Trupti , Singh Narendra Pratap , Carrere Sebastien , Genin Stephane , Peeters Nemo 
Published: May 2014

ABSTRACT

Ralstonia solanacearum
Indian strains Rs-09-161 and Rs-10-244 were isolated from the coastal region of Goa and from the Andaman Islands. We report the draft genome sequences of these representative isolates infecting solanaceous vegetables in India.
Full-Genome Sequence of Human Betacoronavirus 2c Jordan-N3/2012 after Serial Passage in Mammalian Cells
Authors: Frey Kenneth G. , Redden Cassie L. , Bishop-Lilly Kimberly A. , Johnson Reed , Hensley Lisa E. , Raviprakash Kanakatte , Luke Thomas , Kochel Tad , Mokashi Vishwesh P. , Defang Gabriel N. 
Published: May 2014

ABSTRACT
Middle East respiratory syndrome coronavirus (MERS-CoV) is the etiologic agent of a highly lethal pneumonia. Here, we report the full-genome sequence of the Jordan-N3/2012 strain after serial passage in two distinct mammalian cell lines. The genome exhibits noteworthy stability, which may inform the development of vaccines and therapeutics used to treat infection with this virus.
Draft Genome Sequence of Bacillus cereus Strain BcFL2013, a Clinical Isolate Similar to G9241
Authors: Gee Jay E. , Marston Chung K. , Sammons Scott A. , Burroughs Mark A. , Hoffmaster Alex R. 
Published: May 2014

ABSTRACT

Bacillus cereus
strains, such as G9241, causing anthrax-like illnesses have recently been discovered. We report the genome sequence of a clinical strain,
B. cereus
BcFL2013, which is similar to G9241, recovered from a patient in Florida.
Complete Genome Sequence of K14JB01, a Novel Variant Strain of Porcine Epidemic Diarrhea Virus in South Korea
Authors: Cho Yoon-Young , Lim Seong-In , Kim Yong Kwan , Song Jae-Young , Lee Joong-Bok , An Dong-Jun 
Published: May 2014

ABSTRACT
A novel variant strain of porcine epidemic diarrhea virus (PEDV) emerged on pig farms in South Korea during late 2013. Genomic DNA isolated from a K14JB01 strain identified in a diarrheal pig showed high sequence similarity to PEDV strains prevailing in the United States in 2013. This is the first study to identify the complete genome sequence of a novel variant PEDV in South Korea.
Complete Genome Sequence of the Subsurface, Mesophilic Sulfate-Reducing Bacterium Desulfovibrio aespoeensis Aspo-2
Authors: Pedersen Karsten , Bengtsson Andreas , Edlund Johanna , Rabe Lisa , Hazen Terry , Chakraborty Romy , Goodwin Lynne , Shapiro Nicole 
Published: May 2014

ABSTRACT

Desulfovibrio aespoeensis
Aspo-2, DSM 10631
T
, is a mesophilic, hydrogenotrophic sulfate-reducing bacterium sampled from a 600-m-deep subsurface aquifer in hard rock under the island of Äspö in southeastern Sweden. We report the genome sequence of this bacterium, which is a 3,629,109-bp chromosome; plasmids were not found.
Complete Genome Sequence of the Attenuated Novobiocin-Resistant Streptococcus iniae Vaccine Strain ISNO
Authors: Pridgeon Julia W. , Zhang Dunhua , Zhang Lee 
Published: May 2014

ABSTRACT

Streptococcus iniae
ISNO is an attenuated novobiocin-resistant vaccine strain. Its full genome is 2,070,182 bp in length. The availability of this genome will allow comparative genomics to identify potential virulence genes important for pathogenesis of
S. iniae
and potential mechanisms associated with novobiocin resistance in this strain.
Comparative Genomic Analysis of Two Multidrug-Resistant Clinical Isolates of ST395 Epidemic Strain of Pseudomonas aeruginosa Obtained 12 Years Apart
Authors: Valot Benoit , Rohmer Laurence , Jacobs Michael A. , Miller Samuel I. , Bertrand Xavier , Hocquet Didier 
Published: May 2014

ABSTRACT

Pseudomonas aeruginosa
can cause large and prolonged outbreaks in hospitals. We have sequenced and annotated the genomes of two multidrug-resistant
P. aeruginosa
isolates from the same strain obtained 12 years apart from different patients. Genomic analysis provided insight on the genes acquired and lost by
P. aeruginosa
during its spread.
Draft Genome Sequence of Mycobacterium farcinogenes NCTC 10955
Authors: Croce Olivier , Robert Catherine , Raoult Didier , Drancourt Michel 
Published: May 2014

ABSTRACT

We report the draft genome sequence of
Mycobacterium farcinogenes
NCTC 10955 (=DSM 43637
T
), a nontuberculosis species responsible for bovine farcy. The strain described here is composed of 6,139,893 bp, with a G+C content of 65.73%, and contains 5,816 protein-coding genes and 76 RNA genes.
Complete Genome Sequence of Canine Papillomavirus Type 11
Authors: Zhou Dan , Luff Jennifer , Usuda Yukari , Affolter Verena , Moore Peter , Schlegel Richard , Yuan Hang 
Published: May 2014

ABSTRACT

Papillomaviruses with the features of epitheliotropic, nonenveloped, circular, and double-stranded DNA belong to the family
Papillomaviridae
, which contributes to benign and malignant tumors in humans and animals. We report the whole-genome sequence of canine papillomavirus type 11 found at a pigmented plaque located on the skin of a mixed-breed bloodhound.
Metagenomic Approach for Understanding Microbial Population from Petroleum Muck
Authors: Joshi M. N. , Dhebar S. V. , Dhebar S. V. , Bhargava P. , Pandit A. S. , Patel R. P. , Saxena A. K. , Bagatharia S. B. 
Published: May 2014

ABSTRACT
Petroleum products play a major role in fueling the economy of the world but the pollution they create has become a critical issue. Understanding the diversity present in pipeline muck will help with the exploration of new microbial strains with better hydrocarbon degrading capacities for bioremediation of polluted sites. This study provides an analysis of petroleum muck using next generation sequencing.
Higher risk of incident hepatitis C virus among young women who inject drugs compared with young men in association with sexual relationships: a prospective analysis from the UFO Study cohort
Authors: Tracy Daniel , Hahn Judith A , Fuller Lewis Crystal , Evans Jennifer , Briceño Alya , Morris Meghan D , Lum Paula J , Page Kimberly 
Published: May 2014

BackgroundFemale injection drug users (IDUs) may report differences in injection behaviours that put them at greater risk for hepatitis C virus (HCV). Few studies have examined these in association with HCV incidence.MethodsLongitudinal data from a cohort of 417 HCV-uninfected IDU aged 30 or younger were analysed. Cox proportional hazards was used to model female sex as a predictor of new HCV infection. General estimating equation (GEE) analysis was used to model female sex as a predictor of HCV-associated risk behaviour prospectively.ResultsWomen were significantly more likely than men to become infected with HCV during study follow-up (HR 1.4, p<0.05), and were also more likely than men to report high-risk injecting behaviours, especially in the context of sexual and injecting relationships. Sex differences in injecting behaviours appeared to explain the relationship between sex and HCV infection.ConclusionsYoung women’s riskier injection practices lead to their higher rates of HCV infection. Further study on the impact of intimate partnership on women’s risk behaviour is warranted.
Mind the gap between recommendation and implementation—principles and lessons in the aftermath of incident investigations: a semi-quantitative and qualitative study of factors leading to the successful implementation of recommendations
Authors: Wrigstad Jonas , Bergström Johan , Gustafson Pelle 
Published: May 2014

ObjectivesUsing the findings of incident investigations to improve patient safety management is well-established and mandatory under Swedish law. This study seeks to identify the mechanisms behind successful implementation of the recommendations of incident investigations.SettingThis study was based in a university hospital in southern Sweden.ParticipantsA sample of 55 incident investigations from 2008 to 2010 were selected from the hospital's incident reporting system by staff in the office of the chief medical officer. These investigations were initiated by 23 different commissioning bodies and contained 289 separate recommendations. We used a three-stage method: content analysis to code the recommendations, semi-structured interviews with the commissioning bodies focusing on which recommendations had been implemented and why, and data analysis of the coded recommendations together with data from the interviews.ResultsWe found that a clear majority (70%) of the recommendations presented to the commissioning bodies were targeted at the micro-level of the organisation. In nearly half (45%) of all recommendations, actions had been taken and a clear majority (73%) of these were at the micro-level. Changes in the management positions of the commissioning bodies meant that very little further action was taken. Other actions, independent of incident investigations, were often taken within the organisation.ConclusionsWe conclude that two principles (‘close in space’ and ‘close in time’) seem to be important for bridging the gap between recommendation and implementation. The micro-level focus was expected because of the method of investigation used. Adverse events trigger organisational action independently of incident investigations.