bluuebunny/crossref_metadata_2025_split huggingface dataset:
A review on prolificacy genes in sheep
Authors: Abdoli R , Zamani P , Mirhoseini SZ , Ghavi Hossein‐Zadeh N , Nadri S 
Published: August 2016

ContentsOvulation rate and litter size are important reproduction traits in sheep and are of high economic value. Reproduction traits typically have low to medium heritabilities and do not exhibit a noticeable response to phenotypic selection. Therefore, inclusion of genetic information of the genes associated with reproductive ability could efficiently enhance the selection response. The most important major genes affecting prolificacy and their genetic diversities in different sheep breeds were reviewed. Different causative mutations with major effects on reproductive traits including ovulation rate and litter size have been found in various sheep breeds around the world. A general overview of the studies on main prolificacy genes showed that some alleles may express different phenotypic effects in different breeds, and thus, further studies on epistatic effects are necessary for more understanding of genetic control of reproductivity in sheep. Regarding the polygenic control of fertility traits, application of new high‐throughput technologies to find new variants is essential for future studies. Moreover, genomewide association studies and genomic best linear unbiased predictions of breeding values are likely to be effective tools for genetic improvement of sheep reproductive performance traits.
Suicide Risk Among Wounded U.S. Service Members
Authors: Reger Mark A. , Smolenski Derek J. , Skopp Nancy A. , Metzger‐Abamukong Melinda J. , Kang Han K. , Bullman Tim A. , Gahm Gregory A. 
Published: August 2016

The association between suicide and combat injuries sustained during the wars in Iraq and Afghanistan was examined. A retrospective population‐based cohort design was conducted using official military records to identify combat injuries (October 7, 2001, to December 31, 2007). Those who were injured during combat had higher crude suicide rates than those who deployed and were not injured (incidence rate ratio [IRR] = 1.50; confidence interval [CI] = 1.06, 2.12), or never deployed (IRR = 1.46; CI = 1.04, 2.06). After adjusting for demographics, these findings were no longer statistically significant. Although our data did not support an elevated suicide risk among wounded service members, additional research is needed to examine the impact of injury severity.
Frequency and risks associated with Clostridium difficile‐associated diarrhea after pediatric solid organ transplantation: a single‐center retrospective review
Authors: Ciricillo J. , Haslam D. , Blum S. , Kim M.‐O. , Liu C. , Paulsen G. , Courter J. , Danziger‐Isakov L. 
Published: August 2016

AbstractBackgroundMorbidity and mortality related to Clostridium difficile infection (CDI) has increased, but epidemiology and risk factors within pediatric solid organ transplant (SOT) recipients are uncertain.MethodsA retrospective cohort study of SOT recipients age ≤18 years at transplantation from 2010 to 2013 was performed. Patients with CDI were compared with matched CDI‐negative controls with diarrhea.ResultsOf 202 patients, the majority were male (58%) and Caucasian (77%). Kidney (42%) was the most common organ transplanted, followed by liver (38%), heart (17%), and multivisceral/intestine (3%). Age ranged from 3 weeks to 18 years (median 4.7 years, mean 6.6; interquartile range [IQR] 1.5–11.2). In 104 SOT recipients, at least 1 unformed stool was tested; 25 patients were positive for CDI. Most testing occurred by 60 days post transplant (mean 164, median 57, IQR 14–227). First negative tests occurred concurrently (mean 153, median 54, IQR 13–214) to the 25 patients with CDI (mean 199, median 65, IQR 32–238). In univariable analyses, age, gender, ethnicity, obesity, and calcineurin inhibitor choice were not associated with CDI. Liver recipients were more likely to have CDI (18.4% liver, 4.7% kidney, 8.8% heart, P < 0.01). Twenty CDI patients were matched to 35 controls. In multivariable analyses, neither recent hospitalization nor antibiotic duration or intensity was associated with CDI. Acid‐blockade appeared protective (risk ratio 0.13, 95% confidence interval 0.02–0.78).ConclusionsCDI occurs in 12% of pediatric SOT recipients, but 24% of those tested with diarrhea were positive. In patients with diarrhea, prior hospitalization and antibiotic duration or intensity were not associated with CDI.
Cluster Analysis of Campylobacter jejuni Genotypes Isolated from Small and Medium‐Sized Mammalian Wildlife and Bovine Livestock from Ontario Farms
Authors: Viswanathan M. , Pearl D. L. , Taboada E. N. , Parmley E. J. , Mutschall S. K. , Jardine C. M. 
Published: August 2016

SummaryUsing data collected from a cross‐sectional study of 25 farms (eight beef, eight swine and nine dairy) in 2010, we assessed clustering of molecular subtypes of C. jejuni based on a Campylobacter‐specific 40 gene comparative genomic fingerprinting assay (CGF40) subtypes, using unweighted pair‐group method with arithmetic mean (UPGMA) analysis, and multiple correspondence analysis. Exact logistic regression was used to determine which genes differentiate wildlife and livestock subtypes in our study population. A total of 33 bovine livestock (17 beef and 16 dairy), 26 wildlife (20 raccoon (Procyon lotor), five skunk (Mephitis mephitis) and one mouse (Peromyscus spp.) C. jejuni isolates were subtyped using CGF40. Dendrogram analysis, based on UPGMA, showed distinct branches separating bovine livestock and mammalian wildlife isolates. Furthermore, two‐dimensional multiple correspondence analysis was highly concordant with dendrogram analysis showing clear differentiation between livestock and wildlife CGF40 subtypes. Based on multilevel logistic regression models with a random intercept for farm of origin, we found that isolates in general, and raccoons more specifically, were significantly more likely to be part of the wildlife branch. Exact logistic regression conducted gene by gene revealed 15 genes that were predictive of whether an isolate was of wildlife or bovine livestock isolate origin. Both multiple correspondence analysis and exact logistic regression revealed that in most cases, the presence of a particular gene (13 of 15) was associated with an isolate being of livestock rather than wildlife origin. In conclusion, the evidence gained from dendrogram analysis, multiple correspondence analysis and exact logistic regression indicates that mammalian wildlife carry CGF40 subtypes of C. jejuni distinct from those carried by bovine livestock. Future studies focused on source attribution of C. jejuni in human infections will help determine whether wildlife transmit Campylobacter jejuni directly to humans.
Draft Genome Sequence of
Pseudoalteromonas tetraodonis
Strain MQS005, a Bacterium with Potential Quorum-Sensing Regulation
Authors: Pan Yonglong , Wang Yanbo , Yan Xiaoqing , Mazumder Asit , Liang Yan 
Published: August 2016

ABSTRACT

We present here the draft genome sequence of
Pseudoalteromonas tetraodonis
strain MQS005, a bacterium possessing potential quorum-sensing regulatory activity. This strain was isolated from water from the South China Sea, People's Republic of China. The assembly consists of 4,252,538 bp and contains 144 contigs, with a G+C content of 41.85%.
Draft Genome Sequence of
Fonsecaea nubica
Strain CBS 269.64, Causative Agent of Human Chromoblastomycosis
Authors: Costa Flávia F. , de Hoog Sybren , Raittz Roberto T. , Weiss Vinicius A. , Leão Aniele C. R. , Bombassaro Amanda , Sun Jiufeng , Moreno Leandro F. , Souza Emanuel M. , Pedrosa Fabio O. , Steffens Maria Berenice R. , Baura Valter , Tadra-Sfeir Michele Z. , Balsanelli Eduardo , Najafzadeh M. Javad , Gomes Renata R. , Felipe Maria S. , Teixeira Marcus , Santos Germana D. , Xi Liyan , Alves de Castro Mauro Antônio , Vicente Vânia A. 
Published: August 2016

ABSTRACT

On the basis of multilocus phylogenetic data,
Fonsecaea nubica
was described in 2010 as a molecular sibling of
F. monophora
, an established agent of the human skin disease chomoblastomycosis in tropical zones. Genome analysis of these pathogens is mandatory to identify genes involved in the interaction with host and virulence.
Genome Sequence of
Listeria monocytogenes
Strain HPB2088 (Serotype 1/2a), an Environmental Isolate Collected in Canada in 1994
Authors: Pightling Arthur W. , Rand Hugh , Strain Errol , Pagotto Franco 
Published: August 2016

ABSTRACT

Listeria monocytogenes
is a foodborne pathogen that causes severe illness. Thus, ongoing efforts at real-time whole-genome sequencing are of utmost importance. However, it is also important that retrospective analyses that place these data into context be performed. Here, we present the genome sequence of strain HPB2088, which was collected in 1994.
Draft Genome Sequences of Two Ureolytic Bacteria Isolated from Concrete Block Waste
Authors: Park Hongjae , Park Byeonghyeok , Kim Hyun Jung , Park Woojun , Choi In-Geol 
Published: August 2016

ABSTRACT

We sequenced genomes of two ureolytic bacteria,
Bacillus
sp. JH7 and
Sporosarcina
sp. HYO08, which were isolated from concrete waste and have a potential for biocementation applications.
Draft Genome Sequence of Oil-Degrading Bacterium
Gallaecimonas pentaromativorans
Strain YA_1 from the Southwest Indian Ocean
Authors: Xu Yiyuan , Ren Chong , Chen Ruixuan , Zeng Runying 
Published: August 2016

ABSTRACT

Gallaecimonas pentaromativorans
has been previously reported to be capable of degrading crude oil and diesel oil.
G. pentaromativorans
strain YA_1 was isolated from the southwest Indian Ocean and can degrade crude oil. This study reports the draft genome sequence of
G. pentaromativorans
, which can provide insights into the mechanisms of microbial oil biodegradation.
Permanent Draft Genome Sequence of
Nocardia
sp. BMG111209, an Actinobacterium Isolated from Nodules of
Casuarina glauca
Authors: Ghodhbane-Gtari Faten , Beauchemin Nicholas , Gueddou Abdellatif , Hezbri Karima , Ktari Amir , Louati Moussa , Nouioui Imen , Chen Amy , Huntemann Marcel , Ivanova Natalia , Kyrpides Nikos , Markowitz Victor , Mavrommatis Kostas , Pagani Ioanna , Sen Arnab , Wall Luis , Woyke Tanja , Gtari Maher , Tisa Louis S. 
Published: August 2016

ABSTRACT

Nocardia
sp. strain BMG111209 is a non-
Frankia
actinobacterium isolated from root nodules of
Casuarina glauca
in Tunisia. Here, we report the 9.1-Mbp draft genome sequence of
Nocardia
sp. strain BMG111209 with a G + C content of 69.19% and 8,122 candidate protein-encoding genes.
Draft Genome Sequence of the Chloroperoxidase-Producing Fungus
Caldariomyces fumago
Woronichin DSM1256
Authors: Kellner Harald , Pecyna Marek Jan , Buchhaupt Markus , Ullrich René , Hofrichter Martin 
Published: August 2016

ABSTRACT

We report here the draft genome sequence of the chloroperoxidase (EC 1.11.1.10)-producing ascomycete
Caldariomyces fumago
. Its genome was assembled into 511 contigs with a total size of 25 Mb. The G+C content is 51.4%, and 9,806 putative protein-coding genes were predicted. Eight heme-thiolate peroxidase genes, including two chloroperoxidase genes, were found.
Draft Genome Sequence of
Lactococcus garvieae
Strain PAQ102015-99, an Outbreak Strain Isolated from a Commercial Trout Farm in the Northwestern United States
Authors: Nelson Michael C. , Varney Jed S. , Welch Timothy J. , Graf Joerg 
Published: August 2016

ABSTRACT

We announce the draft genome assembly of
Lactococcus garvieae
strain PAQ102015-99, a recently isolated strain from an outbreak of lactococcosis at a commercial trout farm in the northwestern United States. The draft genome comprises 14 contigs totaling 2,068,357 bp with an
N
50
of 496,618 bp and average G+C content of 38%.
Complete Genome Sequence of
Streptococcus agalactiae
Strain S25 Isolated from Peritoneal Liquid of Nile Tilapia
Authors: Mainardi Rafaella Menegheti , Lima Júnior Edson Antônio , Ribeiro Júnior Jose Carlos , Beloti Vanerli , Carmo Anderson Oliveira , Kalapothakis Evanguedes , Gonçalves Daniela Dib , Padua Santiago Benites , Pereira Ulisses Pádua 
Published: August 2016

ABSTRACT

Streptococcus agalactiae
(Lancefield group B; GBS) is one of the major pathogens in fish production, especially in Nile tilapia (
Oreochromis niloticus
). The genomic characteristics of GBS isolated from fish must be more explored. Thus, we present here the genome of GBS S25, isolated from Nile tilapia from Brazil.
Draft Genome Sequences of
Legionella pneumophila
JR32 and Lp01 Laboratory Strains Domesticated in Japan
Authors: Maita Chinatsu , Matushita Mizue , Okubo Torahiko , Matsuo Junji , Miyake Masaki , Nagai Hiroki , Yamaguchi Hiroyuki 
Published: August 2016

ABSTRACT

We report here the draft genome sequences of two
Legionella pneumophila
variant strains (JR32 and Lp01_666) originally derived from a Philadelphia-1 clinical isolate, domesticated in Japan, with distinct susceptibility to amoebae. Detailed genomic analysis will allow us to better understand
Legionella
adaptation and survival mechanisms in host cells.
Draft Genome Sequence of
Burkholderia stabilis
LA20W, a Trehalose Producer That Uses Levulinic Acid as a Substrate
Authors: Sato Yuya , Koike Hideaki , Kondo Susumu , Hori Tomoyuki , Kanno Manabu , Kimura Nobutada , Morita Tomotake , Kirimura Kohtaro , Habe Hiroshi 
Published: August 2016

ABSTRACT

Burkholderia stabilis
LA20W produces trehalose using levulinic acid (LA) as a substrate. Here, we report the 7.97-Mb draft genome sequence of
B. stabilis
LA20W, which will be useful in investigations of the enzymes involved in LA metabolism and the mechanism of LA-induced trehalose production.
Complete Genome Sequence of the Proteorhodopsin-Containing Marine Flavobacterium
Dokdonia donghaensis
DSW-1
T
, Isolated from Seawater off Dokdo in the East Sea (Sea of Korea)
Authors: Kim Kitae , Kwon Soon-Kyeong , Yoon Jung-Hoon , Kim Jihyun F. 
Published: August 2016

ABSTRACT

Dokdonia
spp. have been used for investigating the lifestyles of proteorhodopsin-containing photoheterotrophs and for understanding marine photobiology. Here, we report the complete genome sequence of
Dokdonia donghaensis
DSW-1
T
using the PacBio sequencing platform. It should provide a valuable resource for comparative genomic studies of marine life harboring microbial rhodopsins among others.
Dipeptidyl peptidase-4 inhibition by Saxagliptin prevents inflammation and renal injury by targeting the Nlrp3/ASC inflammasome
Authors: Birnbaum Yochai , Bajaj Mandeep , Qian Jinqiao , Ye Yumei 
Published: August 2016

BackgroundGlucagon-like peptide-1 (GLP-1) receptor activation delays the progression of diabetic nephropathy (DN) in rodents. The NOD-like receptor 3 (Nlrp3) inflammasome plays an important role in DN. Dipeptidyl peptidase-4 inhibitors (DPP4I) inhibit the degradation of endogenous GLP-1 and various other active substances. We assessed whether DPP4I attenuates diabetes-induced activation of the inflammasome and progression of DN in mice with type 2 diabetes mellitus (T2DM) and type 1 diabetes mellitus (T1DM).MethodsBTBR (T2DM), Akita (T1DM) and their matched non-diabetic control (wild-type (WT)) mice received 8-week treatment with Saxagliptin (Saxa) or vehicle.ResultsKidney weight and kidney/body weight ratio increased in the BTBR and Akita mice compared to their WT mice. Saxa attenuated these changes in the BTBR, but not in the Akita mice and had no effect in the WT mice. Serum blood urea nitrogen and creatinine significantly increased in the BTBR and Akita mice. Saxa attenuated the increase in the BTBR and Akita mice. Saxa improved glycemic control in the BTBR mice, but had no effect on glucose levels in the Akita and WT mice. Serum C reactive protein, tumor necrosis factor α (TNFα), interleukin (IL)-1β, IL-6 and IL-18 were significantly higher in the BTBR and Akita mice than in the WT mice. Saxa attenuated the increase in the BTBR and Akita mice. Kidney and adipose protein levels of apoptosis-associated speck-like protein 1, NLRP3, TNFα and Caspase-1 were higher in the BTBR and Akita mice than in the WT mice. Saxa reduced the levels in both types of diabetic mice.ConclusionsSaxa attenuated diabetes-induced activation of the inflammasome and progression of DN. As Saxa did not affect glucose levels in the Akita mice, these effects are independent of glucose lowering.
Investigating the accuracy of parentally reported weights and lengths at 12 months of age as compared to measured weights and lengths in a longitudinal childhood genome study
Authors: Hazrati Sahel , Hourigan Suchitra K , Waller Allison , Yui Yvonne , Gilchrist Nancy , Huddleston Kathi , Niederhuber John 
Published: August 2016

BackgroundChildhood obesity studies rely on parentally reported anthropometrics. However, the accuracy of such data has not been evaluated for 12-month-old children. Moreover, methods to improve the accuracy of reported data have not been assessed in prior studies.MethodsA total of 185 children enrolled in a northern Virginia childhood longitudinal cohort genomic study had parentally completed surveys at 12 months. Measured weights and lengths were recorded for the same children from their 12-month paediatrician visit. Weight for length percentiles were calculated using World Health Organization gender-specific growth charts. The agreement between reported and measured values was examined using Pearson's correlation, paired t-test and κ statistics. The interquartile outlier rule was used to detect and remove outliers.ResultsParentally reported weight was strongly associated with measured weight at 12 months (r=0.90). There was only a moderate correlation between parentally reported and measured lengths (r=0.52) and calculated weight for length percentiles (r=0.65). After removing outliers from parentally reported data, there was an increase in correlation between parentally reported and measured data for weight (r=0.93), length (r=0.69) and weight for length percentiles (r=0.76). Outliers removed compared to all children included were more likely to have maternal education less than a bachelor's degree (p=0.007).ConclusionsAfter removal of outliers from reported data, there is a strong correlation between calculated reported and measured weight for length percentiles suggesting that this may be an effective method to increase accuracy when conducting large-scale obesity studies in young children where study costs benefit from using parentally reported data.
Patterns of cancer screening, incidence and treatment disparities in China: protocol for a population-based study
Authors: Yao Nengliang , Wang Jialin , Cai Yuanchu , Yuan Jing , Wang Haipeng , Gong Jiyong , Anderson Roger , Sun Xiaojie 
Published: August 2016

IntroductionCancer has become the leading cause of death in China. Several knowledge gaps exist with respect to the patterns of cancer care and disparities in China. Chinese healthcare researchers do not have access to cancer research data of high quality. Only cancer incidence and mortality rates have been analysed in China while the patterns of cancer screening and treatment and disparities have not been rigorously examined. Potential disparities in cancer care by socioeconomic status have not been analysed in the previous literature. Population-based estimates of cancer care costs remain unexamined in China. This project will depict the pattern of cancer screening, incidence and treatment in Shandong province and enhance our understanding of causes of disparities in cancer control.Methods and analysisWe will create the first linked database of cancer registry and health insurance claims in China. We obtained cancer registry data on breast, gastrointestinal and lung cancer incidence from 2011 to 2014 and their health insurance claims information from 6 cities/counties of 10.63 million population and validated it with hospital discharge data. A 1600 participant survey will be administered to collect additional information of patients’ socioeconomic status, employment and cancer care costs. Frequency analysis, spatial data exploratory analysis, multivariate logistic regression with instrumental variable, generalised linear regression and subgroup analysis will be used to analyse the following: the receipt of cancer screening, stage at diagnosis, guideline-concordant treatment and cancer care costs. Patient characteristics, tumour features, hospital characteristics, patient comorbidities and county-level descriptors will be used as covariates in the multivariate analysis.Ethics and disseminationThe Institutional Review Board of the School of Public Health of Shandong University approved this study (20140201). Data compiled from this project will be made available to all Chinese healthcare researchers. Study results will be disseminated through peer-reviewed publications and presentations at national and international meetings.
Use and Outcomes of Intravenous Thrombolysis for Acute Ischemic Stroke in Patients ≥90 Years of Age
Authors: Arora Rohan , Salamon Elliott , Katz Jeffrey M. , Cox Margueritte , Saver Jeffrey L. , Bhatt Deepak L. , Fonarow Gregg C. , Peterson Eric D. , Smith Eric E. , Schwamm Lee H. , Xian Ying , Libman Richard B. 
Published: August 2016

Background and Purpose—
Intravenous tissue-type plasminogen activator (tPA) is a proven treatment for acute ischemic stroke, but there has been limited evaluation among patients aged ≥90 years.

Methods—
We analyzed data from the Get With The Guidelines–Stroke national quality improvement registry from January 2009 to April 2013. Frequency, determinants, and outcomes of tPA use were compared among patients aged ≥90 and 3 younger age groups (18–64, 65–79, and 80–89 years).

Results—

Among 35 708 patients from 1178 sites who arrived within 2 hours of time last known well and received tPA, 2585 (7.2%) were ≥90 years. Compared with younger patients, the rate of tPA use among patients without a documented contraindication was lower among patients aged ≥90 years (67.4% versus 84.1% in 18–89-year olds;
P
<0.0001). Discharge outcomes among individuals aged ≥90 years included discharge to home or acute rehabilitation in 31.4%, independent ambulation at discharge in 13.4%, symptomatic hemorrhage in 6.1%, and in-hospital mortality or hospice discharge in 36.4%. On multivariable analysis, good functional outcomes generally occurred less often and mortality more often among patients aged ≥90 years. The risk of symptomatic hemorrhage was increased compared with patients <65 years but was not significantly different than the risk in 66- to 89-year olds.

Conclusions—
The use of intravenous tPA among those aged ≥90 years is lower than in younger patients. When fibrinolytic therapy is used, the risk of symptomatic hemorrhage is not higher than in 66- to 89-year olds; however, mortality is higher and functional outcomes are lower.