bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Genome Sequence of a Tenth Human Polyomavirus
Authors: Buck Christopher B. , Phan Giao Q. , Raiji Manish T. , Murphy Philip M. , McDermott David H. , McBride Alison A. 
Published: September 2012

ABSTRACT

Nine polyomavirus (PyV) species are known to productively infect humans. The circular DNA genomes of PyVs are readily detectable using rolling circle amplification (RCA). RCA-based analysis of condyloma specimens from a patient with
w
arts,
h
ypogammaglobulinemia,
i
nfections, and
m
yelokathexis (WHIM) syndrome demonstrated the presence of a tenth apparently human-tropic polyomavirus species, which we name HPyV10.
Complete Genome Sequence of a Street Rabies Virus from Mexico
Authors: Zhang Guoqing , Fu Zhen F. 
Published: September 2012

ABSTRACT
A canine rabies virus (RABV) has been used as a street rabies virus in laboratory investigations. Its entire genome was sequenced and found to be closely related to that of canine RABV circulating in Mexico. Sequence comparison indicates that the virus is closely related to those in the “cosmopolitan” group, with high homology (89 to 93%) to clade I of rabies viruses. The virus is now termed dog rabies virus-Mexico (DRV-Mexico).
Complete Genome Sequence of Aeromonas hydrophila Phage CC2
Authors: Shen Chan-juan , Liu Yong-jie , Lu Cheng-ping 
Published: September 2012

ABSTRACT

Aeromonas hydrophila
is one of the major pathogenic bacteria for fish and people. To develop an effective antimicrobial agent, we isolated a bacteriophage from sewage, named CC2, and sequenced its genome. Comparative genome analysis of phage CC2 with its relatives revealed that phage CC2 has higher sequence homology to
A. salmonicida
phage 65 than to
A. hydrophila
phage Aeh1. Here, we announce the complete genome sequence of CC2 and report major findings from the genomic analysis.
Complete Genome Sequence of an Avian Leukosis Virus Isolate Associated with Hemangioma and Myeloid Leukosis in Egg-Type and Meat-Type Chickens
Authors: Ji Jun , Li Hongxin , Zhang Huanmin , Xie Qingmei , Chang Shuang , Shang Huiqin , Ma Jingyun , Bi Yingzuo 
Published: September 2012

ABSTRACT
Subgroup J avian leukosis virus (ALV-J) was first isolated from meat-type chickens that developed myeloid leukosis (ML). In recent years, field cases of hemangioma (HE) or HE and ML, rather than ML alone, have been reported in commercial layer flocks exposed to ALV-J with a high incidence in China. Here we report the complete genomic sequence of an ALV-J isolate that caused both HE and ML in egg-type and meat-type chickens in China. These findings will provide additional insights into the molecular characteristics in genomes, host range, and pathogenicity of ALV-J.
Complete Genome Sequence of a Monosense Densovirus Infecting the Cotton Bollworm, Helicoverpa armigera
Authors: Xu Pengjun , Cheng Peng , Liu Zhongfang , Li Yi , Murphy Robert W. , Wu Kongming 
Published: September 2012

ABSTRACT

Densoviruses (DNVs) infecting arthropods are members of the family
Parvoviridae
. Here we report the complete genome sequence of a novel DNV with a monosense genome that infects cotton bollworms (
Helicoverpa armigera
), named HaDNV-1. Alignment and phylogenetic analysis revealed that HaDNV-1 showed high identity with the genus
Iteravirus
.
Radial Artery Free and T Graft Patency as Coronary Artery Bypass Conduit Over a 15-Year Period
Authors: Barner Hendrick B. , Bailey Marci , Guthrie Tracey J. , Pasque Michael K. , Moon Marc R. , Damiano Ralph J. , Lawton Jennifer S. 
Published: September 2012

Background—
The radial artery is often used as the second arterial graft for coronary artery bypass grafting. Little is known about the differences in long-term patency between radial free and T grafts. This study was performed to determine long-term radial artery patency over a 15-year period.

Methods and Results—

Radial arteries were used as free grafts or T grafts for coronary artery bypass grafting over a 15-year period. Patients were contacted to determine if postoperative cardiac catheterization was performed and examination of any reports and films was performed. Grafts were graded as patent, luminal irregularity, or occluded. Each sequential graft was counted separately. Between September 1993 and December 2008, 13 926 patients underwent isolated coronary artery bypass grafting and 3248 patients had at least one radial artery graft used as a conduit. Catheterizations were performed at a mean of 7.4±3.8 years (range, 3 days to 14.4 years) on 372 radial artery grafts (103 free and 269 T) in 215 patients. Kaplan-Meier freedom from occlusion for radial free and T grafts at 1 and 10 years was 97.1% and 75.4% and 99.6% and 62.9%, respectively (
P
=0.146 free versus T). Kaplan-Meier survival to 15 years was not statistically different between free and T graft patients (
P
=0.5).

Conclusions—
In 215 patients with postoperative catheterization after coronary artery bypass grafting with a radial artery graft, radial free and T grafts had similar and acceptable long-term patency to support their use as a coronary artery bypass graft conduit.
Modulation of Transforming Growth Factor-β Signaling and Extracellular Matrix Production in Myxomatous Mitral Valves by Angiotensin II Receptor Blockers
Authors: Geirsson Arnar , Singh Mansher , Ali Rahmat , Abbas Hussain , Li Wei , Sanchez Juan A. , Hashim Sabet , Tellides George 
Published: September 2012

Background—
Little is known about the pathophysiology of myxomatous degeneration of the mitral valve, the pathological hallmark of mitral valve prolapse, associated with symptomatic mitral regurgitation, heart failure, and death. Excess transforming growth factor (TGF)-β signaling is known to cause mitral valve degeneration and regurgitation in a mouse model of Marfan syndrome. We examined if TGF-β signaling is dysregulated in clinical specimens of sporadic mitral valve prolapse compared with explanted nondiseased mitral valves and we tested the effects of angiotensin II receptor blockers on TGF-β signaling in cultured human mitral valve cells.

Methods and Results—
Operative specimens, cultured valve tissues, and cultured valvular interstitial cells were obtained from patients with mitral valve prolapse undergoing mitral valve repair or from organ donors without mitral valve disease. Increased extracellular matrix in diseased valve tissue correlated with an upregulation of TGF-β expression and signaling as evidenced by SMAD2/3 phosphorylation. Both TGF-β ligand and signaling mediators colocalized primarily to valvular interstitial cells suggesting autocrine/paracrine activation. In cultured valve tissue, exogenous TGF-β increased basal extracellular matrix production, whereas serological neutralization of TGF-β inhibited disease-driven extracellular matrix overproduction. TGF-β-induced extracellular matrix production in cultured valvular interstitial cells was dependent on SMAD2/3 and p38 signaling and was inhibited by angiotensin II receptor blockers.

Conclusions—
TGF-β has a profibrotic role in the pathogenesis of sporadic mitral valve prolapse. Attenuation of TGF-β signaling by angiotensin II receptor blockers may represent a mechanistically based strategy to modulate the pathological progression of mitral valve prolapse in patients.
MicroRNA-145 Targeted Therapy Reduces Atherosclerosis
Authors: Lovren Fina , Pan Yi , Quan Adrian , Singh Krishna K. , Shukla Praphulla C. , Gupta Nandini , Steer Brent M. , Ingram Alistair J. , Gupta Milan , Al-Omran Mohammed , Teoh Hwee , Marsden Philip A. , Verma Subodh 
Published: September 2012

Background—
MicroRNA are essential posttranscriptional modulators of gene expression implicated in various chronic diseases. Because microRNA-145 is highly expressed in vascular smooth muscle cells (VSMC) and regulates VSMC fate and plasticity, we hypothesized that it may be a novel regulator of atherosclerosis and plaque stability.

Methods and Results—

Apolipoprotein E knockout mice (
ApoE
−/−
) mice were treated with either a microRNA-145 lentivirus under the control of the smooth muscle cell (SMC)-specific promoter
SM22
α or a
SM22
α control lentivirus before commencing the Western diet for 12 weeks. The SMC-targeted microRNA-145 treatment markedly reduced plaque size in aortic sinuses, ascending aortas, and brachiocephalic arteries. It also significantly increased fibrous cap area, reduced necrotic core area, and increased plaque collagen content. Cellular plaque composition analyses revealed significantly less macrophages in
ApoE
−/−
mice treated with the SMC-specific microRNA-145. These mice also demonstrated marked increases in calponin levels and α-smooth muscle actin–positive SMC areas in their atherosclerotic lesions. Furthermore, lentiviral delivery of microRNA-145 resulted in reduced KLF4 and elevated myocardin expression in aortas from
ApoE
−/−
mice, consistent with an effect of microRNA-145 to promote a contractile phenotype in VSMC.

Conclusions—
VSMC-specific overexpression of microRNA-145 is a novel in vivo therapeutic target to limit atherosclerotic plaque morphology and cellular composition, shifting the balance toward plaque stability vs plaque rupture.
Hybrid Versus Norwood Strategies for Single-Ventricle Palliation
Authors: Baba Kenji , Kotani Yasuhiro , Chetan Devin , Chaturvedi Rajiv R. , Lee Kyong-Jin , Benson Lee N. , Grosse-Wortmann Lars , Van Arsdell Glen S. , Caldarone Christopher A. , Honjo Osami 
Published: September 2012

Background—
Hybrid and Norwood strategies differ substantially in terms of stage II palliative procedures. We sought to compare these strategies with an emphasis on survival and reintervention after stage II and subsequent Fontan completion.

Methods and Results—

Of 110 neonates with functionally single-ventricle physiology who underwent stage I palliation between 2004 and 2010, 75 (69%) infants (Norwood, n=43; hybrid, n=32) who subsequently underwent stage II palliation were studied. Survival and reintervention rates after stage II palliation, anatomic and physiologic variables at pre-Fontan assessment, and Fontan outcomes were compared between the groups. Predictors for reintervention were analyzed. Freedom from death/transplant after stage II palliation was equivalent between the groups (Norwood, 80.4% versus hybrid, 85.6% at 3 years,
P
=0.66). Hybrid patients had a higher pulmonary artery (PA) reintervention rate (
P
=0.003) and lower Nakata index at pre-Fontan evaluation (
P
=0.015). Aortic arch and atrioventricular valve reinterventions were not different between the groups. Ventricular end-diastolic pressure, mean PA pressure, and ventricular function were equivalent at pre-Fontan assessment. There were no deaths after Fontan completion in either group (Norwood, n=25, hybrid, n=14).

Conclusions—
Survival after stage II palliation and subsequent Fontan completion is equivalent between the groups. The hybrid group had a higher PA reintervention rate and smaller PA size. Both strategies achieved adequate physiology for Fontan completion. Evolution of the hybrid strategy requires refinement to provide optimal PA growth.
Safe Genetic Modification of Cardiac Stem Cells Using a Site-Specific Integration Technique
Authors: Lan Feng , Liu Junwei , Narsinh Kazim H. , Hu Shijun , Han Leng , Lee Andrew S. , Karow Marisa , Nguyen Patricia K. , Nag Divya , Calos Michele P. , Robbins Robert C. , Wu Joseph C. 
Published: September 2012

Background—
Human cardiac progenitor cells (hCPCs) are a promising cell source for regenerative repair after myocardial infarction. Exploitation of their full therapeutic potential may require stable genetic modification of the cells ex vivo. Safe genetic engineering of stem cells, using facile methods for site-specific integration of transgenes into known genomic contexts, would significantly enhance the overall safety and efficacy of cellular therapy in a variety of clinical contexts.

Methods and Results—

We used the phiC31 site-specific recombinase to achieve targeted integration of a triple fusion reporter gene into a known chromosomal context in hCPCs and human endothelial cells. Stable expression of the reporter gene from its unique chromosomal integration site resulted in no discernible genomic instability or adverse changes in cell phenotype. Namely, phiC31-modified hCPCs were unchanged in their differentiation propensity, cellular proliferative rate, and global gene expression profile when compared with unaltered control hCPCs. Expression of the triple fusion reporter gene enabled multimodal assessment of cell fate in vitro and in vivo using fluorescence microscopy, bioluminescence imaging, and positron emission tomography. Intramyocardial transplantation of genetically modified hCPCs resulted in significant improvement in myocardial function 2 weeks after cell delivery, as assessed by echocardiography (
P
=0.002) and MRI (
P
=0.001). We also demonstrated the feasibility and therapeutic efficacy of genetically modifying differentiated human endothelial cells, which enhanced hind limb perfusion (
P
<0.05 at day 7 and 14 after transplantation) on laser Doppler imaging.

Conclusions—
The phiC31 integrase genomic modification system is a safe, efficient tool to enable site-specific integration of reporter transgenes in progenitor and differentiated cell types.
WRF Simulations of the Urban Circulation in the Salt Lake City Area for CO2 Modeling
Authors: Nehrkorn Thomas , Henderson John , Leidner Mark , Mountain Marikate , Eluszkiewicz Janusz , McKain Kathryn , Wofsy Steven 
Published: September 2012

AbstractA recent National Research Council report highlighted the potential utility of atmospheric observations and models for detecting trends in concentrated emissions from localized regions, such as urban areas. The Salt Lake City (SLC), Utah, area was chosen for a pilot study to determine the feasibility of using ground-based sensors to identify trends in anthropogenic urban emissions over a range of time scales (from days to years). The Weather Research and Forecasting model (WRF) was combined with a Lagrangian particle dispersion model and an emission inventory to model carbon dioxide (CO2) concentrations that can be compared with in situ measurements. An accurate representation of atmospheric transport requires a faithful modeling of the meteorological conditions. This study examines in detail the ability of different configurations of WRF to reproduce the observed local and mesoscale circulations, and the diurnal evolution of the planetary boundary layer (PBL) in the SLC area. Observations from the Vertical Transport and Mixing field experiment in 2000 were used to examine the sensitivity of WRF results to changes in the PBL parameterization and to the inclusion of an urban canopy model (UCM). Results show that for urban locations there is a clear benefit from parameterizing the urban canopy for simulation of the PBL and near-surface conditions, particularly for temperature evolution at night. Simulation of near-surface CO2 concentrations for a 2-week period in October 2006 showed that running WRF at high resolution (1.33 km) and with a UCM also improves the simulation of observed increases in CO2 during the early evening.
Quick, “Imputation-free” meta-analysis with proxy-SNPs
Authors: Meesters Christian , Leber Markus , Herold Christine , Angisch Marina , Mattheisen Manuel , Drichel Dmitriy , Lacour André , Becker Tim 
Published: September 2012

Abstract

Background
Meta-analysis (MA) is widely used to pool genome-wide association studies (GWASes) in order to a) increase the power to detect strong or weak genotype effects or b) as a result verification method. As a consequence of differing SNP panels among genotyping chips, imputation is the method of choice within GWAS consortia to avoid losing too many SNPs in a MA. YAMAS (Yet Another Meta Analysis Software), however, enables cross-GWAS conclusions prior to finished and polished imputation runs, which eventually are time-consuming.

Results
Here we present a fast method to avoid forfeiting SNPs present in only a subset of studies, without relying on imputation. This is accomplished by using reference linkage disequilibrium data from 1,000 Genomes/HapMap projects to find proxy-SNPs together with in-phase alleles for SNPs missing in at least one study. MA is conducted by combining association effect estimates of a SNP and those of its proxy-SNPs. Our algorithm is implemented in the MA software YAMAS. Association results from GWAS analysis applications can be used as input files for MA, tremendously speeding up MA compared to the conventional imputation approach. We show that our proxy algorithm is well-powered and yields valuable ad hoc results, possibly providing an incentive for follow-up studies. We propose our method as a quick screening step prior to imputation-based MA, as well as an additional main approach for studies without available reference data matching the ethnicities of study participants. As a proof of principle, we analyzed six dbGaP Type II Diabetes GWAS and found that the proxy algorithm clearly outperforms naïve MA on the p-value level: for 17 out of 23 we observe an improvement on the p-value level by a factor of more than two, and a maximum improvement by a factor of 2127.

Conclusions
YAMAS is an efficient and fast meta-analysis program which offers various methods, including conventional MA as well as inserting proxy-SNPs for missing markers to avoid unnecessary power loss. MA with YAMAS can be readily conducted as YAMAS provides a generic parser for heterogeneous tabulated file formats within the GWAS field and avoids cumbersome setups. In this way, it supplements the meta-analysis process.
Empirical evaluation of scoring functions for Bayesian network model selection
Authors: Liu Zhifa , Malone Brandon , Yuan Changhe 
Published: September 2012

AbstractIn this work, we empirically evaluate the capability of various scoring functions of Bayesian networks for recovering true underlying structures. Similar investigations have been carried out before, but they typically relied on approximate learning algorithms to learn the network structures. The suboptimal structures found by the approximation methods have unknown quality and may affect the reliability of their conclusions. Our study uses an optimal algorithm to learn Bayesian network structures from datasets generated from a set of gold standard Bayesian networks. Because all optimal algorithms always learn equivalent networks, this ensures that only the choice of scoring function affects the learned networks. Another shortcoming of the previous studies stems from their use of random synthetic networks as test cases. There is no guarantee that these networks reflect real-world data. We use real-world data to generate our gold-standard structures, so our experimental design more closely approximates real-world situations. A major finding of our study suggests that, in contrast to results reported by several prior works, the Minimum Description Length (MDL) (or equivalently, Bayesian information criterion (BIC)) consistently outperforms other scoring functions such as Akaike's information criterion (AIC), Bayesian Dirichlet equivalence score (BDeu), and factorized normalized maximum likelihood (fNML) in recovering the underlying Bayesian network structures. We believe this finding is a result of using both datasets generated from real-world applications rather than from random processes used in previous studies and learning algorithms to select high-scoring structures rather than selecting random models. Other findings of our study support existing work, e.g., large sample sizes result in learning structures closer to the true underlying structure; the BDeu score is sensitive to the parameter settings; and the fNML performs pretty well on small datasets. We also tested a greedy hill climbing algorithm and observed similar results as the optimal algorithm.
Plasmodium falciparum parasitaemia in the first half of pregnancy, uterine and umbilical artery blood flow, and foetal growth: a longitudinal Doppler ultrasound study
Authors: Griffin Jennifer B , Lokomba Victor , Landis Sarah H , Thorp John M , Herring Amy H , Tshefu Antoinette K , Rogerson Stephen J , Meshnick Steven R 
Published: September 2012

AbstractBackgroundDuring early pregnancy, the placenta develops to meet the metabolic demands of the foetus. The objective of this analysis was to examine the effect of malaria parasitaemia prior to 20 weeks’ gestation on subsequent changes in uterine and umbilical artery blood flow and intrauterine growth restriction.MethodsData were analysed from 548 antenatal visits after 20 weeks’ gestation of 128 women, which included foetal biometric measures and interrogation of uterine and umbilical artery blood flow. Linear mixed effect models estimated the effect of early pregnancy malaria parasitaemia on uterine and umbilical artery resistance indices. Log-binomial models with generalized estimating equations estimated the effect of early pregnancy malaria parasitaemia on the risk of intrauterine growth restriction.ResultsThere were differential effects of early pregnancy malaria parasitaemia on uterine artery resistance by nutritional status, with decreased uterine artery resistance among nourished women with early pregnancy malaria and increased uterine artery resistance among undernourished women with early pregnancy malaria. Among primigravidae, early pregnancy malaria parasitaemia decreased umbilical artery resistance in the late third trimester, likely reflecting adaptive villous angiogenesis. In fully adjusted models, primigravidae with early pregnancy malaria parasitaemia had 3.6 times the risk of subsequent intrauterine growth restriction (95% CI: 2.1, 6.2) compared to the referent group of multigravidae with no early pregnancy malaria parasitaemia.ConclusionsEarly pregnancy malaria parasitaemia affects uterine and umbilical artery blood flow, possibly due to alterations in placentation and angiogenesis, respectively. Among primigravidae, early pregnancy malaria parasitaemia increases the risk ofintrauterinegrowth restriction. The findings support the initiation of malaria parasitaemia prevention and control efforts earlier in pregnancy.