bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pathway-Based Genome-Wide Association Studies for Two Meat Production Traits in Simmental Cattle
Authors: Fan Huizhong , Wu Yang , Zhou Xiaojing , Xia Jiangwei , Zhang Wengang , Song Yuxin , Liu Fei , Chen Yan , Zhang Lupei , Gao Xue , Gao Huijiang , Li Junya 
Published: December 2015

AbstractMost single nucleotide polymorphisms (SNPs) detected by genome-wide association studies (GWAS), explain only a small fraction of phenotypic variation. Pathway-based GWAS were proposed to improve the proportion of genes for some human complex traits that could be explained by enriching a mass of SNPs within genetic groups. However, few attempts have been made to describe the quantitative traits in domestic animals. In this study, we used a dataset with approximately 7,700,000 SNPs from 807 Simmental cattle and analyzed live weight and longissimus muscle area using a modified pathway-based GWAS method to orthogonalise the highly linked SNPs within each gene using principal component analysis (PCA). As a result, of the 262 biological pathways of cattle collected from the KEGG database, the gamma aminobutyric acid (GABA)ergic synapse pathway and the non-alcoholic fatty liver disease (NAFLD) pathway were significantly associated with the two traits analyzed. The GABAergic synapse pathway was biologically applicable to the traits analyzed because of its roles in feed intake and weight gain. The proposed method had high statistical power and a low false discovery rate, compared to those of the smallest P-value and SNP set enrichment analysis methods.
Immobilization of myoglobin on Au nanoparticle-decorated carbon nanotube/polytyramine composite as a mediator-free H2O2 and nitrite biosensor
Authors: Vilian A. T. Ezhil , Veeramani Vediyappan , Chen Shen-Ming , Madhu Rajesh , Kwak Cheol Hwan , Huh Yun Suk , Han Young-Kyu 
Published: December 2015

AbstractA novel composite film was designed for use as a highly selective mediator-free amperometric biosensor and a method was created for accomplishing direct electrochemistry of myoglobin on a multi-walled carbon nanotube and tyramine-modified composite decorated with Au nanoparticles on a glassy carbon electrode. The ultraviolet-visible and electrochemical impedance spectroscopy results showed that myoglobin retained its native conformation in the interaction with Au-PTy-f-MWCNT. The surface coverage of Mb-heme-Fe(II)/(III) immobilized on Au-PTy-f-MWCNT and the heterogeneous electron-transfer rate constant were 2.12 × 10−9 mol cm−2 and 4.86 s−1, respectively, indicating a higher loading capacity of the nanocomposite for direct electron transfer of Mb onto the electrode surface. The proposed Mb/Au-PTy-f-MWCNT biofilm exhibited excellent electrocatalytic behavior toward the reduction of H2O2 and the oxidation of nitrite with linear ranges of 2 to 5000 μM and 1 to 8000 μM and lower detection limits of 0.01 μM and 0.002 μM, respectively. An apparent Michaelis-Menten constant of 0.12 mM indicated that the Mb immobilized on the Au-PTy-f-MWCNT film retained its native activity. This biosensor can be successfully applied to detect H2O2 and nitrite in disinfectant cream, eye drops, pickle juice and milk samples.
Albumin adsorption on CoCrMo alloy surfaces
Authors: Yan Yu , Yang Hongjuan , Su Yanjing , Qiao Lijie 
Published: December 2015

AbstractProteins can adsorb on the surface of artificial joints immediately after being implanted. Although research studying protein adsorption on medical material surfaces has been carried out, the mechanism of the proteins’ adsorption which affects the corrosion behaviour of such materials still lacks in situ observation at the micro level. The adsorption of bovine serum albumin (BSA) on CoCrMo alloy surfaces was studied in situ by AFM and SKPFM as a function of pH and the charge of CoCrMo alloy surfaces. Results showed that when the specimens were uncharged, hydrophobic interaction could govern the process of the adsorption rather than electrostatic interaction and BSA molecules tended to adsorb on the surfaces forming a monolayer in the side-on model. Results also showed that adsorbed BSA molecules could promote the corrosion process for CoCrMo alloys. When the surface was positively charged, the electrostatic interaction played a leading role in the adsorption process. The maximum adsorption occurred at the isoelectric point (pH 4.7) of BSA.
Strong, Multi-Scale Heterogeneity in Earth’s Lowermost Mantle
Authors: Tkalčić Hrvoje , Young Mallory , Muir Jack B. , Davies D. Rhodri , Mattesini Maurizio 
Published: December 2015

AbstractThe core mantle boundary (CMB) separates Earth’s liquid iron outer core from the solid but slowly convecting mantle. The detailed structure and dynamics of the mantle within ~300 km of this interface remain enigmatic: it is a complex region, which exhibits thermal, compositional and phase-related heterogeneity, isolated pockets of partial melt and strong variations in seismic velocity and anisotropy. Nonetheless, characterising the structure of this region is crucial to a better understanding of the mantle’s thermo-chemical evolution and the nature of core-mantle interactions. In this study, we examine the heterogeneity spectrum from a recent P-wave tomographic model, which is based upon trans-dimensional and hierarchical Bayesian imaging. Our tomographic technique avoids explicit model parameterization, smoothing and damping. Spectral analyses reveal a multi-scale wavelength content and a power of heterogeneity that is three times larger than previous estimates. Inter alia, the resulting heterogeneity spectrum gives a more complete picture of the lowermost mantle and provides a bridge between the long-wavelength features obtained in global S-wave models and the short-scale dimensions of seismic scatterers. The evidence that we present for strong, multi-scale lowermost mantle heterogeneity has important implications for the nature of lower mantle dynamics and prescribes complex boundary conditions for Earth’s geodynamo.
Biochemical toxicity and DNA damage of imidazolium-based ionic liquid with different anions in soil on Vicia faba seedlings
Authors: Liu Tong , Zhu Lusheng , Wang Jinhua , Wang Jun , Zhang Jun , Sun Xi , Zhang Cheng 
Published: December 2015

AbstractIn the present study, the toxic effects of 1-octyl-3-methylimidazolium chloride ([Omim]Cl), 1-octyl-3-methylimidazolium bromide ([Omim]Br) and 1-octyl-3-methylimidazolium tetrafluoroborate ([Omim]BF4) in soil on Vicia faba (V. faba) seedlings at 0, 100, 200, 400, 600 and 800 mg kg−1 were assessed for the first time at the cellular and molecular level. Moreover, the toxicity of these three ionic liquids (ILs) was evaluated and the influence of anions on the toxicity of the ILs was assessed. The results showed that even at 100 mg kg−1, the growth of V. faba seedlings was inhibited after exposure to the three ILs and the inhibitory effect was enhanced with increasing concentrations of the three ILs. The level of reactive oxygen species (ROS) was increased after exposure to the three ILs, which resulted in lipid peroxidation, DNA damage and oxidative damage in the cells of the V. faba seedlings. In addition, the anion structure could influence the toxicity of ILs and toxicity of the three tested ILs decreased in the following order: [Omim]BF4 > [Omim]Br > [Omim]Cl. Moreover, oxidative damage is the primary mechanism by which ILs exert toxic effects on crops and ILs could reduce the agricultural productivity.
Assessing the pollution risk of soil Chromium based on loading capacity of paddy soil at a regional scale
Authors: Qu Mingkai , Li Weidong , Zhang Chuanrong , Huang Biao , Zhao Yongcun 
Published: December 2015

AbstractThe accumulation of a trace metal in rice grain is not only affected by the total concentration of the soil trace metal, but also by crop variety and related soil properties, such as soil pH, soil organic matter (SOM) and so on. However, these factors were seldom considered in previous studies on mapping the pollution risk of trace metals in paddy soil at a regional scale. In this study, the spatial nonstationary relationships between rice-Cr and a set of perceived soil properties (soil-Cr, soil pH and SOM) were explored using geographically weighted regression; and the relationships were then used for calculating the critical threshold (CT) of soil-Cr concentration that may ensure the concentration of rice-Cr being below the permissible limit. The concept of “loading capacity” (LC) for Cr in paddy soil was then defined as the difference between the CT and the real concentration of Cr in paddy soil, so as to map the pollution risk of soil-Cr to rice grain and assess the risk areas in Jiaxing city, China. Compared with the information of the concentration of the total soil-Cr, such results are more valuable for spatial decision making in reducing the accumulation of rice-Cr at a regional scale.
Glycan:glycan interactions: High affinity biomolecular interactions that can mediate binding of pathogenic bacteria to host cells
Authors: Day Christopher J. , Tran Elizabeth N. , Semchenko Evgeny A. , Tram Greg , Hartley-Tassell Lauren E. , Ng Preston S. K. , King Rebecca M. , Ulanovsky Rachel , McAtamney Sarah , Apicella Michael A. , Tiralongo Joe , Morona Renato , Korolik Victoria , Jennings Michael P. 
Published: December 2015

Significance
Pathogens use cell surface carbohydrates as a means of attachment to host tissues. In several pathogenic bacteria, truncation of surface carbohydrates, lipooligosaccharide, or lipopolysaccharide have been reported to significantly reduce bacterial adherence to host cells. Here, we show that the lipooligosaccharide/lipopolysaccharide of four distinct bacterial pathogens bind directly to a range of host glycans. Surface plasmon resonance data confirmed binding among 66 different host–glycan:bacterial–glycan pairs. We also demonstrated that bacterial adherence can be competitively inhibited by either host cell or bacterial glycans. Our discovery of high-affinity glycan:glycan interactions in infectious disease may provide new approaches for therapy and prevention. The discovery of the existence of extensive, high-affinity interactions between glycans will alter the perception of the importance of these macromolecular interactions in all biological systems.
Feasibility of Collaborative Care Treatment of Opioid use Disorders with Buprenorphine during Pregnancy
Authors: Mittal Leena , Suzuki Joji 
Published: December 2015

Background Medication-assisted treatment with buprenorphine or methadone is recommended for pregnant patients with opioid use disorders (OUDs) to minimize adverse maternal and neonatal outcomes. Collaborative care approaches have been successfully utilized with office-based opioid treatment with buprenorphine in primary care settings, but research is significantly limited in the obstetric setting. Our aim with this study is to demonstrate the feasibility of a collaborative care model for pregnant patients with opioid use disorder. Methods This is a case series of 16 pregnancies in 14 women initiated on office-based opioid treatment with buprenorphine in a perinatal mental health service embedded in 2 obstetric clinics. Patients are treated by a psychiatrist alongside their prenatal care provider and followed for up to 6 months postpartum and referred to ongoing substance abuse treatment to a community prescriber. Results The average age of the patients was 30.3 years, and an average gestational age of 23.6 weeks at the time of referral. Treatment continued until delivery in 15 (93.8%) pregnancies, with an average duration of treatment of 14.5 weeks. The majority (60%) had a cesarean delivery. Twelve (80%) infants were admitted to the Neonatal Intensive Care Unit (NICU) for monitoring or treatment of neonatal abstinence syndrome, 14 (87.5%) patients continued or resumed treatment with buprenorphine postpartum at the time of discharge from our program, and 13 (81.3%) were referred to a community prescriber. Conclusions A collaborative care approach to buprenorphine treatment is feasible during pregnancy. Further research is needed to improve the treatment of OUD during pregnancy.
Patient Perspectives on An Opioid Overdose Education and Naloxone Distribution Program in the U.S. Department of Veterans Affairs
Authors: Oliva Elizabeth M. , Nevedal Andrea , Lewis Eleanor T. , McCaa Matthew D. , Cochran Michael F. , Konicki P. Eric , Davis Corey S. , Wilder Christine 
Published: December 2015

Background In an effort to prevent opioid overdose mortality among Veterans, Department of Veterans Affairs (VA) facilities began implementing opioid overdose education and naloxone distribution (OEND) in 2013 and a national program began in 2014. VA is the first national health care system to implement OEND. The goal of this study is to examine patient perceptions of OEND training and naloxone kits. Methods Four focus groups were conducted between December 2014 and February 2015 with 21 patients trained in OEND. Participants were recruited from a VA residential facility in California with a substance use disorder treatment program (mandatory OEND training) and a homeless program (optional OEND training). Data were analyzed using matrices and open and closed coding approaches to identify participants’ perspectives on OEND training including benefits, concerns, differing opinions, and suggestions for improvement. Results Veterans thought OEND training was interesting, novel, and empowering, and that naloxone kits will save lives. Some veterans expressed concern about using syringes in the kits. A few patients who never used opioids were not interested in receiving kits. Veterans had differing opinions about legal and liability issues, whether naloxone kits might contribute to relapse, and whether and how to involve family in training. Some veterans expressed uncertainty about the effects of naloxone. Suggested improvements included active learning approaches, enhanced training materials, and increased advertisement. Conclusions OEND training was generally well received among study participants, including those with no indication for a naloxone kit. Patients described a need for OEND and believed it could save lives. Patient feedback on OEND training benefits, concerns, opinions, and suggestions provides important insights to inform future OEND training programs both within VA and in other health care settings. Training is critical to maximizing the potential for OEND to save lives, and this study includes specific suggestions for improving the effectiveness and acceptability of training.
Multi-scale gyrokinetic simulation of tokamak plasmas: enhanced heat loss due to cross-scale coupling of plasma turbulence
Authors: Howard N.T. , Holland C. , White A.E. , Greenwald M. , Candy J. 
Published: December 2015

Abstract
The transport of heat in laboratory and astrophysical plasmas is dominated by the complex nonlinear dynamics of plasma turbulence. In magnetically confined plasmas used for fusion energy research, turbulence is responsible for cross-field transport that limits the performance of tokamak reactors. We report a set of novel gyrokinetic simulations that capture ion and electron-scale turbulence simultaneously, revealing the dynamics of cross-scale energy transfer and zonal flow modification that give rise to heat losses. Multi-scale simulations are required to match experimental ion and electron heat fluxes and electron profile stiffness, establishing the applicability of the newly discovered physics to experiment. Importantly, these results provide a likely explanation for the loss of electron heat from tokamak plasmas, the ‘great unsolved problem’ (Bachelor et al (2007 Plasma Sci. Technol. 9 312–87)) in plasma turbulence and the projected dominant loss channel in ITER.
Numerical analyses of JT-60SA scenarios with the COREDIV code
Authors: Zagórski R. , Giruzzi G. , Gała¸zka K. , Ivanova-Stanik I. , Romanelli M. , Stȩpniewski W. 
Published: December 2015

Abstract
JT-60SA design scenarios have been analyzed with the help of the self-consistent core-edge COREDIV code, with the aim to assess the influence of impurities on the plasma parameters and tokamak performance. In particular, the reduction of divertor target power load due to radiation of sputtered and externally seeded impurities has been investigated. For all scenarios considered, the gradual replacement of carbon by low Z seeding impurity (N, Ne) is observed as the gas influx increases. For high auxiliary power and low density scenarios, the carbon and seeding impurity radiation does not effectively reduce power to plate. Consequently, results with very high

(about 6–8) and impurity concentrations (>9%) are observed. For these scenarios, seeding of the high Z impurity like krypton seems to be more appropriate, in particular when the plasma density is increased.
Severe Cardiac Autonomic Derangement and Altered Ventricular Repolarization Pave the Way to Postoperative Atrial Fibrillation
Authors: Kališnik Jurij Matija , Hrovat Eva , Hrastovec Alenka , Avbelj Viktor , Žibert Janez , Geršak Borut 
Published: December 2015

Objective Postoperative atrial fibrillation (POAF) is a frequent complication after heart surgery. It has been shown that cardiac autonomic derangement plays a significant role in the genesis of atrial fibrillation (AF) and that AF might also be promoted by altered repolarization. Thus, the aim of our study was to determine the levels of cardiac autonomic modulation and repolarization properties in patients developing POAF. Methods Seventy-nine patients scheduled for aortic and/or coronary artery bypass grafting surgery with cardiopulmonary bypass were enrolled prospectively. High-resolution 20-minute electrocardiogram recordings were obtained day before surgery to determine P, PR, QT, and QTc intervals, as well as linear (time and frequency domain) and nonlinear heart rate variability parameters (fractal dimension and detrended fluctuation analysis). QTc interval was calculated using Framingham correction. Results Twenty-nine patients developed POAF (AF group), and 50 did not (non-AF group). Groups were similar regarding demographics, surgery type, and perioperative characteristics, except for older age in the AF group. QT and QTc intervals (Framingham) were longer in the AF group [442 (44) vs 422 (28) milliseconds, P = 0.018; and 448 (44) vs 431 (24) milliseconds, P = 0.031 and P = 0.019, respectively]. Time domain heart rate variability parameter PNN50 (percentage of pairs of adjacent NN intervals differing >50 milliseconds) was higher [14% (21%) vs 8% (16%), P = 0.015], and nonlinear parameter detrended fluctuation analysis α2 was lower in the AF group [0.81 (0.21) vs 0.91 (0.20), P = 0.031]. Conclusions Profound cardiac autonomic derangement, suggestive of parasympathetic excessive modulation, exists preoperatively in patients inclined to POAF after cardiac surgery, whereby parameters PNN50 and α2 differentiated the AF from the non-AF group. Prolonged QTc intervals are associated with an increased risk of POAF.
Total Arterial Minimally Invasive Direct Coronary Artery Bypass Surgery Facilitated by the Trinity Clip Connector
Authors: Stecher David , Bronkers Glenn , Hoefer Imo E. , Pasterkamp Gerard , Buijsrogge Marc P. 
Published: December 2015

Objective This pilot study evaluated the feasibility of total arterial minimally invasive direct coronary artery bypass surgery by using the Trinity Clip anastomotic connector in an acute porcine model. Methods In 3 pigs, the left and right internal thoracic arteries (LITA and RITA) were harvested conventionally and the chest closed subsequently. After a left lateral thoracotomy, the coronary target was positioned and stabilized by an endo-starfish and octopus. A free RITA-to-LITAy-graft, with a LITA-to-left anterior descending coronary artery (LAD) and a free RITA-to-obtuse marginal or posterolateral or posterior descending artery, was constructed using the Trinity Clip. Patency was assessed with angiography (n = 3 anastomoses). Results The anastomotic procedure was feasible via a small lateral thoracotomy, with a fast construction of the y-graft, and successful application of the mounted complex (ie, graft, connector, and laser, temporarily fixated by a fixation clip) onto the LAD. Access to the obtuse marginal artery, posterolateral artery, and posterior descending artery was possible, with successful construction, resulting in patent anastomoses. Conclusions This experimental pilot study demonstrates the feasibility of the anastomotic technique in a total arterial minimally invasive direct coronary artery bypass approach. Revascularization of the anterior, lateral, and inferoposterior regions of the heart is possible. However, visibility during the introduction of the connector was limited, and videoscopic assistance is essential to allow for successful construction. The anastomotic technique has potential to facilitate minimally invasive coronary bypass surgery.
Diversity in Clinical and Biomedical Research: A promise yet to be fulfilled
Authors: Oh Sam S. , Galanter Joshua , Thakur Neeta , Pino-Yanes Maria , Barcelo Nicolas E. , White Marquitta J. , de Bruin Danille M. , Greenblatt Ruth M. , Bibbins-Domingo Kirsten , Wu Alan H.B. , Borrell Luisa N. , Gunter Chris , Powe Neil R. , Burchard Esteban G. 
Published: December 2015

Summary PointsHealth disparities persist across race/ethnicity for the majority ofHealthy People 2010health indicators.Most physicians and scientists are informed by research extrapolated from a largely homogenous population, usually White and male.A growing proportion of Americans are not fully benefiting from clinical and biomedical advances since racial and ethnic minorities make up nearly 40% of the U.S. population.Ignoring the racial/ethnic diversity of the U.S. population is a missed scientific opportunity to fully understand the factors that lead to disease or health.U.S. biomedical research and study populations must better reflect the country’s changing demographics. Adequate representation of diverse populations in scientific research is imperative as a matter of social justice, economics, and science.
Molecular organization of CA1 interneuron classes
Authors: Harris Kenneth D. , Magno Lorenza , Katona Linda , Lönnerberg Peter , Muñoz Manchado Ana B. , Somogyi Peter , Kessaris Nicoletta , Linnarsson Sten , Hjerling-Leffler Jens 
Published: December 2015

AbstractGABAergic interneurons are key regulators of hippocampal circuits, but our understanding of the diversity and classification of these cells remains controversial. Here we analyze the organization of interneurons in the CA1 area, using the combinatorial patterns of gene expression revealed by single-cell mRNA sequencing (scRNA-seq). This analysis reveals a 5-level hierarchy of cell classes. Most of the predicted classes correspond closely to known interneuron types, allowing us to predict a large number of novel molecular markers of these classes. In addition we identified a major new interneuron population localized at the border ofstrata radiatumandlacunosum-molecularethat we term “R2C2 cells” after their characteristic combinatorial expression ofRgs12, Reln, Cxcl14, andCpne5. Several predictions of this classification scheme were verified usingin situhybridization and immunohistochemistry, providing further confidence in the gene expression patterns and novel classes predicted by the single cell data.