bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock
Authors: Alam Nawsad , Goldstein Oriel , Xia Bing , Porter Kathryn A. , Kozakov Dima , Schueler-Furman Ora 
Published: August 2017

AbstractPeptide-protein interactions contribute a significant fraction of the protein-protein interactome. Accurate modeling of these interactions is challenging due to the vast conformational space associated with interactions of highly flexible peptides with large receptor surfaces. To address this challenge we developed a fragment based high-resolution peptide-protein docking protocol. By streamlining the Rosetta fragment picker for accurate peptide fragment ensemble generation, the PIPER docking algorithm for exhaustive fragment-receptor rigid-body docking and Rosetta FlexPepDock for flexible full-atom refinement of PIPER docked models, we successfully addressed the challenge of accurate and efficient global peptide-protein docking at high-resolution with remarkable accuracy. Validation on a representative set of solved peptide-protein complex structures demonstrates the accuracy and robustness of our approach, and opens up the way to high-resolution modeling of many more peptide-protein interactions and to the detailed study of peptide-protein association in general. PIPER-FlexPepDock is freely available to the academic community as a server athttp://piperfpd.furmanlab.cs.huji.ac.il.
Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line
Authors: Nattestad Maria , Goodwin Sara , Ng Karen , Baslan Timour , Sedlazeck Fritz J. , Rescheneder Philipp , Garvin Tyler , Fang Han , Gurtowski James , Hutton Elizabeth , Tseng Elizabeth , Chin Chen-Shan , Beck Timothy , Sundaravadanam Yogi , Kramer Melissa , Antoniou Eric , McPherson John D. , Hicks James , McCombie W. Richard , Schatz Michael C. 
Published: August 2017

AbstractThe SK-BR-3 cell line is one of the most important models for HER2+ breast cancers, which affect one in five breast cancer patients. SK-BR-3 is known to be highly rearranged although much of the variation is in complex and repetitive regions that may be underreported. Addressing this, we sequenced SK-BR-3 using long-read single molecule sequencing from Pacific Biosciences, and develop one of the most detailed maps of structural variations (SVs) in a cancer genome available with nearly 20,000 variants present, most of which were missed by prior efforts. Surrounding the important HER2 locus, we discover a complex sequence of nested duplications and translocations, suggesting a punctuated progression. Full-length transcriptome sequencing further revealed several novel gene fusions within the nested genomic variants. Combining long-read genome and transcriptome sequencing enables an in-depth analysis of how SVs disrupt the transcriptome and sheds new light on the complexity of cancer progression.
Level of awareness among veterinary students of GADVASU towards plagiarism: a case study
Authors: Singh Nirmal 
Published: August 2017

Purpose
Plagiarism is wrecking the academic spheres all around the world. The internet is accused for causing exponential increase in plagiarism. This paper aims to examine the prevalence of plagiarism among veterinary students and assess the impact of the internet on their plagiarism practices, so that the corrective measures can be suggested to ensure the originality of academic and research work.

Design/methodology/approach
A survey of undergraduate and postgraduate students of veterinary science was conducted at Guru Angad Dev Veterinary & Animal Sciences University (GADVASU), Ludhiana using questionnaire as data collection tool. The responses of total 147 students have been analysed using percentage calculations and mean values. The t-test has been applied using SPSS-16 to find the significance of difference in the plagiarism practiced by students using the internet and print sources of information.

Findings
Results revealed the prevalence of plagiarism among both groups of students. There was no significant difference in the frequency level of plagiarism among UG and PG students using both the internet and print sources of information, advocating that the internet has not influenced the plagiarism frequency of students.

Originality/value
This is the first known attempt to examine the plagiarism habits of veterinary students.
Corporate social responsibility, visibility, reputation and financial performance: empirical analysis on the moderating and mediating variables from Korea
Authors: Park SeHyun 
Published: August 2017

PurposeThis paper aims to substantiate the mechanism through which corporate social responsibility (CSR) affects financial performance (FP). Specifically, this paper focuses on the moderating effect of visibility and mediating effect of reputation in the relationship.Design/methodology/approachThis paper investigates 175 Korean firms from 2010 to 2012 that have been listed in the Korean Economic Justice Index for all three years. The hypotheses are tested using various measures of visibility and the Korea’s Most Admired Company index as proxy for reputation. The logistics regression and the ordinary least square are used.FindingsThis paper initially demonstrates that the visibility moderates the correlation between CSR and reputation. On this finding, it further proves that CSR has positive effect on the long-run FP, measured in the Tobin’s Q, both directly and indirectly through reputation. However, the influence is irrelevant in the short run. In sum, visibility moderates the correlation between CSR and reputation, which mediates the CSR-FP relationship in the long run.Practical implicationsThis paper argues for the importance of visibility in practicing CSR, especially when reputation building and financial benefit is sought through CSR.Originality/valueDespite its strategic importance, the visibility of CSR has not been sufficiently studied. Moreover, as scholars have recently suggested that the CSR–FP relationship is rather indirect, there is even more significance in investigating the moderating and mediating variable. Hence, with the intuitive results, this paper lays an integral foundation in the literature.
Ownership and corporate social responsibility in Indian firms
Authors: Panicker Vidya Sukumara 
Published: August 2017

PurposeThe purpose of this paper is to look at the association between different ownership categories and corporate social responsibility (CSR) spending of selected Indian firms.Design/methodology/approachRandom-effects Tobit panel regression is performed on a panel of 4,388 firm years of 1,722 unique firms over a three-year period (2014-2016).FindingsDifferent categories of institutional investors have different preferences for CSR spending of a firm. Promoters of business-group affiliated and unaffiliated firms also behave differently towards CSR activities of their firms.Research limitations/implicationsHeterogeneous behavior of institutional investors is revealed through the study. Foreign institutions and domestic banks are supportive of CSR investments of a firm. Promoters of family firms and group affiliates also diligently plan CSR activities.Practical implicationsManagers cannot ignore the heterogeneities of institutional investors in their investment decisions. Individual investors can align their philanthropic preferences with those of different types of institutional investors or firms.Social implicationsFamily-owned firms play a significant role in CSR activities of emerging economies, while individual promoters are not as attracted by the reputational prospects of CSR.Originality/valueThis paper considers the role of heterogeneities of institutional investors in influencing CSR spending of emerging-economy firms. This heterogeneity has not been previously studied in this context.
Development, validation and reproducibility of a food frequency questionnaire to measure flavonoid intake in older Australian adults
Authors: Kent Katherine , Charlton Karen E. 
Published: August 2017

AimTo develop and assess the validity and reproducibility of a food frequency questionnaire (FFQ) to measure total flavonoid intake, and individual flavonoid subclasses, in older adults.MethodsRetrospective analysis of flavonoid intake in older adults informed the development of a FFQ to measure flavonoid intake and determine the flavonoid subclasses consumed (anthocyanins, flavan‐3‐ols, flavones, flavonols and flavanones). Older adults (n = 42, mean age 75.3 ± 8.6 years) attended two interviews 1 month apart where anthropometrics (height and weight), blood pressure (BP), demographic data and a 93‐item self‐administered FFQ were collected. A 4‐day food record (FR) was randomly administered between the two interview dates, and each food item was assigned a flavonoid and flavonoid subclass content using the United States Department of Agriculture flavonoid database. The criterion validity and reproducibility of the FFQ was assessed against a 4‐day FR using the Wilcoxon signed‐rank sum test, Spearman's correlation coefficient (r), Bland‐Altman Plots and Cohen's kappa.ResultsTotal flavonoid intake was determined (median intake FFQ = 919.3 mg/day, FR = 781.4 mg/day). Tests of validity indicated that the FFQ consistently overestimated total flavonoid intake compared with the 4‐day FR. There was a significant difference in estimates between the FFQ and the 4‐day FR for total flavonoid intake (Wilcoxon signed‐rank sum P < 0.001; Bland‐Altman plots indicated large bias and wide limits of agreement), but they were well correlated (Spearman's r 0.93, P < 0.001; Cohen's kappa κ = 0.619, P < 0.001). For individual flavonoid subclasses, the tests of validity indicated greater discrepancy compared with 4‐day FR. The FFQ showed high reproducibility for estimating total flavonoid intake (FFQ1vsFFQ2: Wilcoxon signed‐rank sum test, P > 0.05; Spearman's r 0.91, P < 0.001; Bland‐Altman plots visually showed small, non‐significant bias and wide limits of agreement; and Cohen's kappa κ = 0.619, P < 0.001), with a small mean percentage difference (6.7%). For individual flavonoid subclasses, the tests of reproducibility between FFQ1 and FFQ2 showed similarly high reproducibility.ConclusionsThe developed FFQ appears suitable for satisfactorily ranking individuals according to total flavonoid intake. The FFQ shows limitations for estimating absolute total flavonoid intake and intake of flavonoid subclasses in comparison to a 4‐day FR in terms of overestimating intake. Refinement and further validation of this tool may be required.
Effects of adults body size and larvae diet on the fecundity and percent fertility of eggs laid by Xylotrechus arvicola (Coleoptera: Cerambycidae) females, insect pest in Spanish vineyards
Authors: Rodríguez‐González Álvaro , Peláez Horacio J. , González‐López Óscar , Mayo Sara , Casquero Pedro A. 
Published: August 2017

AbstractXylotrechus arvicola is a pest of grape in some vine‐producing regions of the Iberian Peninsula. Biological parameters and relationships (fecundity and percent fertility of eggs in relationship to body size) of females obtained in the laboratory and captured in vineyards were studied. In laboratory conditions, the mean developmental time of larvae ranged from 384 to 392 days and pupal stage varied between 12 to 14 days. Body size (BS) of X. arvicola females was significantly bigger than males. Fecundity was greater in the laboratory (147 eggs) than in the field (50 eggs) females, but the percent fertility of the laboratory eggs was lower (16 eggs). Laboratory females showed a bigger relationship between the production of eggs and BS than females captured in vineyards. Wild females (PDO Ribera del Duero and Tierra de León) had a positive relationship between the percent fertility of eggs and the BS. No correlation between the percent fertility of eggs and the BS was displayed by females captured in PDO Toro, but these females had a higher percent fertility (53 eggs) than the others PDO's. These biological parameters and relationships studied suggest that the artificial diet may lack certain essential nutrients that vine varieties can provide that favor the fertility of eggs. This explains why wild females have the potential to become a problem pest in the Tempranillo grape variety, with bilateral cordon and bush vines training systems that have the highest incidence of this cerambycid.
Identification and elucidation of in vivo function of two alanine racemases from Pseudomonas putida KT2440
Authors: Duque Estrella , Daddaoua Abdelali , Cordero Baldo F. , De la Torre Jesús , Antonia Molina‐Henares Maria , Ramos Juan‐Luis 
Published: August 2017

SummaryThe genome of Pseudomonas putida KT2440 contains two open reading frames (ORFs), PP_3722 and PP_5269, that encode proteins with a Pyridoxal phosphate binding motif and a high similarity to alanine racemases. Alanine racemases play a key role in the biosynthesis of D‐alanine, a crucial amino acid in the peptidoglycan layer. For these ORFs, we generated single and double mutants and found that inactivation of PP_5269 resulted in D‐alanine auxotrophy, while inactivation of PP_3722 did not. Furthermore, as expected, the PP_3722/PP_5269 double mutant was a strict auxotroph for D‐alanine. These results indicate that PP_5269 is an alr allele and that it is the essential alanine racemase in P. putida. We observed that the PP_5269 mutant grew very slowly, while the double PP_5269/PP_3722 mutant did not grow at all. This suggests that PP_3722 may replace PP_5269 in vivo. In fact, when the ORF encoding PP_3772 was cloned into a wide host range expression vector, ORF PP_3722 successfully complemented P. putida PP_5269 mutants. We purified both proteins to homogeneity and while they exhibit similar KM values, the Vmax of PP_5269 is fourfold higher than that of PP_3722. Here, we propose that PP_5269 and PP_3722 encode functional alanine racemases and that these genes be named alr‐1 and alr‐2 respectively.
Antidote to cannabinoid intoxication: the CB1 receptor inverse agonist, AM251, reverses hypothermic effects of the CB1 receptor agonist, CB‐13, in mice
Authors: Pryce Gareth , Baker David 
Published: August 2017

Background and PurposeCannabis is a recreational drug leading to intoxication, following stimulation of cannabinoid CB1 receptors. However, more recently, herbs mixed with synthetic cannabinoids sometimes known as ‘Spice’ and ‘Black Mamba’ have been increasingly used, and their high CB1 receptor affinity has led not only to marked intoxication but also life‐threatening complications and an increasing number of deaths. Although many studies have indicated that prophylactic treatment with CB1 receptor antagonists can block cannabimimetic effects in animals and humans, the aim of this study was to determine whether CB1 receptor antagonism could reverse physical cannabimimetic effects.Experimental ApproachCannabimimetic effects, measured by the hypothermic response following sedation and hypomotility, were induced by the synthetic CB1 receptor agonist CB‐13 (1‐naphthalenyl[4‐(pentyloxy)‐1‐naphthalenyl]methanone) in Biozzi Antibody High mice. The CB1 receptor antagonist/inverse agonist AM251 (N‐(piperidin‐1‐yl)‐5‐(4‐iodophenyl)‐1‐(2, 4‐dichlorophenyl)‐4‐methyl‐1H‐pyrazole‐3‐carboxamide) was administered 20 min after the injection of CB‐13 and its effects on the cannabimimetic responses were assessed.Key ResultsIn this study, the CNS‐related cannabimimetic effects, as measured by the hypothermic effect, induced by the CB1 receptor agonist were therapeutically treated and were rapidly reversed by the CB1 receptor antagonist/inverse agonist. There was also a subjective reversal of visually evident sedation.Conclusions and ImplicationsCannabinoid receptor antagonists have been widely used and so may provide an acceptable single‐dose antidote to cannabinoid intoxication. This use may save human life, where the life‐threatening effects are mediated by cannabinoid receptors and not off‐target influences of the synthetic cannabinoids or non‐cannabinoids within the recreational drug mixture.
Parental Cultural Socialization and Adolescent Private Regard: Exploring Mediating Pathways Through Daily Experiences
Authors: Wang Yijie , Cham Heining , Aladin Meera , Yip Tiffany 
Published: August 2017

Using longitudinal experience sampling data from 214 ethnic/racial minority adolescents (Wave 1 Mage = 15.24), the present study investigated how the longitudinal effect of parental cultural socialization on adolescent private regard was mediated through various daily pathways and novel constructs. Both the mean levels and variability of adolescents' ethnic feelings (i.e., private regard) and social interactions (i.e., intragroup contact) in daily situations, as well as the situational association between intragroup contact and private regard, emerged as mediators. Greater cultural socialization promoted greater and more stable ethnic feelings and interactions, as well as their situational association, all of which promoted private regard over time. This study provides a framework to explore how development occurs in daily lives.
For Better or for Worse? Positive and Negative Parental Influences on Young Children's Executive Function
Authors: Hughes Claire , Devine Rory T. 
Published: August 2017

Despite rapidly growing research on parental influences on children's executive function (EF), the uniqueness and specificity of parental predictors and links between adult EF and parenting remain unexamined. This 13‐month longitudinal study of 117 parent–child dyads (60 boys; Mage at Time 1 = 3.94 years, SD = 0.53) included detailed observational coding of parent–child interactions and assessed adult and child EF and child verbal ability (VA). Supporting a differentiated view of parental influence, negative parent–child interactions and parental scaffolding showed unique and specific associations with child EF, whereas the home learning environment and parental language measures showed global associations with children's EF and VA.
Leaving like an Englishman: Assisting institutional reform in post‐communist Ukraine
Authors: Leitch Duncan 
Published: August 2017

AbstractScholars of Development Studies have largely distanced themselves from research into external advice on governance reform in Ukraine, regarding post‐communist reconstruction as a political rather than developmental project. This article suggests that these seemingly distinct fields of donor intervention have more in common than is usually thought. It examines the influence of external advice on an issue which has particular resonance in the light of recent events in Ukraine, the relationship between Kyiv and the regions. It is argued that the impact of international assistance in this area has been negligible, largely due to institutional factors on the donor side, and that the most persuasive explanations for this are to be found in the literature of Development Studies.
Opportunities and challenges for modelling epidemiological and evolutionary dynamics in a multihost, multiparasite system: Zoonotic hybrid schistosomiasis in West Africa
Authors: Borlase Anna , Webster Joanne P. , Rudge James W. 
Published: August 2017

AbstractMultihost multiparasite systems are evolutionarily and ecologically dynamic, which presents substantial trans‐disciplinary challenges for elucidating their epidemiology and designing appropriate control. Evidence for hybridizations and introgressions between parasite species is gathering, in part in line with improvements in molecular diagnostics and genome sequencing. One major system where this is becoming apparent is within the GenusSchistosoma, where schistosomiasis represents a disease of considerable medical and veterinary importance, the greatest burden of which occurs in sub‐Saharan Africa. Interspecific hybridizations and introgressions bring an increased level of complexity over and above that already inherent within multihost, multiparasite systems, also representing an additional source of genetic variation that can drive evolution. This has the potential for profound implications for the control of parasitic diseases, including, but not exclusive to, widening host range, increased transmission potential and altered responses to drug therapy. Here, we present the challenging case example of haematobium groupSchistosomaspp. hybrids in West Africa, a system involving multiple interacting parasites and multiple definitive hosts, in a region where zoonotic reservoirs of schistosomiasis were not previously considered to be of importance. We consider how existing mathematical model frameworks for schistosome transmission could be expanded and adapted to zoonotic hybrid systems, exploring how such model frameworks can utilize molecular and epidemiological data, as well as the complexities and challenges this presents. We also highlight the opportunities and value such mathematical models could bring to this and a range of similar multihost, multi and cross‐hybridizing parasites systems in our changing world.
High‐Growth Firms in the Southern U.S.: Where is the Growth?
Authors: Kalafsky Ronald V. , Rice Murray D. 
Published: August 2017

AbstractPolicymakers across the Southern U.S. have directed considerable attention to regional economic development plans, with mixed results. Questions remain over what types of industries, firms, and/or policies can drive long‐range growth. Over the past two decades, researchers have started to focus on high‐growth firms (HGFs) due to their potential innovation spillovers and job creation prospects, both of which drive further economic development. Employing databases from the Inc. 500, this study explores the dynamics of HGFs within Southern and comparative contexts. The first goal of this paper is to explore Southern HGF activity in comparison with the U.S. at‐large. The second is to examine the geographical characteristics of HGFs within the South, which will include an exploration of locations, industrial mix, and the factors that could encourage HGF development and agglomeration. This paper will also analyze the longer‐term ownership and acquisition patterns of HGFs across the South. Are such firms remaining embedded in the South or moving elsewhere through mergers or acquisitions? The paper concludes with a discussion of the impacts of HGFs on regional economic development and moreover, whether existing policies are conducive to these firms.
Simple Tests Compare Well with a Hand‐held Audiometer for Hearing Loss Screening in Primary Care
Authors: Strawbridge William J. , Wallhagen Margaret I. 
Published: August 2017

ObjectivesTo compare hearing loss screening results of four simple tests with those of hand‐held audiometry.DesignCross‐sectional study of individuals screened during intake for physicals and other routine procedures.SettingTwo primary care clinics in the San Francisco Bay area.ParticipantsOlder adults not wearing hearing aids (N = 125, mean age 72.9, 63% female).MeasurementsDirect question about hearing loss, indirect question, finger‐rub test, whisper test, and audiometric results using a hand‐held audiometer.ResultsSensitivity was 91% for the finger‐rub test compared with 89% for the direct question, 85% for the indirect question, and 79% for the whisper test. For specificity, the whisper test was highest, followed by the finger rub, indirect, and direct.ConclusionSimple screening procedures can be used to identify older adults with hearing loss in primary care and facilitate early referral for additional testing and treatment.