bluuebunny/crossref_metadata_2025_split huggingface dataset:
HiC‐3DViewer: a new tool to visualize Hi‐C data in 3D space
Authors: Djekidel Mohamed Nadhir , Wang Mengjie , Zhang Michael Q. , Gao Juntao 
Published: December 2016

BackgroundAlthough significant progress has been made to map chromatin structure at unprecedented resolution and scales, we are short of tools that enable the intuitive visualization and navigation along the three‐dimensional (3D) structure of chromatins. The available tools people have so far are generally script‐based or present basic features that do not easily enable the integration of genomic data along with 3D chromatin structure, hence, many scientists find themselves in the obligation to hack tools designed for other purposes such as tools for protein structure study.MethodsWe present HiC‐3DViewer, a new browser‐based interactive tool designed to provide an intuitive environment for investigators to facilitate the 3D exploratory analysis of Hi‐C data along with many useful annotation functionalities. Among the key features of HiC‐3DViewer relevant to chromatin conformation studies, the most important one is the 1D‐to‐2D‐to‐3D mapping, to highlight genomic regions of interest interactively. This feature enables investigators to explore their data at different levels/angels. Additionally, investigators can superpose different genomic signals (such as ChIP‐Seq, SNP) on the top of the 3D structure.ResultsAs a proof of principle we applied HiC‐3DViewer to investigate the quality of Hi‐C data and to show the spatial binding of GATA1 and GATA2 along the genome.ConclusionsAs a user‐friendly tool, HiC‐3DViewer enables the visualization of inter/intra‐chromatin interactions and gives users the flexibility to customize the look‐and‐feel of the 3D structure with a simple click. HiC‐3DViewer is implemented in Javascript and Python, and is freely available at: http://bioinfo.au.tsinghua.edu.cn/member/nadhir/HiC3DViewer/. Supplementary information (User Manual, demo data) is also available at this website.
Effect of platelet‐rich plasma on reconstruction with nerve autografts
Authors: Teymur Hakan , Tiftikcioglu Yigit Ozer , Cavusoglu Turker , Tiftikcioglu Bedile Irem , Erbas Oytun , Yigitturk Gurkan , Uyanikgil Yigit 
Published: December 2016

AbstractDespite advances in understanding of peripheral nerve injuries and regeneration and advances in surgical techniques, successful outcomes cannot be guaranteed after reconstructive surgery. Platelet‐rich plasma (PRP) has been reported to have positive effects on nerve regeneration, as well as on tissue healing. The present study was designed to evaluate the effect of PRP on nerve‐grafted defects. Sprague–Dawley rats were divided into four surgery groups (n= 7 in each). A 1‐cm long nerve defect was created in the upper thigh and then reconstructed using a nerve autograft in all groups. The wet muscle weights, electromyographic findings, and histomorphologic changes were evaluated 10 weeks later. As shown by both the electromyographic (p< 0.001) and histomorphologic findings (p< 0.001), PRP had more positive effects on nerve gap reconstruction in Group 3 then Group 4 as compared to the control groups. The present study is novel in that it evaluated the regeneration effect of PRP on a large nerve defect reconstructed with a nerve graft rather than primary repair. The results are encouraging for further experimental studies on the role of PRP in nerve healing.
Collectivism-oriented HRM and individual creative contribution: The roles of value congruence and task interdependence
Authors: Chen Silu , Zhang Guanglei , Jiang Wanxing , Shi Shengping , Liu Tao 
Published: December 2016

AbstractThis study deals with the issue whether collectivism-oriented human resource management (HRM) system influences individual creative contribution to research teams in particular in an Asia-Pacific context. It is argued that, given certain environmental factors, such as high person-organization value congruence among team members and task interdependence, the collectivism-oriented HRM system should have a positive effect on individual creative contribution to the research teams. A multi-level theoretical model is proposed accordingly, which is then tested with data from 40 research teams and 168 individuals in Chinese universities. The results demonstrated that collectivism-oriented HRM helps to enhance individual creative contribution through the path of value congruence. Moreover, the relationship between value congruence and individual creative contribution was moderated by task interdependence. These findings offer novel insight into how an organization can develop its HRM system and improve individual creative contribution in research teams.
Plasma phylloquinone, menaquinone-4 and menaquinone-7 levels and coronary artery calcification
Authors: Torii S. , Ikari Y. , Tanabe K. , Kakuta T. , Hatori M. , Shioi A. , Okano T. 
Published: December 2016

AbstractVitamin K is considered to be involved in the pathological mechanisms of coronary artery calcification (CAC). Correlation between CAC and plasma vitamin K levels was studied. A total of 103 patients, with at least one coronary risk factor, were studied. CAC was measured using 64-slice multislice computed tomography (MSCT) and divided into three groups: none (CAC score = 0; n 25), mild to moderate (0 < CAC score < 400; n 52) and severe (CAC score > 400; n 26). Phylloquinone (PK) and menaquinone (MK)-4 and MK-7 were measured by HPLC-tandem MS. Mean age of patients was 64 (sd 13) years, of which 57 % were male. Median CAC score was 57·2. Median levels of PK, MK-4 and MK-7 were 1·33, 0 and 6·99 ng/ml, showing that MK-7 was the dominant vitamin K in this population. MK-7 showed a significant inverse correlation with uncarboxylated osteocalcin (ucOC, P = 0·014), protein induced by vitamin K absence of antagonist-2 (PIVKA-2, P = 0·013), intact parathyroid hormone (P = 0·007) and bone-specific alkaline phosphatase (P = 0·018). CAC showed an inverse correlation with total circulating uncarboxylated matrix Gla protein (t-ucMGP, P = 0·018) and Hb (P = 0·05), and a positive correlation with age (P < 0·001), creatinine, collagen type 1 cross-linked N-terminal telopeptide (NTX, P = 0·03), pulse wave velocity (P < 0·001) and osteoprotegerin (P < 0·001). However, CAC did not have a significant correlation with plasma levels of PK, MK-4 or MK-7. In conclusion, plasma MK-7, MK-4 or PK level did not show significant correlation with CAC despite the association between plasma vitamin K levels and vitamin K-dependent proteins such as ucOC or PIVKA-2.
Efficacy of an SMS-Based Smoking Intervention Using Message Self-Authorship: A Pilot Study
Authors: DeStasio Krista L. , Hill Anne P. , Berkman Elliot T. 
Published: December 2016

Introduction: Text-message-based interventions hold great potential for intervention and are increasingly feasible, given advances in information technology.Aims: This pilot randomized controlled trial (RCT) aims to compare the efficacy of self-versus expert-authored content delivered via text-messaging for smoking cessation.Methods: Sixty-two participants aged 25–66 attended laboratory sessions pre- and post-30 days of text-messaging intervention. Participants were randomised to one of two experimental conditions – self-authorship (SA) only and SA with implementation intentions (SA+ii) – or active control. Participants composed 30–60 brief motivational cessation messages for use during their cessation attempt. SA+ii participants were further instructed to anticipate obstacles and form simple if-then plans to overcome them. Experimental groups received their self-authored texts during the intervention phase, whereas control participants received expert-authored messages.Results: Overall, smoking decreased as measured by change in exhaled carbon monoxide (CO), F(1,59) = 4.43, p = 0.04. The SA+ii group showed slightly greater CO reduction (M = 3.63, SD = 5.39) than control (M = 0.03, SD = 5.80; t(40) = 2.08, p = 0.04). SA alone (M = 1.97, SD = 9.30) was not more effective than control.Conclusions: SA does not appear to increase efficacy. However, this pilot supports prior research, indicating that text-based interventions can increase smoking cessation success and may decrease psychological symptoms of withdrawal. Much research is needed to identify ways to bolster intervention efficacy.
Reproductive policy and the social construction of motherhood
Authors: Stabile Bonnie 
Published: December 2016

Background. Reproductive technologies allow women to embrace or forgo motherhood, but a woman’s ability to make autonomous reproductive choices depends on access to these technologies. In the United States, public policies — laws, regulations, appropriations, and rulings — have either broadened or narrowed this access.Question. Have U.S. public policies affecting reproductive choices conformed to attitudinal distinctions about motherhood itself?Methods. I identified policies covering infertility, contraception, and abortion and examined them contextually within the Ingram-Schneider social construction framework.Findings. Women’s choices fell within social construction quadrants as being positively portrayed and powerful; negatively portrayed but powerful; positively portrayed but powerless; and negatively portrayed and powerless. Married heterosexual women embracing motherhood were likely to be viewed positively and to reap benefits. Women forgoing motherhood, poor women, and women seeking to form nontraditional families were likely to be viewed negatively and to bear burdens; critical among these burdens was restriction of access to technologies that could be used to support a decision to avoid motherhood or to achieve motherhood through nontraditional methods.Conclusion. Yes, U.S. public policies affecting reproductive choices have conformed to attitudinal distinctions about motherhood itself. These policies may also have altered those choices.
Evidence for marine redox control on spatial colonization of early animals during Cambrian Age 3 (c. 521–514 Ma) in South China
Authors: JIN CHENGSHENG , LI CHAO , ALGEO THOMAS J. , CHENG MENG , LEI LIDAN , ZHANG ZIHU , SHI WEI 
Published: December 2016

AbstractThe early Cambrian Period was a key interval in Earth history with regard to changes in both ocean chemistry and animal evolution. Although increasing ocean ventilation has been widely assumed to have played a key role in the rapid appearance, diversification and spatial colonization of early animals, this relationship is in fact not firmly established. Here, we report a high-resolution Fe-C-S-Al-Ti geochemical study of the lower Cambrian Wangjiaping section from an outer-shelf setting of the Yangtze Sea of South China. Iron speciation data document a redox transition from dominantly euxinic to ferruginous conditions during Cambrian Age 3 (c. 521–514 Ma). Interpretation of coexisting pyrite sulphur isotope (δ34Spy) records from Wangjiaping reveals relatively high marine sulphate availability at Wangjiaping. Furthermore, Wangjiaping section shows lower δ34Spy (‒2.1±5.3‰) and lower TOC (2.4±1.1%) values but higher positive correlation (R2 = 0.66, p < 0.01) between TOC and Fepy/FeHR relative to deeper sections reported previously, suggesting that euxinia developed at Wangjiaping in response to increasing marine productivity and organic matter-sinking fluxes. Our reconstructed redox conditions and fossils at Wangjiaping in comparison with previously well-studied strata in the inner-shelf Xiaotan and Shatan sections suggest that planktonic and benthic planktonic trilobites with bioturbation appeared in the oxic water columns, whereas only planktonic trilobites without bioturbation occurred within the anoxic (even euxinic) water columns during Cambrian Age 3. This finding indicates that spatial heterogeneity of redox conditions in the shelves had an important effect on early animal distribution in the Yangtze Block.
ASSESSMENT OF KNOWLEDGE, ATTITUDE AND PRACTICE TOWARDS CONSANGUINEOUS MARRIAGES AMONG A COHORT OF MULTIETHNIC HEALTH CARE PROVIDERS IN SAUDI ARABIA
Authors: Alnaqeb Dhekra , Hamamy Hanan , Youssef Amira M. , Al-Rubeaan Khalid 
Published: December 2016

SummaryThis study aimed to assess knowledge, attitude and practice related to consanguinity among multiethnic health care providers in the Kingdom of Saudi Arabia. Using a cross-sectional study design, a validated, self-administered close-ended questionnaire was randomly distributed to health care providers in different health institutions in the country between 1st August 2012 and 31st July 2013. A total of 1235 health care providers completed the study questionnaire. Of the 892 married participants (72.23% of total), 11.43% were married to a first cousin, and were predominantly Arabs, younger than 40 years and male. Only 17.80% of the patients seen by the health care providers requested consanguinity related counselling. A knowledge barrier was expressed by 27.49% of the participants, and 85.67% indicated their willingness to have more training in basic genetic counselling. A language barrier was expressed as a limiting factor to counselling for consanguinity among non-Arabs. The health care providers had a major dearth of knowledge that was reflected in their attitude and practice towards consanguinity counselling. This finding indicates the need for more undergraduate and postgraduate medical and nursing education and training in the counselling of consanguineous couples. It is recommended that consanguinity counselling is included in the current premarital screening and counselling programmes in the Kingdom.
Oligopeptidase B and B2: comparative modelling and virtual screening as searching tools for new antileishmanial compounds
Authors: SODERO ANA CAROLINA R. , DOS SANTOS ANA CAROLINA G. O. , MELLO JULIANA F. R. E , DE JESUS JÉSSICA B. , DE SOUZA ALESSANDRA M. T. , RODRIGUES MARIA ISABEL C. , DE SIMONE SALVATORE G. , RODRIGUES CARLOS R. , DE MATOS GUEDES HERBERT L. 
Published: December 2016

SUMMARYLeishmaniasis are diseases caused by parasites of the genus Leishmania and transmitted to humans by the bite of infected insects of the subfamily Phlebotominae. Current drug therapy shows high toxicity and severe adverse effects. Recently, two oligopeptidases (OPBs) were identified in Leishmania amazonensis, namely oligopeptidase B (OPB) and oligopeptidase B2 (OPB2). These OPBs could be ideal targets, since both enzymes are expressed in all parasite lifecycle and were not identified in human. This work aimed to identify possible dual inhibitors of OPB and OPB2 from L. amazonensis. The three-dimensional structures of both enzymes were built by comparative modelling and used to perform a virtual screening of ZINC database by DOCK Blaster server. It is the first time that OPB models from L. amazonensis are used to virtual screening approach. Four hundred compounds were identified as possible inhibitors to each enzyme. The top scored compounds were submitted to refinement by AutoDock program. The best results suggest that compounds interact with important residues, as Tyr490, Glu612 and Arg655 (OPB numbers). The identified compounds showed better results than antipain and drugs currently used against leishmaniasis when ADMET in silico were performed. These compounds could be explored in order to find dual inhibitors of OPB and OPB2 from L. amazonensis.
Challenges to the Independence of the International Judiciary: Reflections on the International Court of Justice
Authors: KEITH KENNETH J. 
Published: December 2016

AbstractThe International Court of Justice and other international tribunals have a much more prominent role in settling international disputes than they did 50 years ago. It follows that the measures for the protection of the independence of the institutions and their members are even more important. Those protections include the qualifications judges are to have, the methods of their election and selection, their commitment to their responsibilities, and their methods of work. Also important are the reactions to their decisions by states, particularly the parties, the wider international community and the contribution of the rulings of the institutions to the clarification of the law and its development.
Adolescent cannabis use, change in neurocognitive function, and high-school graduation: A longitudinal study from early adolescence to young adulthood
Authors: Castellanos-Ryan Natalie , Pingault Jean-Baptiste , Parent Sophie , Vitaro Frank , Tremblay Richard E. , Séguin Jean R. 
Published: December 2016

AbstractThe main objective of this prospective longitudinal study was to investigate bidirectional associations between adolescent cannabis use (CU) and neurocognitive performance in a community sample of 294 young men from ages 13 to 20 years. The results showed that in early adolescence, and prior to initiation to CU, poor short-term and working memory, but high verbal IQ, were associated with earlier age of onset of CU. In turn, age of CU onset and CU frequency across adolescence were associated with (a) specific neurocognitive decline in verbal IQ and executive function tasks tapping trial and error learning and reward processing by early adulthood and (b) lower rates of high-school graduation. The association between CU onset and change in neurocognitive function, however, was found to be accounted for by CU frequency. Whereas the link between CU frequency across adolescence and change in verbal IQ was explained (mediated) by high school graduation, the link between CU frequency and tasks tapping trial and error learning were independent from high school graduation, concurrent cannabis and other substance use, adolescent alcohol use, and externalizing behaviors. Findings support prevention efforts aimed at delaying onset and reducing frequency of CU.
E2-25K SUMOylation inhibits proteasome for cell death during cerebral ischemia/reperfusion
Authors: Jeong Eun Il , Chung Hae Won , Lee Won Jea , Kim Seo-Hyun , Kim Hyunjoo , Choi Seon-Guk , Jung Yong-Keun 
Published: December 2016

AbstractCerebral ischemia/reperfusion (I/R) causes brain damage accompanied by ubiquitin accumulation and impairment of proteasome activity. In this study, we report that E2-25K, an E2-conjugating enzyme, is SUMOylated during oxidative stress and regulates cerebral I/R-induced damage. Knockdown of E2-25K expression protects against oxygen/glucose deprivation and reoxygenation (OGD/R)-induced neuronal cell death, whereas ectopic expression of E2-25K stimulates it. Compared with the control mice, cerebral infarction lesions and behavioral/neurological disorders are ameliorated in E2-25K knockout mice during middle cerebral artery occlusion and reperfusion. In particular, E2-25K is SUMOylated at Lys14 under oxidative stress, OGD/R and I/R to prompt cell death. Further, E2-25K downregulates the proteasome subunit S5a to impair proteasome complex and thus restrain proteasome activity under oxidative stress. This proteasome inhibitory activity of E2-25K is dependent on its SUMOylation. These results suggest that E2-25K has a crucial role in oxidative stress and cerebral I/R-induced damage through inhibiting proteasome via its SUMOylation.
Unrestrained AMPylation targets cytosolic chaperones and activates the heat shock response
Authors: Truttmann Matthias C. , Zheng Xu , Hanke Leo , Damon Jadyn R. , Grootveld Monique , Krakowiak Joanna , Pincus David , Ploegh Hidde L. 
Published: December 2016

Significance
The stability of the proteome is essential to cellular and organismic health and lifespan. To maintain proteostasis, cells are equipped with a network of chaperones that support folding of nascent proteins, as well as refolding of unfolded or misfolded proteins. Aging and age-associated diseases progressively increase the accumulation of misfolded, damaged, and aggregated proteins, thus taxing the chaperoning machinery to its limits. Here, we describe how AMPylation of cytosolic heat shock proteins (HSP) leads to a collapse of proteostasis, the induction of a strong heat shock response, inhibition of translation, as well as the formation of protein aggregates. AMPylation-mediated inhibition of HSP70 may represent a strategy for targeted ablation of this chaperone.
Who wins the championship? Market value and team composition as predictors of success in the top European football leagues
Authors: Gerhards Jürgen , Mutz Michael 
Published: December 2016

ABSTRACT
Processes of commercialisation and globalisation have changed professional football and the composition of football teams fundamentally. Against the background of these shifting conditions we investigate to what extent the success of football teams in their national leagues is determined by: (a) the monetary value of the team expressed in its market value, (b) the inequality within the team, (c) the cultural diversity of the team, and (d) the degree of fluctuation among the team members. The empirical analysis refers to five football seasons, spanning from 2011/2012 until 2015/2016, and includes the twelve most important European football leagues. The findings demonstrate that success in national football championships is highly predictable. The market value of a team is by far the most important single predictor, whereas different features of a team's composition – inequality, cultural diversity, and fluctuation – are less decisive. However, the market value of a team does not play the same role in all of the leagues. The lower the degree of financial inequality in a league, the lower the impact of the market value on teams’ performance.
Ex Vivo Model to Decipher the Impact of Extracorporeal Membrane Oxygenation on Beta-lactam Degradation Kinetics
Authors: Leven Cyril , Fillâtre Pierre , Petitcollin Antoine , Verdier Marie-Clémence , Laurent Jérôme , Nesseler Nicolas , Launey Yoann , Tattevin Pierre , Bellissant Eric , Flécher Erwan , Lemaitre Florian 
Published: December 2016

Background:
As a consequence of drug sequestration, increase in volume of distribution, or alteration of elimination, extracorporeal membrane oxygenation (ECMO) might lead to inadequate plasma concentrations of vital drugs. The aim of this experimental study was to develop an ex vivo model to better characterize the impact of ECMO procedure on beta-lactam antibiotics pharmacokinetics.

Methods:
Plasma concentrations of cefotaxime, ceftazidime, cefepime, piperacillin, oxacillin, amoxicillin, and ceftriaxone were measured in an ex vivo ECMO circuit primed with whole human blood and compared with controls stored in glass tubes and polyvinyl chloride tubing. Serial blood samples were collected over 48 hours, and the concentrations of beta-lactam antibiotics were quantified using a validated high-performance liquid chromatography assay. The concentrations' decay rate over time was compared between the ECMO circuits and controls using nonlinear mixed-effect modeling.

Results:
Cefotaxime concentrations decreased markedly: 86% of the initial concentration remained after 4 hours and only 21% after 48 hours (P < 0.05 for the comparison in rate of decrease with both glass and polyvinyl chloride controls). There was no difference in the rate of decrease between ECMO circuit and controls for the other beta-lactam antibiotics. The average drug recoveries from the ECMO circuits at 48 hours were as follows: ceftazidime, 73%; cefepime, 67%; piperacillin, 71%; oxacillin, 46%; and amoxicillin, 72%. Concentrations of ceftriaxone remained stable throughout the 48-hour study both in ECMO circuits and in controls.

Conclusions:
Significant losses of cefotaxime were observed, whereas ceftazidime, cefepime, piperacillin, oxacillin, and amoxicillin decrease was moderate and similar to that of the control group, and ceftriaxone concentrations remained unchanged. These results are reassuring for the use of beta-lactam antibiotics in critically ill patients treated with ECMO.