bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inference of the worldwide invasion routes of the pinewood nematodeBursaphelenchus xylophilususing approximate Bayesian computation analysis
Authors: Mallez Sophie , Castagnone Chantal , Lombaert Eric , Castagnone-Sereno Philippe , Guillemaud Thomas 
Published: October 2018

AbstractPopulation genetics have been greatly beneficial to improve knowledge about biological invasions. Model-based genetic inference methods, such as approximate Bayesian computation (ABC), have brought this improvement to a higher level and are now essential tools to decipher the invasion routes of any invasive species. In this paper, we performed ABC random forest analyses to shed light on the pinewood nematode (PWN) worldwide invasion routes and to identify the source of European populations. Originating from North America, this microscopic worm has been invading Asia since 1905 and Europe since 1999, causing tremendous damage on pine forests. Using microsatellite data, we demonstrated the existence of multiple introduction events in Japan (at least two involving individuals originating from the USA) and China (one involving individuals originating from the USA and one involving individuals originating from Japan). We also found that Portuguese samples had a Japanese origin. We observed some discrepancies between descriptive genetic methods and the ABC method, which are worth investigating and are discussed here. The ABC method helped clarify the worldwide history of the PWN invasion, even though the results still need to be considered with some caution because the features of the PWN and the genetic markers used probably push the ABC method to its very limits.
Directed evolution of split APEX peroxidase
Authors: Han Yisu , Martell Jeffrey D. , Branon Tess C. , Boassa Daniela , Shechner David M. , Ellisman Mark H. , Ting Alice Y. 
Published: October 2018

AbstractAPEX is an engineered peroxidase that catalyzes the oxidation of a wide range of substrates, facilitating its use in a variety of applications, from subcellular staining for electron microscopy to proximity biotinylation for spatial proteomics and transcriptomics. To further advance the capabilities of APEX, we used directed evolution to engineer a split APEX tool (sAPEX). Twenty rounds of FACS-based selections from yeast-displayed fragment libraries, using three different yeast display configurations, produced a 200-amino acid N-terminal fragment (with 9 mutations relative to APEX2) called “AP” and a 50-amino acid C-terminal fragment called “EX”. AP and EX fragments were each inactive on their own but reconstituted to give peroxidase activity when driven together by a molecular interaction. We demonstrate sAPEX reconstitution in the mammalian cytosol, on engineered RNA motifs within telomerase noncoding RNA, and at mitochondria-endoplasmic reticulum contact sites.
Oxidation-induced destabilization of the fibrinogenαC-domain dimer investigated by molecular dynamics simulations
Authors: Pederson Eric N. , Interlandi Gianluca 
Published: October 2018

AbstractUpon activation, fibrinogen is converted to insoluble fibrin, which assembles into long strings called protofibrils. These aggregate laterally to form a fibrin matrix that stabilizes a blood clot. Lateral aggregation of protofibrils is mediated by theαC domain, a partially structured fragment located in a disordered region of fibrinogen. Polymerization ofαC domains links multiple fibrin molecules with each other enabling the formation of thick fibrin fibers and a fibrin matrix that is stable but can also be digested by enzymes. How-ever, oxidizing agents produced during the inflammatory response have been shown to cause thinner fibrin fibers resulting in denser clots, which are harder to proteolyze and pose the risk of deep vein thrombosis and lung embolism. It has been postulated that oxidation of Met476located within theαC domain hinders its ability to polymerize disrupting the lateral aggregation of protofibrils and leading to the observed thinner fibers. HowαC domains assemble into polymers is still unclear and yet this knowledge would shed light on the mechanism through which oxidation weakens the lateral aggregation of protofibrils. This study used temperature replica exchange molecular dynamics simulations to investigate theαC-domain dimer and how this is affected by oxidation of Met476. The results suggest that multiple binding modes between two alphaC domains can occur and that oxidation decreases the likelihood of dimer formation. Furthermore, the side chain of Met476acts as a docking spot betweenαC domains and this function is abrogated by its conversion to methionine sulfoxide.
Anti-tumor effects of antimicrobial peptides, targets of the innate immune system, against hematopoietic tumors inDrosophila mxcmutants
Authors: Araki Mayo , Awane Rie , Sato Tetsuya , Ohkawa Yasuyuki , Inoue Yoshihiro H. 
Published: October 2018

AbstractThe innate immune response is the first line of defense against microbial infections. InDrosophila, three immune pathways induce the synthesis of antimicrobial peptides (AMPs) in the fat body. Recently, it has been reported that certain cationic AMPs exhibit selective cytotoxicity against human cancer cells. However, little is known about their anti-tumor effects.Drosophila mxcmbn1mutants exhibit malignant hyperplasia in a larval hematopoietic organ called the lymph gland (LG). Here, using RNA-Seq analysis, we found that many immunoresponsive genes, including AMP genes, were up-regulated in the mutants. Down-regulation of these pathways by either aTollor animdmutation enhanced the tumor phenotype of themxcmutants. Conversely, ectopic expression of each of five different AMPs in the fat body significantly suppressed the LG hyperplasia phenotype in the mutants. Thus, we propose that theDrosophilainnate immune system can suppress progression of hematopoietic tumors by inducing AMP gene expression. Overexpression of any one of these five AMPs resulted in enhanced apoptosis in the mutant LGs, while no apoptosis signals were detected in controls. We observed that two AMPs, Drosomycin and Defensin, were taken up by circulating hemocyte-like cells, which were associated with LG regions showing reduced cell-to-cell adhesion in the mutants; another AMP, diptericin, was directly localized on the tumors without intermediating hemocytes. These results lead us to conclude that the AMPs have a specific cytotoxic effect that enhance apoptosis exclusively in the tumor cells.Summary statement:Antimicrobial peptides can be associated with tumor cells generated in a hematopoietic tissue inDrosophila mxcmutants and have an anti-tumor effect in suppressing their growth.
Divalent cations can control a switch-like behavior in heterotypic and homotypic RNA coacervates
Authors: Onuchic Paulo L. , Milin Anthony N. , Alshareedah Ibraheem , Deniz Ashok A. , Banerjee Priya R. 
Published: October 2018

AbstractLiquid-liquid phase separation (LLPS) of RNA-protein complexes plays a major role in the cellular function of membraneless organelles (MLOs). MLOs are sensitive to changes in cellular conditions, such as fluctuations in cytoplasmic ion concentrations. To investigate the effect of these changes on MLOs, we studied the influence of divalent cations on the physical and chemical properties of RNA coacervates. Using a model arginine-rich peptide-RNA system, we predicted and observed that variations in signaling cations exert interaction-dependent effects on RNA LLPS. Changing the ionic environment has opposing effects on the propensity for heterotypic peptide-RNA and homotypic RNA LLPS, which results in a switch between coacervate types. Furthermore, divalent ion variations continuously tune the microenvironments and fluid properties of heterotypic and homotypic droplets. Our results may provide a generic mechanism for modulating the biochemical environment of RNA coacervates in a cellular context.
Increasing the Capping Efficiency of the Sindbis Virus nsP1 Protein Negatively Affects Viral Infection
Authors: LaPointe Autumn T. , Moreno-Contreras Joaquín , Sokoloski Kevin J. 
Published: October 2018

AbstractAlphaviruses are arthropod-borne RNA viruses that are capable of causing severe disease and are a significant burden to public health. Alphaviral replication results in the production of both capped and noncapped viral genomic RNAs, which are packaged into virions during the infections of vertebrate and invertebrate cells. However, the roles that the noncapped genomic RNAs (ncgRNAs) play during alphaviral infection have yet to be exhaustively characterized. Here, the importance of the ncgRNAs to alphaviral infection was assessed by using mutants of the nsP1 protein of Sindbis virus (SINV), which altered the synthesis of the ncgRNAs during infection by modulating the protein’s capping efficiency. Specifically, point mutants at residues Y286A and N376A decreased capping efficiency, while a point mutant at D355A increased the capping efficiency of the SINV genomic RNA during genuine viral infection. Viral growth kinetics were significantly reduced for the D355A mutant relative to wild type infection, whereas the Y286A and N376A mutants showed modest decreases in growth kinetics. Overall genomic translation and nonstructural protein accumulation was found to correlate with increases and decreases in capping efficiency. However, genomic, minus strand, and subgenomic viral RNA synthesis was largely unaffected by the modulation of alphaviral capping activity. In addition, translation of the subgenomic vRNA was found to be unimpacted by changes in capping efficiency. The mechanism by which decreased presence of ncgRNAs reduced viral growth kinetics was through the impaired production of viral particles. Collectively, these data illustrate the importance of ncgRNAs to viral infection and suggests that they play in integral role in the production of viral progeny.ImportanceAlphaviruses have been the cause of both localized outbreaks and large epidemics of severe disease. Currently, there are no strategies or vaccines which are either safe or effective for preventing alphaviral infection or treating alphaviral disease. This deficit of viable therapeutics highlights the need to better understand the mechanisms behind alphaviral infection in order to develop novel antiviral strategies for alphaviral disease. In particular, this study details a previously uncharacterized aspect of the alphaviral life cycle, the importance of noncapped genomic viral RNAs to alphaviral infection. This offers new insights into the mechanisms of alphaviral replication and the impact of the noncapped genomic RNAs on viral packaging.
Mortality in trauma patients admitted during, before, and after national academic emergency medicine and trauma surgery meeting dates in Japan
Authors: Yumoto Tetsuya , Naito Hiromichi , Ihoriya Hiromi , Yorifuji Takashi , Nakao Atsunori 
Published: October 2018

AbstractAnnually, many physicians attend national academic meetings. While participating in these meetings can have a positive impact on daily medical practice, attendance may result in reduced medical staffing during the meeting dates. We sought to examine whether there were differences in mortality after trauma among patients admitted to the hospital during, before, and after meeting dates. Using the Japan Trauma Data Bank, we analyzed in-hospital mortality in patients with traumatic injury admitted to the hospital from 2004 to 2015 during the dates of two national academic meetings - the Japanese Association for Acute Medicine (JAAM) and the Japanese Association for the Surgery of Trauma (JAST). We compared the data with that of patients admitted with trauma during identical weekdays in the weeks before and after the meetings, respectively. We used multiple logistic regression analysis to compare outcomes among the three groups. A total of 7,491 patients were included in our analyses, with 2,481, 2,492, and 2,518 patients in the during, before, and after meeting dates groups, respectively; their mortality rates were 7.3%, 8.0%, and 8.5%, respectively. After adjusting for covariates, no significant differences in in-hospital mortality were found among the three groups (adjusted odds ratio [95% CI] of the before meeting dates and after meeting dates groups; 1.18 [0.89-1.56] and 1.23 [0.93-1.63], respectively, with the during meeting dates group as the reference category). No significant differences in in-hospital mortality were found among trauma patients admitted during, before, and after the JAAM and JAST meeting dates.
How important is the transitional yield (t-yield)? An analysis of reforms to organic crop insurance
Authors: Delbridge Timothy A. , King Robert P. 
Published: October 2018

PurposeThe USDA’s Risk Management Agency (RMA) made several changes to the crop insurance products available to organic growers for the 2014 crop year. Most notably, a 5 percent premium surcharge was removed and organic-specific transitional yields (t-yields) were issued for the first time. The purpose of this paper is to use farm-level organic crop yield data to analyze the impact of these reforms on producer insurance outcomes and compare the insurance options for new organic growers.Design/methodology/approachThis study uses a unique panel data set of organic corn and soybean yields to analyze the impact of organic crop insurance reforms. Actual Production History values and premium rates are calculated for each farm and crop yield sequence. Producer loss ratios and subsidized premium wedges are compared for yield, revenue and area-risk products before and after the instituted reforms.FindingsResults indicate that RMA succeeded in improving the actuarial soundness of the organic insurance program, though further refinement of organic t-yields may be necessary to accurately reflect the yield potential of organic producers and avoid reductions in program participation.Originality/valueThis paper provides insight into the effectiveness of reforms intended to improve the actuarial soundness of organic crop insurance and demonstrates the effect that the reforms are likely to have on new and existing organic farms. Because this analysis uses data collected independently of RMA and includes farms that may or may not have purchased crop insurance, it avoids the self-selection problems that might affect analyses using crop insurance program data.
Scholarly book publishers’ ratings and lists in Finland and Spain
Authors: Mañana Rodriguez Jorge , Pölönen Janne 
Published: October 2018

Purpose
The purpose of this paper is twofold: first, to compare the lists of publishers in SPI (Spain) and the lists of VIRTA (Finland), in order to determine some of the potential uses of a merged list, such as complementing each other; and, second, to assess the effects of cross-field variability in the SPI rankings on the potential uses identified in the previous objective.

Design/methodology/approach
VIRTA and SPI lists were matched and compared in terms of level and number of submissions (VIRTA) and prestige (SPI).

Findings
There is a set of international publishers common to both information systems, but most publishers are nationally oriented. This type of publisher is still highly relevant for scholars. Consequently, a merge of national lists would provide useful information for all stakeholders involved in terms of grounding information for the rating of foreign, non-international publishers. Nevertheless, several issues should be considered in an eventual merging process, such as the decisions related to the use of field-specific rankings or general rankings.

Practical implications
If merged, ratings ought to be kept separately. Ratings of national publishers can be imputed in other systems’ evaluation process, thus making the merging process potentially useful.

Originality/value
This research explores obstacles and opportunities for merging scholarly publishers’ lists from an empirical perspective. It provides groundwork for future efforts toward supra-national combinations of publishers’ lists.
The associations among market orientation, technology orientation, entrepreneurial orientation and organizational performance
Authors: Masa’deh Ra’ed , Al-Henzab Jawaher , Tarhini Ali , Obeidat Bader Yousef 
Published: October 2018

PurposeThe purpose of this paper is to explore the relationship between three variables of strategic orientation (market orientation, technology orientation entrepreneurial orientation) and organizational performance in the Jordanian pharmaceutical sector.Design/methodology/approachThis study employed a quantitative research design where 252 questionnaires were collected form respondents operating in various pharmaceutical companies in Jordan to obtain necessary data to test the hypotheses developed for the study. Multiple regressions were used to analyze the research data.FindingsThe results of the analysis revealed that strategic orientations were positively and significantly related to organizational performance. The findings also showed that market orientation contributed the most to the enhancement of organizational development followed by technology orientation and finally entrepreneurship orientation.Practical implicationsThese findings contribute to the understanding of the importance of employing multiple strategic orientations in order to enhance organizational performance, particularly in pharmaceutical companiesOriginality/valueThis is the first study which adequately covers the relationship between three variables of strategic orientation (market orientation, technology orientation, entrepreneurial orientation) and organizational performance in the Jordanian pharmaceutical sector.
Proposed the pricing model as an alternative Islamic benchmark
Authors: Ahmed Essia Ries , Islam Md Aminul , Alabdullah Tariq Tawfeeq Yousif , bin Amran Azlan 
Published: October 2018

PurposeThe purpose of this paper is to find applicable Islamic pricing benchmarks (IPBs) instead of the market interest rates which are currently used in Islamic finance as benchmark.Design/methodology/approachThe suggested model (Islamic pricing benchmark model (IPBM)) obviously reveals the feasibility and practical effectiveness of a substitute to London Interbank Offered Rate (LIBOR) and as an evaluator tool to suggested investment projects. The model is a suggested mechanism which could be used as an alternative choice to the conventional borrowing based on the forbiddenRibaor on interest. The suggested IPBM depends on estimating the rate of return for any project on consideration of the cash flows in future which is expected to be relative to the invested capital.FindingsThe IPBM approach might be applied to financial tools, where the fund owner bears the loss since it is not because of negligence. An instrument to help identify the investment for target rates of return (as an alternative choice to LIBOR) to identify a breakeven point based on expected cash flows for the project to be financed instead of based on seeking the indicators of interest orRiba(as LIBOR). This feature of the IPBM model as an Islamic benchmark renders it as aShariahpricing mechanism for the Islamic financial products.Practical implicationsThe IPBM could be used as a financial instrument to assist in identifying the investment for the target return rates to determine a breakeven point based on expected cash flows for the project to be funded instead of being based on seeking the interest indicators orRiba(as LIBOR). This feature as an Islamic benchmark is considered as aShariahpricing mechanism for the Islamic financial products. In particular, the proposed model incorporates theShariahparameters. In that, it is hoped that the Islamic financial instruments will be more comprehensive in theirShariahcompliance and thereby may bring more credibility to the Islamic financial system in general.Originality/valueThis paper highlights several important issues related to the IPBMs in Islamic financial institutions which are not widely discussed among researchers. This study contributes to finding an alternative IPB for the Islamic financial products which is currently using the conventional interest rate (LIBOR) as its benchmark. The current study provides empirical evidence for the possibility of relying on the IPBM as an Islamic benchmark to price Islamic financial transactions.
Benchmarking performance of governance quality in Indian states using MCDM techniques
Authors: Raj Alok , Khanna Rupika 
Published: October 2018

PurposeThe purpose of this paper is to benchmarking the governance performance of Indian states.Design/methodology/approachThis paper provides a framework to measure governance performance at the state level. Using the data on 28 key indicators, the authors evaluate Indian states on seven broad dimensions of governance quality covering several aspects of public service delivery, regulatory quality and law and order. The empirical methodology involves the application of multi-criteria decision making techniques in two steps. The authors, first develop suitable weights of the identified dimensions and criteria under each dimension by applying the inputs of an expert-based decision-panel in a best-worst framework. Next, using these weights, the authors evaluate ranking of each state using TOPSIS and PROMETHEE-II methods.FindingsThe results indicate wide disparities in the governance performance of Indian states. Based on different indicators, the paper evaluates the rank of all the major Indian states. Results reveal that “Social Service Delivery(S)” is the most influencing dimension for the development of a state. Overall, the authors find Andra Pradesh, NCT of Delhi and Goa to be the leading states in terms of governance quality.Research limitations/implicationsThe paper provides policy makers with easy to use operational indicators to analyse the governance performance of Indian states. These would help in better monitoring of these states through competitive goal-setting for continuous improvement.Originality/valueTo the best of the authors’ knowledge, this study is the first formal assessment of governance quality in the Indian states in a multi-criteria framework. To this end, the paper addresses the issue of wide regional disparities in the country. The findings of the paper provide powerful insights to policy makers in setting up appropriate strategies to eliminate these disparities.
Agentic work behaviour and thriving at work: role of decision making authority
Authors: Sia Surendra Kumar , Duari Pravakar 
Published: October 2018

PurposeThe purpose of this paper is to examine the contribution of agentic work behaviour and decision-making authority (DMA) to thriving at work and, more importantly, the moderating role of DMA in the relationship between agentic behaviour and thriving.Design/methodology/approachThe study has been carried out upon a random sample of 330 employees below supervisory level from manufacturing companies located at Odisha (a state located at the eastern part of India). After verifying the significance of correlation among the study variables through Pearson’s product moment correlation, moderated regression analyses were carried out to examine the independent contribution of agentic work behaviour and DMA to thriving as well as the moderating contribution of DMA towards thriving.FindingsResults reveal that the three dimensions of agentic work behaviour, namely, task focus, exploration and heedful relation, have a direct positive contribution towards thriving at workplace. As far as the moderation is concerned, it is observed that the thriving level is higher for the employees having high DMA irrespective of the level of agentic work behaviour at each dimension.Research limitations/implicationsThe findings imply for designing interventions to enhance task focus, super-ordinate relationship and interest for learning. In addition, the organisations should provide autonomy to employees for decision making.Originality/valueThe study is first of its kind in the Indian context upon employee thriving. In this study, the authors have not only investigated the separate independent contribution of agentic behaviour and DMA, but also their interacting contribution to employee thriving.