bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deficiencies in tRNA synthetase editing activity cause cardioproteinopathy
Authors: Liu Ye , Satz Jakob S. , Vo My-Nuong , Nangle Leslie A. , Schimmel Paul , Ackerman Susan L. 
Published: November 2014

SignificanceMisfolded proteins are a hallmark of diverse human cardiac disorders including desmin-related cardiomyopathy and systemic amyloidosis. Defects in translational fidelity can cause neurodegeneration, however the consequences of mistranslation in other tissues, including the heart, are unknown. The fidelity of protein synthesis is largely ensured by aminoacyl-tRNA synthetases, and many tRNA synthetases contain editing domains that hydrolyze mischarged tRNAs, preventing incorporation of incorrect amino acids into proteins. Here, we show that diminished editing efficacy of the alanyl-tRNA synthetase causes misfolded protein aggregation and cell death in the mammalian heart. These results illuminate the importance of translational fidelity in cardiac homeostasis and suggest that genetic factors that disrupt the accuracy of translation may contribute to proteinopathies of the heart and other tissues.
Wnts produced by Osterix-expressing osteolineage cells regulate their proliferation and differentiation
Authors: Tan Si Hui , Senarath-Yapa Kshemendra , Chung Michael T. , Longaker Michael T. , Wu Joy Y. , Nusse Roeland 
Published: November 2014

Significance
Despite the importance of Wnt signaling in bone biology, there is a knowledge gap in the identity of the cells that produce the Wnt ligands and the functions of Wnts produced by specific cell types. In our study, we comprehensively characterized the expression patterns of all 19 Wnts in the developing mouse bone by in situ hybridization, and further showed that Osterix-expressing cells can produce Wnts and respond to Wnt signaling. Additionally, we found that Wnts produced by these Osterix-expressing cells regulate their differentiation and proliferation. Through providing a better understanding of how Wnt signaling contributes to bone biology, our findings also have clinical implications for the mechanism of the osteoporotic drug that targets Sclerostin, a Wnt signaling antagonist.
A Review on Attachment and Adolescent Substance Abuse: Empirical Evidence and Implications for Prevention and Treatment
Authors: Schindler Andreas , Bröning Sonja 
Published: November 2014

Background This paper reviews research on the relation of attachment and substance use disorders (SUD) in adolescence. Based on a theoretical introduction, we review evidence for a possible general link between SUD and insecure attachment, for links between specific forms of SUD and specific patterns of attachment, and for studies on family patterns of attachment in adolescence. Methods Using medical and psychological databases, we identified 10 studies on adolescent SUD and another 13 studies on adult SUD. Results Empirical evidence strongly supports the assumption of insecure attachment in SUD samples. With regard to specific patterns of attachment, results mainly point towards fearful and dismissing-avoidance, whereas single studies report preoccupied and unresolved patterns. Results indicate different patterns of attachment in different groups of substance abusers, that is, fearful-avoidant attachment in heroin addicts and more heterogeneous results in abusers of other substances. Explorative data suggest different types of insecure family attachment patterns, which might imply different functions of substance abuse and lead to different treatment recommendations. Methodological problems such as poor assessment of SUD and the use of different measures of attachment limit comparability. Conclusions Although a lot of research is still needed to address the unknowns in the relation between attachment and SUD, there is strong evidence for a general link between SUD and insecure attachment. Data on connections between different patterns of attachment and different pathways towards SUD are less conclusive but mainly point to disorganized and externalizing pathways. Evidence suggests that fostering attachment security might improve the outcome of state-of-the-art approaches in both early interventional treatment and prevention. Implications for individual and family approaches are outlined.
Expenditure Response to Increases in In‐Kind Transfers: Evidence from the Supplemental Nutrition Assistance Program
Authors: Beatty Timothy K.M. , Tuttle Charlotte J. 
Published: November 2014

AbstractEconomic theory predicts that households who receive less in Supplemental Nutrition Assistance Program benefits than they spend on food will treat SNAP benefits as if they were cash. However, empirical tests of these predictions draw different conclusions. In this study, we reexamine this question using recent increases in Supplemental Nutrition Assistance Program benefits, the largest of which was due to the American Recovery and Reinvestment Act of 2009. We find that increases in benefits cause households to increase their food budget share by more than would be predicted by theory. Results are robust to a host of specification tests.
Efficient searching and annotation of metabolic networks using chemical similarity
Authors: Pertusi Dante A. , Stine Andrew E. , Broadbelt Linda J. , Tyo Keith E.J. 
Published: November 2014

AbstractMotivation: The urgent need for efficient and sustainable biological production of fuels and high-value chemicals has elicited a wave of in silico techniques for identifying promising novel pathways to these compounds in large putative metabolic networks. To date, these approaches have primarily used general graph search algorithms, which are prohibitively slow as putative metabolic networks may exceed 1 million compounds. To alleviate this limitation, we report two methods—SimIndex (SI) and SimZyme—which use chemical similarity of 2D chemical fingerprints to efficiently navigate large metabolic networks and propose enzymatic connections between the constituent nodes. We also report a Byers–Waterman type pathway search algorithm for further paring down pertinent networks.Results: Benchmarking tests run with SI show it can reduce the number of nodes visited in searching a putative network by 100-fold with a computational time improvement of up to 105-fold. Subsequent Byers–Waterman search application further reduces the number of nodes searched by up to 100-fold, while SimZyme demonstrates ∼90% accuracy in matching query substrates with enzymes. Using these modules, we have designed and annotated an alternative to the methylerythritol phosphate pathway to produce isopentenyl pyrophosphate with more favorable thermodynamics than the native pathway. These algorithms will have a significant impact on our ability to use large metabolic networks that lack annotation of promiscuous reactions.Availability and implementation: Python files will be available for download at http://tyolab.northwestern.edu/tools/.Contact: k-tyo@northwestern.eduSupplementary information: Supplementary data are available at Bioinformatics online.
genomation: a toolkit to summarize, annotate and visualize genomic intervals
Authors: Akalin Altuna , Franke Vedran , Vlahoviček Kristian , Mason Christopher E. , Schübeler Dirk 
Published: November 2014

Abstract
Summary: Biological insights can be obtained through computational integration of genomics data sets consisting of diverse types of information. The integration is often hampered by a large variety of existing file formats, often containing similar information, and the necessity to use complicated tools to achieve the desired results. We have built an R package, genomation, to expedite the extraction of biological information from high throughput data. The package works with a variety of genomic interval file types and enables easy summarization and annotation of high throughput data sets with given genomic annotations.
Availability and implementation: The software is currently distributed under MIT artistic license and freely available at http://bioinformatics.mdc-berlin.de/genomation, and through the Bioconductor framework.
Contact: dirk.schubeler@fmi.ch, chm2042@med.cornell.edu, altuna.akalin@fmi.ch, or aakalin@gmail.com
QuasR: quantification and annotation of short reads in R
Authors: Gaidatzis Dimos , Lerch Anita , Hahne Florian , Stadler Michael B. 
Published: November 2014

Abstract
Summary: QuasR is a package for the integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification. QuasR supports different experiment types (including RNA-seq, ChIP-seq and Bis-seq) and analysis variants (e.g. paired-end, stranded, spliced and allele-specific), and is integrated in Bioconductor so that its output can be directly processed for statistical analysis and visualization.
Availability and implementation: QuasR is implemented in R and C/C++. Source code and binaries for major platforms (Linux, OS X and MS Windows) are available from Bioconductor (www.bioconductor.org/packages/release/bioc/html/QuasR.html). The package includes a ‘vignette’ with step-by-step examples for typical work ﬂows.
Contact: michael.stadler@fmi.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
The non-thermal superbubble in IC 10: the generation of cosmic ray electrons caught in the act
Authors: Heesen Volker , Brinks Elias , Krause Martin G. H. , Harwood Jeremy J. , Rau Urvashi , Rupen Michael P. , Hunter Deidre A. , Chyży Krzysztof T. , Kitchener Ged 
Published: November 2014

Abstract
Superbubbles are crucial for stellar feedback, with supposedly high (of the order of 10 per cent) thermalization rates. We combined multiband radio continuum observations from the Very Large Array (VLA) with Effelsberg data to study the non-thermal superbubble (NSB) in IC 10, a starburst dwarf irregular galaxy in the Local Group. Thermal emission was subtracted using a combination of Balmer Hα and VLA 32 GHz continuum maps. The bubble's non-thermal spectrum between 1.5 and 8.8 GHz displays curvature and can be well fitted with a standard model of an ageing cosmic ray electron population. With a derived equipartition magnetic field strength of 44 ± 8 μG, and measuring the radiation energy density from Spitzer MIPS maps as 5 ± 1 × 10−11 erg cm−3, we determine, based on the spectral curvature, a spectral age of the bubble of 1.0 ± 0.3 Myr. Analysis of the LITTLE THINGS H i data cube shows an expanding H i hole with 100 pc diameter and a dynamical age 3.8 ± 0.3 Myr, centred to within 16 pc on IC 10 X-1, a massive stellar mass black hole (M &gt; 23 M⊙). The results are consistent with the expected evolution for a superbubble with a few massive stars, where a very energetic event like a Type Ic supernova/hypernova has taken place about 1 Myr ago. We discuss alternatives to this interpretation.
Waves in Ship Prices and Investment
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Authors: Greenwood Robin , Hanson Samuel G. 
Published: November 2014

Abstract
We study the link between investment boom and bust cycles and returns on capital in the dry bulk shipping industry. We show that high current ship earnings are associated with high used ship prices and heightened industry investment in new ships, but forecast low future returns. We propose and estimate a behavioral model of industry cycles that can account for the evidence. In our model, firms overextrapolate exogenous demand shocks and partially neglect the endogenous investment response of their competitors. As a result, firms overpay for ships and overinvest in booms and are disappointed by the subsequent low returns. Formal estimation of the model suggests that modest expectational errors can result in dramatic excess volatility in prices and investment.
Genetic landscape of populations along the Silk Road: admixture and migration patterns
Authors: Mezzavilla Massimo , Vozzi Diego , Pirastu Nicola , Girotto Giorgia , d’Adamo Pio , Gasparini Paolo , Colonna Vincenza 
Published: November 2014

ABSTRACTBackgroundThe ancient Silk Road has been a trading route between Europe and Central Asia from the 2nd century BCE to the 15th century CE. While most populations on this route have been characterized, the genetic background of others remains poorly understood, and little is known about past migration patterns. The scientific expedition “Marco Polo” has recently collected genetic and phenotypic data in six regions (Georgia, Armenia, Azerbaijan, Uzbekistan, Kazakhstan, Tajikistan) along the Silk Road to study the genetics of a number of phenotypes.ResultsWe characterized the genetic structure of these populations within a worldwide context. We observed a West-East subdivision albeit the existence of a genetic component shared within Central Asia and nearby populations from Europe and Near East. We observed a contribution of up to 50% from Europe and Asia to most of the populations that have been analyzed. The contribution from Asia dates back to ~25 generations and is limited to the Eastern Silk Road. Time and direction of this contribution are consistent with the Mongolian expansion era.ConclusionsWe clarified the genetic structure of six populations from Central Asia and suggested a complex pattern of gene flow among them. We provided a map of migration events in time and space and we quantified exchanges among populations. Altogether these novel findings will support the future studies aimed at understanding the genetics of the phenotypes that have been collected during the Marco Polo campaign, they will provide insights into the history of these populations, and they will be useful to reconstruct the developments and events that have shaped modern Eurasians genomes.
Do corporate social responsibility practices yield different business benefits in eastern and western contexts?
Authors: Wei Yu-Chen , P. Egri Carolyn , Yeh-Yun Lin Carol 
Published: November 2014

Purpose– The purpose of this paper is to investigate the extent to which societal culture has a moderating effect on the business benefits of corporate social responsibility (CSR).Design/methodology/approach– A cross-national research design was conducted using survey data collected from 164 firms in Taiwan and 196 firms in Canada.Findings– We found societal differences in the positive influence of CSR on corporate image and employee commitment. Specifically, we found that the relationships between CSR (customer-oriented and employee-oriented) and corporate image were stronger for Taiwanese firms than for Canadian firms. In addition, employee CSR was found to be more strongly associated with higher employee commitment in Taiwan than in Canada. While customer CSR was associated with enhanced customer loyalty, this relationship was similar for firms in both countries.Research limitations/implications– Multi-informants for data collection and longitudinal research design in future research would be required for further understanding of the relationships among the variables in this study.Practical implications– This paper suggests that the business benefits of customer and employee CSR practices may yield relatively greater competitive advantages in East Asian countries where CSR is not as established or taken for granted as in Western countries.Originality/value– This study draws on the strategic perspective to investigate the value of CSR practices yielding different business benefits in contrasting cultural contexts.
The relative informational efficiency of stocks, options and credit default swaps during the financial crisis
Authors: Amadori Maria Chiara , Bekkour Lamia , Lehnert Thorsten 
Published: November 2014

Purpose– This paper aims to investigate informational efficiency of stock, options and credit default swap (CDS) markets. Previous research suggests that informed traders prefer equity option and CDS markets over stock markets to exploit their informational advantage. As a result, equity and credit derivative markets contribute more to price discovery compared to stock markets.Design/methodology/approach– In this study, the authors investigate the dynamics behind informed investors’ trading decisions in European stock, options and CDS markets. This allows to identify the predictive explanatory power of the unique information contained in each market with respect to future stock, CDS and option market movements.Findings– A lead-lag relation is found between the CDS market and the other markets, in which changes in CDS spreads are able to consistently forecast changes in stock prices and equity options’ implied volatilities, indicating how the fast-growing CDS market seems to play a special role in the price discovery process. Moreover, in contrast to results of US studies, the stock market is found to forecast changes in the other two markets, suggesting that investors also prefer stock market involvement to exploit their information advantages before moving to CDS and option markets. Interestingly, these patterns have only emerged during the recent financial crisis, while before the crisis, the option market was found to be of major importance in the price discovery process.Originality/value– The authors are the first to study the lead-lag relationship among European stock, option and CDS markets for a large sample period covering the financial crisis.
Ethics and values
Authors: Feikis Jonelle , McHugh Avery , Lane Samuel 
Published: November 2014

Purpose– The purpose of this paper is to examine the similarities and differences in the ethics and values seen within the USA, Brazil, Canada and the United Kingdom. By comparing these three countries to the USA, we can conclude the appropriate means in which to conduct business and research with any of the corresponding countries. This, in turn, will serve as a major asset to global business alike and prove to be monumental in the ways it breaks down cultural barriers to promote the sanctity of business worldwide.Design/methodology/approach– The USA, Brazil, Canada and the United Kingdom were examined extensively on each of their ethics and values to fully grasp what the literature of previous empirical research stated. Throughout the literary research, data and surveys can be found to further emphasize the value and reliability of empirical research. Through the collaboration of thoughts and the literature that was discovered, we can draw conclusions about the similarities and differences between the USA, Brazil, Canada and the United Kingdom. It is clear that among the different countries ethics, values and cultural norms come into play when partaking in business.Findings– There were many similarities and differences that lied between the different countries. Of those similarities, it was especially noticeable between the USA, Canada and the United Kingdom. This is due to the fact that these three countries have similar forms of common law governmental systems that are established and help form moral guidelines and parameters for doing business. Despite the fact that both the United Kingdom and Canada are under the rule of a Constitutional Monarchy, it is apparent that because the USA, United Kingdom and Canada have a free market economy all three operate at a similar capacity in terms of business.Originality/value– This paper is original and provides value by taking a unique review of literature and reviewing previous research on the topic. Specific suggestions for future research are offered at the end of this paper.
Comparison and Chemometric Analysis of the Phenolic Compounds and Organic Acids Composition of Chinese Wines
Authors: Tang Ke , Ma Lei , Han Ye‐Hui , Nie Yao , Li Ji‐Ming , Xu Yan 
Published: November 2014

AbstractCharacteristics of 106 wines from 5 major grape varieties and 3 typical geographic regions in China were investigated by means of profiling of organic acids and phenolic compounds analysis. An ultra‐performance liquid chromatography method was developed and thus, large number of samples could be determined in a quick and reliable way. The results showed that different origins and varieties were characteristic of various profiles of organic acid and phenolic compounds. In order to investigate possible correlation between organic acids and phenolic compounds content and grape variety and/or geographical origin, analysis of variance and linear discriminant analysis (LDA) were conducted. A satisfactory LDA result for red wines according to geographic origin was obtained, in which the correct classification was 100% and the leave‐one‐out validation accuracy was 90%. The corresponding results of white wines were 91% and 86%, respectively. When LDA was processed, according to grape varieties, the proportionality of successfully classified wines was 96%, while the leave‐one‐out validation accuracy was 94%. The organic acids and phenolic compounds profiles were useful in the classification of Chinese wines according to grape variety and geographic origin.
Widespread Effects of Alcohol on White Matter Microstructure
Authors: Fortier Catherine B. , Leritz Elizabeth C. , Salat David H. , Lindemer Emily , Maksimovskiy Arkadiy L. , Shepel Juli , Williams Victoria , Venne Jonathan R. , Milberg William P. , McGlinchey Regina E. 
Published: November 2014

BackgroundEvidence suggests that chronic misuse of alcohol may preferentially affect the integrity of frontal white matter (WM) tracts, which can impact executive functions important to achieve and maintain abstinence.MethodsGlobal and regional WM microstructure was assessed using diffusion magnetic resonance measures of fractional anisotropy (FA) for 31 abstinent alcoholics (ALC) with an average of 25 years of abuse and approximately 5 years of sobriety and 20 nonalcoholic control (NC) participants. Data processing was conducted with FreeSurfer and FSL processing streams. Voxelwise processing of the FA data was carried out using tract‐based spatial statistics. Clusters of significance were created to provide a quantitative summary of highly significant regions within the voxelwise analysis.ResultsWidespread, bilateral reductions in FA were observed in ALC as compared to NC participants in multiple frontal, temporal, parietal, and cerebellar WM tracts. FA in the left inferior frontal gyrus was associated with drinking severity.ConclusionsThis study found widespread reductions in WM integrity in a group of ALC compared to NC participants, with most pronounced effects in frontal and superior tracts. Decreased FA throughout the frontostriatal circuits that mediate inhibitory control may result in impulsive behavior and inability to maintain sobriety.
Fn14 Receptor Appears as a Modulator Of Ovarian Steroid‐Related Regulation Of Goat Endometrial Epithelial Cell IL‐18 expression
Authors: Lei Mingzhu , Qin Lijuan , Wang Aihua , Jin Yaping , Zhao Xianjun , Qi Xuefeng 
Published: November 2014

ProblemTumor necrosis factor‐like weak inducer of apoptosis (TWEAK)/fibroblast growth factor‐inducible 14 (Fn14) interactions affect the regulation of cytotoxic/immunotrophic pathways that are themselves under control of IL‐18. The effect of Fn14 on regulation of endometrium IL‐18 expression, however, remains unclear.Method and studyThe aim was to determine the mode of ovarian steroid action in regulating Fn14 expression by goat endometrial epithelial cells (EECs) in the presence and absence of endometrial stromal cells (ESCs). The possible role of Fn14 on the expression of IL‐18 by EECs was also evaluated.ResultsOpposite effects of E2 and/or P4 on the regulation of both Fn14 mRNA and protein expression by EECs were observed in the presence and absence of ESCs. Fn14 knockdown by blocking antibody or siRNA resulted in a decrease of IL‐18 mRNA and protein levels in EECs cocultured with ESCs, and no significant difference of the IL‐18 mRNA and protein levels in the EECs was observed between steroid treatment group and control group.ConclusionThese findings confirm the importance of steroids in controlling Fn14 expression in goat EECs. Furthermore, Fn14 appears as a novel modulator of the steroid‐related IL‐18 expression in EECs in the presence of ESCs.