bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome variants associated with RNA splicing variation in bovine are extensively shared between tissues
Authors: Xiang Ruidong , Hayes Ben J. , Jagt Christy J. Vander , MacLeod Iona M. , Khansefid Majid , Bowman Phil J. , Yuan Zehu , Prowse-Wilkins Claire P. , Reich Coralie M. , Mason Brett A. , Garner Josie B. , Marett Leah C. , Chen Yizhou , Bolormaa Sunduimijid , Daetwyler Hans D. , Chamberlain Amanda J. , Goddard Michael E. 
Published: November 2017

AbstractBackgroundMammalian phenotypes are shaped by numerous genome variants, many of which may regulate gene transcription or RNA splicing. To identify variants with regulatory functions in cattle, an important economic and model species, we used sequence variants to map a type of expression quantitative trait loci (expression QTLs) that are associated with variations in the RNA splicing, i.e., sQTLs. To further the understanding of regulatory variants, sQTLs were compare with other two types of expression QTLs, 1) variants associated with variations in gene expression, i.e., geQTLs and 2) variants associated with variations in exon expression, i.e., eeQTLs, in different tissues.ResultsUsing whole genome and RNA sequence data from four tissues of over 200 cattle, sQTLs identified using exon inclusion ratios were verified by matching their effects on adjacent intron excision ratios. sQTLs contained the highest percentage of variants that are within the intronic region of genes and contained the lowest percentage of variants that are within intergenic regions, compared to eeQTLs and geQTLs. Many geQTLs and sQTLs are also detected as eeQTLs. Many expression QTLs, including sQTLs, were significant in all four tissues and had a similar effect in each tissue. To verify such expression QTL sharing between tissues, variants surrounding (±1Mb) the exon or gene were used to build local genomic relationship matrices (LGRM) and estimated genetic correlations between tissues. For many exons, the splicing and expression level was determined by the same cis additive genetic variance in different tissues. Thus, an effective but simple-to-implement meta-analysis combining information from three tissues is introduced to increase power to detect and validate sQTLs. sQTLs and eeQTLs together were more enriched for variants associated with cattle complex traits, compared to geQTLs. Several putative causal mutations were identified, including an sQTL at Chr6:87392580 within the 5th exon of kappa casein (CSN3) associated with milk production traits.ConclusionsUsing novel analytical approaches, we report the first identification of numerous bovine sQTLs which are extensively shared between multiple tissue types. The significant overlaps between bovine sQTLs and complex traits QTL highlight the contribution of regulatory mutations to phenotypic variations.
Suboptimal eye movements for seeing fine details
Authors: Ağaoğlu Mehmet N. , Sheehy Christy K. , Tiruveedhula Pavan , Roorda Austin , Chung Susana T. L. 
Published: November 2017

AbstractHuman eyes are never stable, even during attempts of maintaining gaze on a visual target. Considering transient response characteristics of retinal ganglion cells, a certain amount of motion of the eyes is required to efficiently encode information and to prevent neural adaptation. However, excessive motion of the eyes leads to insufficient exposure to the stimuli which creates blur and reduces visual acuity. Normal miniature eye movements fall in between these extremes but it is unclear if they are optimally tuned for seeing fine spatial details. We used a state-of-the-art retinal imaging technique with eye tracking to address this question. We sought to determine the optimal gain (stimulus/eye motion ratio) that corresponds to maximum performance in an orientation discrimination task performed at the fovea. We found that miniature eye movements are tuned, but may not be optimal, for seeing fine spatial details.
Secondary metabolites and the antimicrobial potential of five differentColeusspecies in response to salinity stress
Authors: Kotagiri Divya , Khasim Beebi Shaik , Viswanatha Chaitanya Kolluru 
Published: November 2017

AbstractSalinity is one of the major abiotic stresses that affects the growth and productivity of plants. The presence of soluble salts at high concentration near the root system restricts the uptake of water by plants. Plants grown under saline conditions possess higher amounts of secondary metabolites compared with those grown under normal conditions. The use of traditional medicine to treat infectious diseases is increasing day by day throughout the world. Developing novel drugs with antimicrobial potential from the source of medicinal plants is receiving attention to replace the use of synthetic drugs and to combat the growth of multi-drug resistant strains. Thus screening of medicinal plant extracts is carried out to evaluate their antimicrobial potency. The present study aimed at determining the secondary metabolites and antimicrobial potential of leaf, stem and root ethanol and chloroform extracts of five differentColeusspecies;C.aromaticus, C.amboinicus, Cbarbatus, C.forskohliiandC.zeylanicussubjected to salinity stress. The up regulation in the content of plant bioactive compounds along with the antimicrobial activities of ethanol and chloroform extracts under the influence of salinity stress have been observed during the study inColeus.The leaf, stem and root extracts of all the fiveColeusspecies showed good antimicrobial activity against the tested pathogenic strains. The leaf extracts ofColeusshowed higher inhibitory activity compared to the stem and root extracts. Ethanol extracts showed higher anti-microbial activity ranging from 1.5-100 mg/ml compared with the chloroform extracts ranging from 0.97-250 mg/ml respectively. The study revealed that the increased antimicrobial activity with increasing salinity might be due to the up regulation of secondary metabolites. The leaf, stem and root extracts ofColeusshowed effective antimicrobial activity against the pathogenic strains even under saline conditions is due to the up regulation of secondary metabolites which provides a scope of developing novel drugs to treat infectious diseases.
PWWP INTERACTOR OF POLYCOMBS (PWO1) links PcG-mediated gene repression to the nuclear lamina inArabidopsis
Authors: Mikulski Pawel , Hohenstatt Mareike L. , Farrona Sara , Smaczniak Cezary , Kaufmann Kerstin , Angenent Gerco , Schubert Daniel 
Published: November 2017

AbstractPolycomb group (PcG) proteins facilitate chromatin-mediated gene repression through the modification of histone tails in a wide range of eukaryotes, including plants and animals. One of the PcG protein complexes, Polycomb Repressive Complex 2 (PRC2), promotes repressive chromatin formation via tri-methylation of lysine-27 on histone H3 (H3K27me3). The animal PRC2 is implicated in impacting subnuclear distribution of chromatin as its complex components and H3K27me3 are functionally connected with the nuclear lamina (NL) - a peripheral protein mesh that resides underneath the inner nuclear membrane (INM) and consists of lamins and lamina-associated proteins. In contrast to animals, NL in plants has an atypical structure and its association with PRC2-mediated gene repression is largely unknown. Here, we present a connection between lamin-like protein, CROWDED NUCLEI 1 (CRWN1), and a novel PRC2-associated component, PWWP INTERACTOR OF POLYCOMBS 1 (PWO1), inArabidopsis thaliana. We show that PWO1 and CRWN1 proteins associate physically with each other, act in the same pathway to maintain nuclear morphology and control expression of similar set of target genes. Moreover, we demonstrate that PWO1 proteins form speckle-like foci located partially at the subnuclear periphery inNicotiana benthamianaandArabidopsis thaliana. Ultimately, as CRWN1 and PWO1 are plant-specific, our results argue that plants developed an equivalent, rather than homologous, mechanism of linking PRC2-mediated chromatin repression and nuclear lamina.
Age-accelerated cognitive decline in asymptomatic adults with CSF β-amyloid
Authors: Clark Lindsay R. , Berman Sara E. , Norton Derek , Koscik Rebecca L. , Jonaitis Erin , Blennow Kaj , Bendlin Barbara B. , Asthana Sanjay , Johnson Sterling C. , Zetterberg Henrik , Carlsson Cynthia M. 
Published: November 2017

ABSTRACTObjectiveCompare cognitive and hippocampal volume (HCV) trajectories in asymptomatic middle-aged and older adults with positive cerebrospinal fluid (CSF) markers of β-amyloid (Aβ) or tau to adults without an AD-associated biomarker profile.Method392 adults enrolled in a longitudinal cohort study (Wisconsin Registry for Alzheimer’s Prevention or Wisconsin Alzheimer’s Disease Research Center) completed a lumbar puncture and at least two biennial or annual neuropsychological evaluations. Cutoffs for Aβ42, total tau, and phosphorylated tau were developed via receiver operating characteristic curve analyses on a sample of 78 participants (38 dementia, 40 controls). These cutoffs were applied to a separate sample of 314 cognitively healthy adults (mean age at CSF collection = 61.5) and mixed-effects regression analyses tested linear and quadratic interactions of biomarker group × age at each visit on cognitive and HCV outcomes.Results215 participants (69%) were biomarker negative (preclinical AD Stage 0), 46 (15%) were Aβ+ only (preclinical AD Stage 1), 25 (8%) were Aβ+ and tau+ (preclinical AD Stage 2), and 28 (9%) were tau+ only. Both Stage 1 and Stage 2 groups exhibited greater rates of linear decline on story memory and processing speed measures, and non-linear decline on list-learning and set-shifting measures compared to Stage 0. The tau+ only group did not significantly differ from Stage 0 in rates of cognitive decline.ConclusionIn an asymptomatic at-risk cohort, elevated CSF Aβ (with or without elevated tau) was associated with greater rates of cognitive decline, with the specific pattern of decline varying across cognitive measures.
Naked mole-rat transcriptome signatures of socially-suppressed sexual maturation and links of reproduction to aging
Authors: Bens Martin , Szafranski Karol , Holtze Susanne , Sahm Arne , Groth Marco , Kestler Hans A. , Hildebrandt Thomas B. , Platzer Matthias 
Published: November 2017

AbstractNaked mole-rats (NMRs) are eusocially organized in colonies. Although breeders carry the additional metabolic load of reproduction, they are extremely long-lived and remain fertile throughout their lifespan. Comparative transcriptome analysis of ten organs from breeders and non-breeders of the eusocial long-lived NMR and the polygynous shorter-lived guinea pig provide comprehensive and unbiased molecular evidence that sexual maturation in NMR is socially suppressed. After transition into breeders, transcriptomes are markedly sex-specific, show pronounced feedback signaling via gonadal steroids and have similarities to reproductive phenotypes in African cichlid fish. Further, NMRs show functional enrichment of status-related expression differences associated with aging. Lipid metabolism and oxidative phosphorylation – molecular networks known to be linked to aging – were identified among most affected gene sets. Further, a transcriptome pattern associated with longevity is reinforced in NMR breeders contradicting the disposable soma theory of aging and potentially contributing to their exceptional long life- and healthspan.
Bacterial adaptation to diet is a key evolutionary force shaping Drosophila-Lactobacillus symbiosis
Authors: Martino Maria Elena , Joncour Pauline , Leenay Ryan , Gervais Hugo , Shah Malay , Hughes Sandrine , Gillet Benjamin , Beisel Chase , Leulier François 
Published: November 2017

AbstractAnimal-microbe facultative symbioses play a fundamental role in ecosystem and organismal health (1–3). Yet, due to the flexible nature of their association, the selection pressures acting on animals and their facultative symbionts remain elusive (4, 5). Here, by applying experimental evolution to a well-established model of facultative symbiosis: Drosophila melanogaster associated with Lactobacillus plantarum, one of its growth promoting symbiont (6, 7), we show that the diet, instead of the host, is a predominant driving force in the evolution of this symbiosis and identify the mechanism resulting from the bacterial adaptation to the diet, which confers host growth benefits. Our study reveals that adaptation to the diet can be the foremost step in the determination of the evolutionary course of a facultative symbiosis.
Hyperactivation of extracellular signal-regulated kinase (ERK) by RAS-mediated signaling or inhibition of dual specificity phosphatase 6 (DUSP6) is associated with toxicity in lung adenocarcinoma cells with mutations in KRAS or EGFR
Authors: Unni Arun M. , Harbourne Bryant , Oh Min Hee , Wild Sophia , Lockwood William W. , Varmus Harold 
Published: November 2017

AbstractWe recently described the synthetic lethality that results when mutant KRAS and mutant EGFR are coexpressed in human lung adenocarcinoma (LUAD) cells, revealing the biological basis for the mutual exclusivity of KRAS and EGFR mutations in lung cancers. We have now further defined the biochemical events responsible for the toxic effects of signaling through the RAS pathway. By combining pharmacological and genetic approaches, we have developed multiple lines of evidence that signaling through extracellular signal-regulated kinases (ERK1/2) mediates the toxicity. These findings imply that tumors with mutant oncogenes that drive signaling through the RAS pathway must restrain the activity of ERK1/2 to avoid cell toxicities and enable tumor growth. In particular, a dual specificity phosphatase, DUSP6, regulates phosphorylated (P)-ERK levels in lung adenocarcinoma cells, providing negative feedback to the RAS signaling pathway. Accordingly, inhibition of DUSP6 is cytotoxic in LUAD cells driven by either mutant KRAS or mutant EGFR, phenocopying the effects of co-expression of mutant KRAS and EGFR. Together, these data suggest that targeting DUSP6 or other feedback regulators of the EGFR-KRAS-ERK pathway may offer a strategy for treating certain cancers by exceeding an upper threshold of RAS-mediated signaling.
Insulin-Like Peptides Regulate Feeding Preference and Metabolism in Drosophila
Authors: Semanyuk Uliana , Gospodaryov Dmytro , Feden’ko Hrystyna , Yurkevych Ihor , Vaiserman Alexander , Storey Kenneth , Simpson Stephen , Lushchak Oleh 
Published: November 2017

SUMMARYFruit flies have eight identified Drosophila insulin-like peptides (DILPs) involved in regulation of carbohydrate concentrations in hemolymph as well as accumulation of storage metabolites. In the present study, we investigated diet-dependent roles of DILPs encoded by genes dilp1–5, and dilp7 in regulation of insect appetite, food choice, accumulation of triglycerides, glycogen, glucose, and trehalose in fruit fly body and carbohydrates in hemolymph. We found that dilp2 gene predominantly influences body glycogen level, dilp3 – trehalose level in hemolymph, while dilp5 and dilp7 affect triglyceride level. Fruit fly appetite was found to be regulated by dilp3 and dilp7 genes. Our data contribute to the understanding of Drosophila as a model for further studies of metabolic diseases and may serve as a guide for uncovering the evolution of metabolic regulatory pathways.HIGHLIGHTSDifferent Drosophila insulin-like peptides play distinctive roles in metabolism, physiology and appetite regulation.Lack of Dilp2 and Dilp5 abrogates glycogen accumulation on high carbohydrate dietsLack of Dilp3 leads to build-up of trehalose in haemolymph on high-carbohydrate-low-protein dietsLack of Dilp3 and Dilp7 leads to increased consumption of protein on low-carbohydrate-high-protein dietsGRAPHICAL ABSTRACT
Couple dynamics in family holidays decision-making process
Authors: Rojas-de-Gracia María-Mercedes , Alarcón-Urbistondo Pilar , González Robles Eva María 
Published: November 2017

PurposeFamily holiday decision-making (FHDM) is a process composed of several stages. This paper aims to describe two objectives: to identify at each stage the roles in couples, the main decision-maker in the case of family holidays; and to determine the most influential variables.Design/methodology/approachTo identify the roles played by the partners, a frequency analysis has been conducted, which provides a graphic representation of the so-called feasibility triangles. The technique selected to identify the variables that explained the decision structure was binary logistic regression. In total, 375 useful dyads of questionnaires were received.FindingsHolidays follow a joint decision-making process in the initiation phase and in the final decision, while the search for information is carried out equally by either partner. The woman’s work situation, the type of destination travelled to and the difference in education levels between them are the variables that best explain how couples decide on their family holidays.Practical implicationsA better understanding of the FHDM process will help tourism companies to improve their marketing campaigns.Originality/valueThe characteristics of the sample composed of 375 couples whose members completed a questionnaire separately have allowed not have to rely on one response per household, which adds reliability to the results. This sample is higher than the one of many reference publications on the subject. Furthermore, this paper revealed differences between male and female perception.
Exploring travelers’ decision-making styles
Authors: Atadil Hilmi A. , Sirakaya-Turk Ercan , Meng Fang , Decrop Alain 
Published: November 2017

PurposeThe purpose of this study is to profile market segments using travelers’ decision-making styles (DMS) as segmentation bases and to identify similarities and differences between traveler segments regarding a series of psychographic and attitudinal characteristics.Design/methodology/approachData are gathered from a sample of 426 travelers in Dubai and Shanghai via self-reported surveys. Analyses included factor, k-means cluster, discriminant and MANOVA.FindingsStudy findings reveal significant differences among the rational, adaptive and daydreamer decision-makers’ segments in their behavioral and attitudinal characteristics with respect to tourism involvement and destination images.Practical implicationsFindings provide important practical implications for generating effective marketing and positioning strategies based on the identified attitudinal characteristics of the traveler segments for destination marketing organizations.Originality/valueA stream of recent tourism studies shows a strong relationship between tourism involvement and destination images, yet very little research has tackled the issue of how these critical variables can be affected by individuals’ decision-making styles. This study explores and tests the relationships among DMS, tourism involvement and destination image using a factor-cluster approach.
The effect of reporting quality on stock returns of listed companies on the Tehran Stock Exchange
Authors: Salehi Mahdi , Tagribi Masomeh , Farhangdoust Shayan 
Published: November 2017

Purpose
The purpose of this paper is to examine the effect of earnings quality (as a proxy for financial reporting quality) of companies listed on the Tehran Stock Exchange (TSE) and the quality of their financial information disclosure on stock returns.

Design/methodology/approach
The authors test the hypotheses by conducting panel data analysis on a sample of 1,680 firm-year observations from companies listed on the TSE during 2009-2014. The authors also conduct the variance inflation factor and unit root tests to control for the severity of multicollinearity in their ordinary least squares regression analysis and whether the time series variables are non-stationary and possess a unit root.

Findings
Using Francis et al. (2005) and modified Jones (1991) models as measures for earnings quality, the results are indicative of a significant and positive relationship between firms’ earnings quality and their stock returns. However, the research findings suggest that earnings management as well as disclosure quality (DQ) is not significantly associated with firms’ stock return.

Research limitations/implications
Although the authors controlled for some of the factors affecting stock returns, there are still some other factors such as the operating environment, institutional setting and/or information uncertainty that could influence stock returns, and accordingly, the authors were not able to exclude their possibility and get the most robust results. Moreover, there are several models proposed in different studies for measuring earnings quality which have led to mixed results particularly without a general consensus on what a good model is, and whether earnings quality is a priced risk factor.

Originality/value
Taken as a whole, the paper could provide new insights into the determinants of stock returns which has rarely been considered by prior finance literature. Furthermore, the unique institutional context of the paper could contribute substantially to the literature on the relationship between financial reporting and DQ and stock returns.
Conditional volatility nexus between stock markets and macroeconomic variables
Authors: Abbas Ghulam , McMillan David G. , Wang Shouyang 
Published: November 2017

PurposeThe purpose of this paper is to analyse the relation between stock market volatility and macroeconomic fundamentals for G-7 countries using monthly data over the period from July 1985 to June 2015.Design/methodology/approachThe empirical methodology is based on two steps: in the first step, the authors obtain the conditional volatilities of stock market returns and macroeconomic variables through the GARCH family of models. The authors also incorporate the impact of early 2000s dotcom and the global financial crises. In the second step, the authors estimate multivariate vector autoregressive model to analyze the dynamic relation between stock markets return and macroeconomic variables.FindingsThe overall results for G-7 countries indicate a weak volatility transmission from macroeconomic factors to stock market volatility at individual level but the collective impact of volatility transmission is highly significant. Although, the results of block exogeneity indicate a bidirectional causality except UK, but the causal linkage is quite weak from stock market to macroeconomic variables. Moreover, the local financial variables excluding interest rate are closely integrated, and the volatility of industrial production growth and oil price are identified as the most significant macroeconomic factors that could possibly influence the directions of stock markets.Originality/valueThis research establishes the nature of the links between stock market and macroeconomic volatility. Research to date has been unable to satisfactorily establish the empirical nature of such links. The authors believe this paper begins to do this.