bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovery and functional annotation of quantitative trait loci affecting resistance to sea lice in Atlantic salmon
Authors: Robledo Diego , Gutiérrez Alejandro P. , Barría Agustín , Lhorente Jean P. , Houston Ross D. , Yáñez José M. 
Published: October 2018

ABSTRACTSea lice (Caligus rogercresseyi) are ectoparasitic copepods which have a large negative economic and welfare impact in Atlantic salmon (Salmo salar) aquaculture, particularly in Chile. A multi-faceted prevention and control strategy is required to tackle lice, and selective breeding contributes via cumulative improvement of host resistance to the parasite. While host resistance has been shown to be heritable, little is yet known about the individual loci that contribute to this resistance, the potential underlying genes, and their mechanisms of action. In this study we took a multifaceted approach to identify and characterise quantitative trait loci (QTL) affecting hose resistance in a population of 2,688 Caligus-challenged Atlantic salmon post-smolts from a commercial breeding programme. We used low and medium density genotyping to collect genome-wide SNP marker data for all animals. Moderate heritablility estimates of 0.28 and 0.24 were obtained for lice density (as a measure of host resistance) and growth during infestation respectively. Three QTL explaining between 7 and 13 % of the genetic variation in resistance to sea lice (as represented by the traits of lice density) were detected on chromosomes 3, 18 and 21. Characterisation of these QTL regions was undertaken using RNA sequencing and pooled whole genome sequencing data. This resulted in the identification of a shortlist of potential underlying causative genes, and candidate functional mutations for further study. For example, candidates within the chromosome 3 QTL include a putative premature stop mutation in TOB1 (an anti-proliferative transcription factor involved in T cell regulation) and an uncharacterized protein which showed significant differential allelic expression (implying the existence of a cis-acting regulatory mutation). While host resistance to sea lice is polygenic in nature, the results of this study highlight significant QTL regions together explaining a moderate proportion of the heritability of the trait. Future investigation of these QTL may enable improved knowledge of the functional mechanisms of host resistance to sea lice, and incorporation of functional variants to improve genomic selection accuracy.
The CryoEM Structure of the Ribosome Maturation Factor Rea1
Authors: Sosnowski Piotr , Urnavicius Linas , Boland Andreas , Fagiewicz Robert , Busselez Johan , Papai Gabor , Schmidt Helgo 
Published: October 2018

AbstractThe biogenesis of the 60S ribosomal subunit is initiated in the nucleus where rRNAs and proteins form pre-60S particles. These pre-60S particles mature by transiently interacting with various assembly factors. The ~5000 amino-acid AAA+ ATPase Rea1 (or Midasin) generates force to mechanically remove assembly factors from pre-60S particles, which promotes their export to the cytosol. Here we present three Rea1 cryoEM structures. We visualize the Rea1 engine, a hexameric ring of AAA+ domains, and identify an α-helical bundle of AAA2 as a major ATPase activity regulator. The α-helical bundle interferes with nucleotide induced conformational changes that create a docking site for the substrate binding MIDAS domain of Rea1 on the AAA+ ring. Furthermore, we reveal the architecture of the Rea1 linker, which is involved in force generation and extends from the AAA+ ring. The data presented here provide insights into the mechanism of one of the most complex ribosome maturation factors.
Single synapse indicators of impaired glutamate clearance derived from fast iGluu imaging of cortical afferents in the striatum of normal and Huntington (Q175) mice
Authors: Dvorzhak Anton , Helassa Nordine , Török Katalin , Schmitz Dietmar , Grantyn Rosemarie 
Published: October 2018

ABSTRACTChanges in the balance between glutamate (Glu) release and uptake may stimulate synaptic reorganization and even synapse loss. In the case of neurodegeneration, a mismatch between astroglial Glu uptake and presynaptic Glu release could be detected if both parameters were assessed independently and at a single synapse level. This has now become possible due to a new imaging assay with the genetically encoded ultrafast Glu sensor iGluu. We report findings from individual corticostriatal synapses in acute slices prepared from mice aged >1 year. Contrasting patterns of short-term plasticity and a size criterion identified 2 classes of terminals, presumably corresponding to the previously defined IT and PT synapses. The latter exhibited a higher degree of frequency potentiation/residual Glu accumulation and were selected for our first iGluu single synapse study in Q175 mice, a model of Huntington’s disease (HD). It was found that in HD the time constant of perisynaptic [Glu] decay (TauD, as indicator of uptake) and the peak iGluu amplitude (as indicator of release) were prolonged and reduced, respectively. Treatment of WT preparations with the astrocytic Glu uptake blocker TFB-TBOA (100 nM) mimicked the TauD changes in homozygotes (HOM). Considering the largest TauD values encountered in WT, about 40% of PT terminals tested in Q175 heterozygotes (HET) can be classified as dysfunctional. Moreover, HD but not WT synapses exhibited a positive correlation between TauD and the peak amplitude of iGluu. Finally, EAAT2 immunoreactivity was reduced next to corticostriatal terminals. Thus, astrocytic Glu transport remains a promising target for therapeutic intervention.SIGNIFICANCE STATEMENTAlterations in astrocytic Glu uptake can play a role in synaptic plasticity and neurodegeneration. Until now, sensitivity of synaptic responses to pharmacological transport block and the resulting activation of NMDA receptors were regarded as reliable evidence for a mismatch between synaptic uptake and release. But the latter parameters are interdependent. Using a new genetically encoded sensor to monitor [Glu] at individual corticostriatal synapses we can now quantify the time constant of perisynaptic [Glu] decay (as indicator of uptake) and the maximal [Glu] elevation next to the active zone (as indicator of Glu release). The results provide a positive answer to the hitherto unresolved question whether neurodegeneration (e.g. Huntington’s disease) associates with a glutamate uptake deficit at tripartite excitatory synapses.
Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes
Authors: Guglielmini Julien , Woo Anthony , Krupovic Mart , Forterre Patrick , Gaia Morgan 
Published: October 2018

AbstractGiant and large eukaryotic double-stranded DNA viruses from the Nucleo-Cytoplasmic Large DNA Virus (NCLDV) assemblage represent a remarkably diverse and potentially ancient component of the eukaryotic virome. However, their origin(s), evolution and potential roles in the emergence of modern eukaryotes remain a subject of intense debate. Since the characterization of the mimivirus in 2003, many big and giant viruses have been discovered at a steady pace, offering a vast material for evolutionary investigations. In parallel, phylogenetic tools are constantly being improved, offering more rigorous approaches for reconstruction of deep evolutionary history of viruses and their hosts. Here we present robust phylogenetic trees of NCLDVs, based on the 8 most conserved proteins responsible for virion morphogenesis and informational processes. Our results uncover the evolutionary relationships between different NCLDV families and support the existence of two superclades of NCLDVs, each encompassing several families. We present evidence strongly suggesting that the NCLDV core genes, which are involved in both informational processes and virion formation, were acquired vertically from a common ancestor. Among them, the largest subunits of the DNA-dependent RNA polymerase were seemingly transferred from two clades of NCLDVs to proto-eukaryotes, giving rise to two of the three eukaryotic DNA-dependent RNA polymerases. Our results strongly suggest that these transfers and the diversification of NCLDVs predated the emergence of modern eukaryotes, emphasizing the major role of viruses in the evolution of cellular domains.
A focus on details? Inconsistent results on auditory and visual local-to-global processing in absolute pitch musicians
Authors: Wenhart T. , Altenmüller E. 
Published: October 2018

AbstractAbsolute pitch, the ability to name or produce a musical tone without a reference, is a rare ability which is often related to early musical training and genetic components. However, it remains a matter of debate why absolute pitch is relatively common in autism spectrum disorders and why absolute pitch possessors exhibit higher autistic traits. By definition absolute pitch (which involves the analysis of single tones) is characterized by a focus on a local scale than relative pitch (involving relations between tones, intervals, melodies).This study investigated whether a detail-oriented cognitive style, a concept borrowed from the autism literature (weak central coherence theory), might provide a framework to explain this joint occurrence. Two local-to-global experiments in vision (hierarchically constructed letters) and audition (hierarchically constructed melodies) as well as a pitch adjustment test measuring absolute pitch proficiency were conducted in 31 absolute pitch and 33 relative pitch professional musicians. Analyses revealed inconsistent group differences among reaction time, accuracy and speed-accuracy-composite-scores of experimental conditions (local vs. global, and congruent vs. incongruent stimuli). Furthermore, amounts of interference of global form on judgements of local elements and vice versa were calculated. Interestingly, reduced global-to-local interference in audition was associated with greater absolute pitch ability and in vision with higher autistic traits. Results are partially in line with the idea of a detail-oriented cognitive style in absolute pitch musicians. The inconsistency of the results might be due to limitations of global-to-local paradigms in measuring cognitive style and due to heterogeneity of absolute pitch possessors. In summary, this study provides further evidence for a multifaceted pattern of various and potentially interacting factors on the acquisition of absolute pitch.
Engineered developmental niche enables predictive phenotypic screening in human dystrophic cardiomyopathy
Authors: Macadangdang Jesse R. , Miklas Jason W. , Smith Alec S.T. , Choi Eunpyo , Leung Winnie , Wang Yuliang , Guan Xuan , Lee Soowan , Salick Max R. , Regnier Michael , Mack David , Childers Martin K. , Ruohola-Baker Hannele , Kim Deok-Ho 
Published: October 2018

ABSTRACTDirected differentiation of human pluripotent stem cells (hPSCs) into cardiomyocytes typically produces cells with structural, functional, and biochemical properties that most closely resemble those present in the fetal heart. Here we establish an in vitro engineered developmental cardiac niche to produce matured hPSC-derived cardiomyocytes (hPSC-CMs) with enhanced sarcomere development, electrophysiology, contractile function, mitochondrial capacity, and a more mature transcriptome. When this developmental cardiac niche was applied to dystrophin mutant hPSC-CMs, a robust disease phenotype emerged, which was not observed in non-matured diseased hPSC-CMs. Matured dystrophin mutant hPSC-CMs exhibited a greater propensity for arrhythmia as measured via beat rate variability, most likely due to higher resting cytosolic calcium content. Using a custom nanopatterned microelectrode array platform to screen functional output in hPSC-CMs exposed to our engineered developmental cardiac niche, we identified calcium channel blocker, nitrendipine, mitigated hPSC-CM arrhythmogenic behavior and correctly identified sildenafil as a false positive. Taken together, we demonstrate our developmental cardiac niche platform enables robust hPSC-CM maturation allowing for more accurate disease modeling and predictive drug screening.
An Efficient Computational Approach for Constructing the Allele Frequency Spectrum of Populations with Arbitrary Complex History
Authors: Chen Hua 
Published: October 2018

AbstractThe allele frequency spectrum (AFS), or site frequency spectrum, is commonly used to summarize the genomic polymorphism pattern of a sample, which is informative for inferring population history and detecting natural selection. Recently, Chen and Chen (2013) developed a method for analytically deriving the AFS for populations with temporally varying size through the coalescence time-scaling function. However, their approach is only applicable for population history scenarios in which the analytical form of the time-scaling function is tractable. In this paper, we propose a computational approach to extend the method to populations with arbitrary complex history by numerically approximating the time-scaling function. We demonstrate the performance of the approach by constructing the AFS for two population history scenarios: the logistic growth model and the Gompertz growth model, for which the AFS are unavailable with existing approaches.
Pentatricopeptide repeat poly(A) binding protein from mitochondria of trypanosomes
Authors: Mesitov Mikhail V. , Yu Tian , Suematsu Takuma , Sement Francois M. , Zhang Liye , Yu Clinton , Huang Lan , Aphasizheva Inna 
Published: October 2018

AbstractIn Trypanosoma brucei, most mitochondrial mRNAs undergo U-insertion/deletion editing, and 3′ adenylation and uridylation. The internal sequence changes and terminal extensions are coordinated: Pre-editing addition of the short (A) tail protects the edited transcript against 3′-5′ degradation, while post-editing A/U-tailing renders mRNA competent for ribosome recruitment. Participation of a poly(A) binding protein (PABP) in coupling of editing and 3′ modification processes has been inferred, but its identity and mechanism of action remained elusive. We report identification of KPAF4, a pentatricopeptide repeat-containing PABP which sequesters the A-tail and impedes exonucleolytic degradation. Conversely, KPAF4 inhibits uridylation of A-tailed transcripts and, therefore, premature A/U-tailing of partially-edited mRNAs. This quality check point prevents translation of incompletely edited mRNAs. Our findings also implicate the RNA editing substrate binding complex (RESC) in mediating the interaction between the 5′ end bound pyrophosphohydrolase MERS1 and 3′ end associated KPAF4 to enable mRNA circularization. This event is critical for transcript stability during the editing process.
Comparison of efficiency and technology across the banking systems of Vietnam, China and India
Authors: Nguyen Thanh Pham Thien 
Published: October 2018

Purpose
Given some similarities in the banking industry and economic condition across Vietnam, China and India, the purpose of this paper is to estimate and compare the cost and revenue efficiency of banks across these three countries over the period 1995–2011.

Design/methodology/approach
This study employs the meta-frontier of Battese et al. (2004) and O’Donnell et al. (2008) which envelops the three country-frontiers to measure the cost and revenue efficiency of banks in these three countries.

Findings
This study finds that Chinese banks adopt the most advanced cost-reducing and revenue-increasing technology when providing banking products to their customers, followed by Indian banks. Indian banks are as cost-efficient as Chinese banks, but more cost-efficient than Vietnamese banks. Indian banks are as revenue-efficient as Vietnamese banks, but less revenue-efficient than Chinese banks. Over the analysis period, banks in the three countries have employed the more advanced technology in reducing costs, and they have become more cost-efficient. Nonetheless, for revenue side, the improvement in revenue efficiency and adopted technology are observed only in Chinese banks. The main source of meta-cost and meta-revenue inefficiency of these banking systems stems from undertaking inferior technology rather than managerial ability. Results from comparison across bank types show that state-owned banks (SOBs) are more cost and revenue-efficient than privately owned banks, with Indian and Chinese SOBs being the most cost- and revenue-efficient, respectively.

Practical implications
To improve meta-cost efficiency, Chinese and Indian banks would constitute a relevant benchmark for Vietnamese banks, while to improve meta-revenue efficiency, Chinese banks would be considered as a relevant benchmark for Vietnamese and Indian banks.

Originality/value
This is the first study which utilizes meta-frontier to compare cost and revenue efficiency and technology across banks in Vietnam, China and India.
A model for supply chain risk management in the automotive industry using fuzzy analytic hierarchy process and fuzzy TOPSIS
Authors: Salehi Heidari Samira , Khanbabaei Mohammad , Sabzehparvar Majid 
Published: October 2018

Purpose
One of the most important issues in supply chain (SC) management is the identification and management of the risk involved in it. The purpose of this paper is to propose a comprehensive model of supply chain risk management (SCRM) in the product life cycle (PLC) and the operational process cycle (OPC). To decrease the risks in a fuzzy environment, the model considers the organizational performance factors (OPF) and the risk operational practices (ROP).

Design/methodology/approach
Fuzzy analytic hierarchy process is used to determine the weights of the relationships between the PLC, OPC and OPF in the hierarchical structure of the decision problem. In addition, the fuzzy technique for order preference by similarity to ideal solution is employed to recognize the priority of ROPs in dealing with the performance factors. The integrated framework is evaluated using the case study of an automotive company in Iran.

Findings
The results demonstrated that the proposed model can be used to formulate an appropriate method for prioritizing defined alternatives to decrease risk and improve the organizational performance in SCRM under fuzzy conditions.

Research limitations/implications
A major limitation of the study is that a few of the selected criteria for risk assessment are focused only on economic factors. Another limitation of the current study is related to the PLC, OPC and OPF being based on the work of Xia and Chen (2011).

Practical implications
The current study identified the more important stage in the PLC. More significant process in each stage of the PLC and weightier risk factors in each process of the OPC were determined. Some strategies for reducing risk in each stage of the PLC were presented. The best alternatives for reducing risks in SC were indicated.

Originality/value
It is worth mentioning that previous studies have not applied multiple criteria and alternatives to decrease the risks involved in the PLC and OPC parts of the SC under fuzzy conditions. However, it should be stated that some academics have used these techniques separately, in other specialized areas of the SC.
The view, brew and loo: perceptions of botanic gardens?
Authors: Catahan Nicholas , Woodruffe-Burton Helen 
Published: October 2018

PurposeThis is an exploratory and qualitative study to consider approaches to capture, analyse and monitor perceptions from big data, to inform and contribute to place management research and practice of botanic gardens (BGs). This paper aims to address the ongoing significant threat to BGs due to funding being cut and the need to inform and develop sustainable revenue streams for their survival.Design/methodology/approachGuiding research questions for this study were: ‘What are the perceived strengths and areas for development for 2 BGs via a Leximancer Automatic Content Analysis (ACA) of TripAdvisor online reviews; and do they match BGs purpose of scientific research, conservation, display and education?’ A content analysis of 582 online reviews from 2007 to 2017 follows qualitative methodology techniques using a combination of manual and automatic text analysis (Leximancer text mining software). These approaches enabled a comparison of online TripAdvisor reviews with Likert-type or rating scale items of 1 to 5 stars.FindingsInsights revealed the use of Leximancer and TripAdvisor (or similar innovations) as tools for potential place management, place marketing communications and monitoring purposes. Predominant perceptions extracted from reviews are not concerned with documented collections of living plants for the purposes of scientific discovery, conservation, display and education. Reviews clearly focus more upon aesthetics, facilities and services, which support previous studies. Overall, reviews highlighted positive sentiments towards the BGs.Research limitations/implicationsLimitations link to limited data across two BGs, synthesis and meaning of complex perceptions, matters of subjectivity and time needed to interpret information. Implications enable insights into BG “place” gleaned from big data in the form of user-generated content and electronic Word-Of-Mouth using Leximancer; viewed as a measure alongside management action plans. Future studies could strengthen debate and action regarding the use of Leximancer, and also public perception of BGs’ core functions, importance and value. The research supports potential to monitor and transform perceptions, values and beliefs. Outcomes could eventually inform policy and generate a much-needed shift in funds and resources for BGs by highlighting their relevance and value to society.Originality/valueAn empirical and methodological contribution via peer reviewed studies of visitor perceptions via online reviews of Britain’s BGs “place” and “space” analysed with Leximancer have never been published. This study critically explores potential visitor and place management needs of BGs. Managers can make better use of big data from social media platforms/digital channels, using a novel type of data analytical software like Leximancer for strategic planning; with more informed approaches to place management, innovation and development. A key contribution of this study is this ACA methodological approach for place management.
BRI and its digital dimension: twists and turns
Authors: Kozłowski Krzysztof 
Published: October 2018

Purpose
The purpose of this paper is to analyze the perspectives of the People’s Republic of China (PRC) Belt and Road strategy. The challenge in terms of studying the New Silk Road concept comes from the fact of dramatic difference between the declared ambitions of the Chinese state and the elusive character of concrete Chinese involvement, in particular as far as the digital dimension of the strategy is concerned.

Design/methodology/approach
The goal will be achieved by comparing the Chinese expansion in the Post-Soviet Central Asia with nowadays declarations concerning the digital version of the New Silk Road. For China, the Post-Soviet Central Asia was the first frontier approached on the basis of genuinely own integration strategy: the New Silk Road Diplomacy, which later evolved into the New Silk Road concept. An overview of Chinese activity in the region tells a lot about its grand strategy of today.

Findings
To paraphrase T.S. Kuhn, what one sees depends on not only what one is looking at but also what one has learned to notice. The Post-Soviet Central Asia shows the way Beijing thinks about integration. PRC achieved the most by basing on the free rider effect: concentrating on economic expansion, while other Powers provided relative regional security and stability.

Originality/value
The comparison of the beginnings of the New Silk Diplomacy in the 1990s with the plans of the New Digital Road gives a unique angle to grasp the specific features of the Chinese approach to international integration.