bluuebunny/crossref_metadata_2025_split huggingface dataset:
Frequent non-allelic gene conversion on the human lineage and its effect on the divergence of gene duplicates
Authors: Harpak Arbel , Lan Xun , Gao Ziyue , Pritchard Jonathan K. 
Published: May 2017

AbstractGene conversion is the copying of genetic sequence from a “donor” region to an “acceptor”. In non-allelic gene conversion (NAGC), the donor and the acceptor are at distinct genetic loci. Despite the role NAGC plays in various genetic diseases and the concerted evolution of gene families, the parameters that govern NAGC are not well-characterized. Here, we survey duplicate gene families and identify converted tracts in 46% of them. These conversions reflect a large GC-bias of NAGC. We develop a sequence evolution model that leverages substantially more information in duplicate sequences than used by previous methods and use it to estimate the parameters that govern NAGC in humans: a mean converted tract length of 250bp and a probability of 2.5×10−7per generation for a nucleotide to be converted (an order of magnitude higher than the point mutation rate). Despite this high baseline rate, we show that NAGC slows down as duplicate sequences diverge—until an eventual “escape” of the sequences from its influence. As a result, NAGC has a small average effect on the sequence divergence of duplicates. This work improves our understanding of the NAGC mechanism and the role that it plays in the evolution of gene duplicates.
Insight into the mechanism of protein thermostability based on the residue interaction degrees
Authors: Ge Huihua , Chu Yunmeng , Zhang Guangya 
Published: May 2017

ABSTRACTUnderstanding the basis of protein thermostability raises a general question: which residue with specific interaction degrees is more important to the protein thermostability? A strictly selected dataset of 131 pairs of thermophilic (TPs) and mesophilic proteins (MPs) was constructed. There were 6.4% and 8.4% of the total residues in sequences did not interact with others in TPs and MPs. The amino acid contents in sequences are closest to those with the interaction degrees of 3 according to the Chi-squared distances. Only Glu, Gln and the amide residues showed significant differences in sequences, which was the same as identified at low residue interaction degrees. However, we observed significant Phe, Lys, Leu, Gln and the charged, aliphatic, aromatic, positive charged and small residues at high interaction degree. Among them, Phe was rarely reported previously although aromatic residues were well-known contributor to protein thermostability. Finally, we took aspartate transcarbamylases as an example to explain how a residue with various interaction degrees contributed differently to their thermostability. Our results clearly demonstrated the differences of amino acids in sequence between TPs and MPs could only represent those involved in low interaction degrees. Much more residues with significant differences existed at high interaction degrees even if they had few significant amino acids in sequences. The interaction degree-based method should be an alternative tool in extracting valuable eigenvalues for predicting proteins attributes in bioinformatics. It could also provide a new perspective for studying the thermostability of proteins and engineering novel thermostable proteins.List of abbreviationsTPsthermophilic proteinsMPsmesophilic proteinsOGToptimal growth temperatureASAabsolute surface areas
Heat shock protein 70 (Hsp70) is involved in the Zika virus cellular infection process
Authors: Pujhari Sujit , Macias Vanessa M. , Nissly Ruth H. , Nomura Masashi , Kuchipudi Suresh V. , Rasgon Jason L. 
Published: May 2017

AbstractZika virus (ZIKV) is a historically neglected flavivirus that has recently caused epidemics in the western hemisphere. ZIKV has been associated with severe symptoms including infant microcephaly and Guillain Barré syndrome, stimulating interest in understanding factors governing ZIKV infection. Heat shock protein 70 (Hsp70) has been shown to be an infection factor for multiple viruses. We investigated the role of Hsp70 in the ZIKV infection process. We localized Hsp70 protein to the Vero cell membrane surface by confocal microscopy and demonstrated that, inside the cell, there is significant co-localization between Hsp70 and ZIKV E protein. Inducing and suppressing Hsp70 expression increased and decreased ZIKV production, respectively. Antibody blocking cell surface-localized Hsp70 decreased ZIKV cell infection rates and production of infectious virus particles, as did competition with recombinant Hsp70 protein. Our data suggest that Hsp70 is an important factor in the ZIKV infection process. Understanding the interactions between Hsp70 and ZIKV may lead to novel therapeutics for ZIKV infection, particularly for pregnant women and fetuses.
Arousal dependent modulation of thalamo-cortical functional interaction
Authors: Stitt Iain , Zhou Zhe Charles , Radtke-Schuller Susanne , Fröhlich Flavio 
Published: May 2017

Summary paragraphCognition and behavior emerge from the dynamic interaction of widely distributed, but functionally specialized brain networks. However, it remains unclear how network-level interactions dynamically reorganize to support ever-shifting cognitive and behavioral demands. Here, we investigate how the interaction between posterior parietal cortex (PPC) and lateral posterior (LP) / Pulvinar is shaped by ongoing fluctuations in pupil-linked arousal, which is a non-invasive measure related to neuromodulatory tone in the brain. We found that fluctuations in pupil-linked arousal tracked the dynamic interaction between PPC and LP/Pulvinar characterized by changes in the direction and carrier frequency of oscillatory interaction. Active visual exploration by saccadic eye movements elicited similar transitions in thalamo-cortical interaction. These findings suggest a common network substrate of both spontaneous activity and active vision. Thus, neuromodulators may play a role in dynamically sculpting the patterns of thalamo-cortical functional interaction that underlie visual processing.
Ultra-accurate Genome Sequencing and Haplotyping of Single Human Cells
Authors: Chu Wai Keung , Edge Peter , Lee Ho Suk , Bansal Vikas , Bafna Vineet , Huang Xiaohua , Zhang Kun 
Published: May 2017

AbstractAccurate detection of variants and long-range haplotypes in genomes of single human cells remains very challenging. Common approaches require extensivein vitroamplification of genomes of individual cells using DNA polymerases and high-throughput short-read DNA sequencing. These approaches have two notable drawbacks. First, polymerase replication errors could generate tens of thousands of false positive calls per genome. Second, relatively short sequence reads contain little to no haplotype information. Here we report a method, which is dubbed SISSOR (Single-Stranded Sequencing using micrOfluidic Reactors), for accurate single-cell genome sequencing and haplotyping. A microfluidic processor is used to separate the Watson and Crick strands of the double-stranded chromosomal DNA in a single cell and to randomly partition megabase-size DNA strands into multiple nanoliter compartments for amplification and construction of barcoded libraries for sequencing. The separation and partitioning of large single-stranded DNA fragments of the homologous chromosome pairs allows for the independent sequencing of each of the complementary and homologous strands. This enables the assembly of long haplotypes and reduction of sequence errors by using the redundant sequence information and haplotype-based error removal. We demonstrated the ability to sequence single-cell genomes with error rates as low as 10−8and average 500kb long DNA fragments that can be assembled into haplotype contigs with N50 greater than 7Mb. The performance could be further improved with more uniform amplification and more accurate sequence alignment. The ability to obtain accurate genome sequences and haplotype information from single cells will enable applications of genome sequencing for diverse clinical needs.
Coordinated Changes In The Accumulation Of Metal Ions In Maize (Zea mays ssp. mays L.) In Response To Inoculation With The Arbuscular Mycorrhizal FungusFunneliformis mosseae
Authors: Ramirez-Flores M. Rosario , Rellan-Alvarez Ruben , Wozniak Barbara , Gebreselassie Mesfin-Nigussie , Jakobsen Iver , Olalde-Portugal Victor , Baxter Ivan , Paszkowski Uta , Sawers Ruairidh J.H. 
Published: May 2017

AbstractArbuscular mycorrhizal symbiosis is an ancient interaction between plants and fungi of the phylum Glomeromycota. In exchange for photosynthetically fixed carbon, the fungus provides the plant host with greater access to soil nutrients via an extensive network of root-external hyphae. Here, to determine the impact of the symbiosis on the host ionome, the concentration of nineteen elements was determined in the roots and leaves of a panel of thirty maize varieties, grown under phosphorus limiting conditions, with, or without, inoculation with the fungusFunneliformis mosseae.Although the most recognized benefit of the symbiosis to the host plant is greater access to soil phosphorus, the concentration of a number of other elements responded significantly to inoculation across the panel as a whole. In addition, variety-specific effects indicated the importance of plant genotype to the response. Clusters of elements were identified that varied in a coordinated manner across genotypes, and that were maintained between non-inoculated and inoculated plants.AbbreviationsNCnon-colonizedMmycorrhizalSDWshoot dry weightICP-MSinductively coupled plasma mass spectrometryPCprincipal component
Distinct temporal filters in mitral cells and external tufted cells of the olfactory bulb
Authors: Vaaga Christopher E , Westbrook Gary L 
Published: May 2017

AbstractShort-term synaptic plasticity is a critical regulator of neural circuits, and largely determines how information is temporally processed. In the olfactory bulb, afferent olfactory receptor neurons respond to increasing concentrations of odorants with barrages of action potentials, and their terminals have an extraordinarily high release probability (Sicard, 1986; Murphyet al.,2004). These features suggest that during naturalistic stimuli, afferent input to the olfactory bulb is subject to strong synaptic depression, presumably truncating the postsynaptic response to afferent stimuli. To examine this issue, we used single glomerular stimulation in mouse olfactory bulb slices to measure the synaptic dynamics of afferent-evoked input at physiological stimulus frequencies. In cell-attached recordings, mitral cells responded to high frequency stimulation with sustained responses, whereas external tufted cells responded transiently. Consistent with previous reports (Murphyet al., 2004), olfactory nerve terminals onto both cell types had a high release probability (0.7), from a single pool of slowly recycling vesicles, indicating that the distinct responses of mitral and external tufted cells to high frequency stimulation did not originate presyaptically. Rather, distinct temporal response profiles in mitral cells and external tufted cells could be attributed to slow dendrodendritic responses in mitral cells, as blocking this slow current in mitral cells converted mitral cell responses to a transient response profile, typical of external tufted cells. Our results suggest that despite strong axodendritic synaptic depression, the balance of axodendritic and dendrodendritic circuitry in external tufted cells and mitral cells, respectively, tunes the postsynaptic responses to high frequency, naturalistic stimulation.Key PointsThe release probability of the ORN is reportedly one of the highest in the brain (Murphy et al., 2004), which is predicted to impose a transient temporal filter on postsynaptic cells.Mitral cells responded to high frequency ORN stimulation with sustained transmission, whereas external tufted cells responded transiently.The release probability of ORNs (0.7) was equivalent across mitral and external tufted cells and could be explained by a single pool of slowly recycling vesicles.The sustained response in mitral cells resulted from dendrodendritic amplification in mitral cells, which was blocked by NMDA and mGluR1 receptor antagonists, converting mitral cell responses to transient response profiles.Our results suggest that although the afferent ORN synapse shows strong synaptic depression, dendrodendritic circuitry in mitral cells produces robust amplification of brief afferent input, thus the relative strength of axodendritic and dendrodendritic input determines the postsynaptic response profile.
A destination’s gastronomy as a means for holiday well-being
Authors: Björk Peter , Kauppinen-Räisänen Hannele 
Published: May 2017

Purpose
To provide insights into holiday well-being, the purpose of this paper is to examine two inevitable traveller activities related to destinations’ gastronomy: pre-trip food information sourcing and the daily meals consumed.

Design/methodology/approach
A survey was carried out among 243 Finnish travellers. The findings are based on univariate analysis (t-test, ANOVA and regression analysis).

Findings
Pre-trip behaviour to ensure holiday well-being is based on travellers’ interests in food, an emotional desire for a sense of safety and a functional desire for convenience, while they collect information from the internet and guidebooks about recommended food places and local food as well as food safety and price level. Travellers’ place the highest importance on dinner for their holiday well-being, especially foodies – those travellers with a keen interest in food. Breakfast is the second most important meal contributing to holiday well-being.

Practical implications
These findings inform destination marketing organisations about what food dimensions they should emphasise in destination gastronomy-related marketing communication for tour operators and hotel and local restaurants about the essence of dinner and breakfast for holiday well-being.

Originality/value
The study provides insights into the role of destinations’ gastronomy in holiday well-being, which deserves to be studied in the current era of experiences and food interest.
Consumer-perceived quality characteristics of chicken meat and chicken meat products in Southeast Europe
Authors: Skunca Dubravka , Tomasevic Igor , Zdolec Nevijo , Kolaj Rezear , Aleksiev Georgi , Djekic Ilija 
Published: May 2017

Purpose
The purpose of this paper is to analyse consumer perception of quality characteristics of chicken meat and chicken meat products in Southeast European countries (Albania, Bosnia and Herzegovina, Bulgaria, Croatia, FYR of Macedonia, Montenegro, and Serbia).

Design/methodology/approach
Results were collected from a field survey by using data obtained from a questionnaire directed at 2,368 consumers during 2015.

Findings
This study identified four consumer segments: “typical”, “selective”, “chicken meat preparers” and “uninterested” chicken meat consumers.

Originality/value
Older consumers (50 years) have higher interest in chicken meat quality characteristics, while women are “chicken meat preparers”. Chicken meat consumers who prefer particular chicken parts and consume chicken meat because it is nutritious are found among the working population, while the most number of consumers “uninterested” in chicken meat come from Serbia.
Specialty food retailing: examining the role of products’ perceived quality
Authors: Calvo-Porral Cristina , Lévy-Mangin Jean-Pierre 
Published: May 2017

Purpose
The purpose of this paper is to address the following issue: “Does the products’ perceived quality influences the consumer behaviour in the specialty retailing setting?”

Design/methodology/approach
For this purpose, the authors propose and empirically test a conceptual model on the creation of consumer satisfaction and loyalty in specialty retailing, to examine the influence of products’ quality perception and its potential moderating role. Data were analysed through structural equation modelling on a sample of 592 consumers

Findings
The findings show that the store-based attributes have different influence on customer satisfaction and loyalty, according to the quality perception of products, and suggest the moderating role of products’ perceived quality.

Practical implications
Retailing managers may use the product’s perceived quality as a segmentation variable in the specialty food retailing context.

Originality/value
The major contribution of this paper is the empirical analysis of one subjective customer-based variable in the specialty retailing setting.
Using the Voluntary Retirement Scheme as an HR tool
Authors: Chaudhary Narendra Singh , Bhushan Bharat 
Published: May 2017

Purpose
The purpose of this paper is to highlight the significance of the voluntary retirement scheme (VRS) as a management tool for organisational restructuring.

Design/methodology/approach
The paper presents the personal view of the author, based on research findings and practical experience.

Findings
The paper advances the viewpoint that to attain the competitive edge and to survive in the current turbulent times, it is essential for the management to right size their organisations. It is imperative for them to look for the right kind of strategies to overcome the redundancy. They have to choose the most viable options considering its financial and legal implications. This would not only help management in maintaining the healthy industrial relations but also enhance the overall organisational profitability and well-being.

Practical implications
The paper highlights the pros and cons of the VRS. It reflects the financial and legal implications of the same on the employer and employees in the organisations.

Originality/value
This paper depicts how VRS (acts as a management tool and helps in improving organisational efficiency. It basically talks about exercising the VRS and its related legislation in an Indian context.
Open access journals: a bibliometric study in SSCI
Authors: Ma Tsu-Jui , Lee Gwo-Guang 
Published: May 2017

PurposeThe purpose of this paper is to describe a bibliometric study of journal articles in Social Sciences Citation Index (SSCI) related to open access journals. Publication trends from 1993 to 2016, core journals, prolific authors and article citation frequencies were examined to provide librarians and scholars with a basic reference of relevant resources.Design/methodology/approachAmong articles published in journals which have been listed in SSCI during 1993-2016, titles were searched for the term “open access journal”. The data were evaluated in response to five research questions concerning topics including publication trends from 1993 to 2016, core journals, prolific authors and article citation frequencies.FindingsIn total, 115 articles on open access journals were authored by 215 individuals from 1993 to 2016. The 115 articles analyzed were cited 842 times in 57 journals.Originality/valueThis paper describes a bibliometric study on open access journal publication, which has rarely been performed within the specific context of document supply issues. It provides a foundation for further research on titles as well as resources for librarians and scholars.
Resource sharing at the American University of Beirut: challenges and opportunities
Authors: Chalhoub Carla 
Published: May 2017

Purpose
This study aims to determine the effectiveness of the resource sharing initiative through signing reciprocal agreements, joining consortia and subscribing to OCLC at the American University of Beirut (AUB) Libraries.

Design/methodology/approach
Statistical analysis of interlibrary loan transactions over the past five years was conducted.

Findings
Joining local, regional and international consortia, signing reciprocal agreements with two institutions and subscribing to OCLC Worldshare ILL have maximized access to resources by reducing the cost allocated to ILL and expanded the DDS services to allow unlimited requests to all members of the AUB community.

Originality/value
Academic libraries are still facing budget cuts while they are expected to deliver better services to their communities. The implication of the statistics gathered discloses a constant need for finding ways to support resource sharing and to align with the University’s mission of fostering life-long learners by supporting research and maximizing access to resources.
Graph-theoretic node importance mining in world city networks: methods and applications
Authors: Xue Shan , Xiong Li , Lu Zhao , Wu Jia 
Published: May 2017

PurposeThis study aims to review the literature on graph-theoretic mining methods for node importance in both static and dynamic world city networks, which is correspondingly categorised by graph-theoretic node importance mining on network topologies and transmission mechanisms.Design/methodology/approachThe authors overview the graph-theoretic indicators of node importance: centrality and power. Then, the methods of graph-theoretic node importance mining on network topologies are assessed with node relevance, centrality- and power-based measurements, heterogeneous fusion and other miscellaneous approaches. The latest progress in transmission mechanisms is also reviewed in this study involving network evolution, node immunisation and robustness in dynamics. Finally, the findings are analysed and future directions in this field are suggested.FindingsThe method development of node importance mining is driven by complex application-based problems within a transmission mechanism. Fusion measurements, based on centrality and power, are extended by other graph mining techniques in which power has a significant role. In conclusion, the trends of node importance mining focus on power-embedded fusion measurements in the transmission mechanism-based complex applications.Originality/valueThis is the first systematic literature review of node importance from the view of graph-theoretic mining.
A surrogate-based generic classifier for Chinese TV series reviews
Authors: Ma Yufeng , Xia Long , Shen Wenqi , Zhou Mi , Fan Weiguo 
Published: May 2017

Purpose
The purpose of this paper is automatic classification of TV series reviews based on generic categories.

Design/methodology/approach
What the authors mainly applied is using surrogate instead of specific roles or actors’ name in reviews to make reviews more generic. Besides, feature selection techniques and different kinds of classifiers are incorporated.

Findings
With roles’ and actors’ names replaced by generic tags, the experimental result showed that it can generalize well to agnostic TV series as compared with reviews keeping the original names.

Research limitations/implications
The model presented in this paper must be built on top of an already existed knowledge base like Baidu Encyclopedia. Such database takes lots of work.

Practical implications
Like in digital information supply chain, if reviews are part of the information to be transported or exchanged, then the model presented in this paper can help automatically identify individual review according to different requirements and help the information sharing.

Originality/value
One originality is that the authors proposed the surrogate-based approach to make reviews more generic. Besides, they also built a review data set of hot Chinese TV series, which includes eight generic category labels for each review.