bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient Multivariate Analysis Algorithms for Longitudinal Genome-wide Association Studies
Authors: Ning Chao , Wang Dan , Zhou Lei , Wei Julong , Liu Yuanxin , Kang Huimin , Zhang Shengli , Zhou Xiang , Xu Shizhong , Liu Jian-Feng 
Published: August 2018

AbstractMotivationCurrent dynamic phenotyping system introduces time as an extra dimension to genome-wide association studies (GWAS), which helps to explore the mechanism of dynamical genetic control for complex longitudinal traits. However, existing methods for longitudinal GWAS either ignore the covariance among observations of different time points or encounter computational efficiency issues.ResultsWe herein developed efficient genome-wide multivariate association algorithms (GMA) for longitudinal data. In contrast to existing univariate linear mixed model analyses, the proposed new method has improved statistic power for association detection and computational speed. In addition, the new method can analyze unbalanced longitudinal data with thousands of individuals and more than ten thousand records within a few hours. The corresponding time for balanced longitudinal data is just a few minutes.Availability and ImplementationWe wrote a software package to implement the efficient algorithm named GMA (https://github.com/chaoning/GMA), which is available freely for interested users in relevant fields.
Integrating Mendelian randomization and multiple-trait colocalization to uncover cell-specific inflammatory drivers of autoimmune and atopic disease
Authors: McGowan Lucy M. , Smith George Davey , Gaunt Tom R. , Richardson Tom G. 
Published: August 2018

AbstractImmune mediated diseases (IMDs) arise from a lack of immune tolerance, causing chronic inflammation. Despite their growing prevalence, targeted therapies to treat IMDs are lacking. Cytokines and their receptors, which mediate inflammation, have been associated with IMD susceptibility. However, the complex signalling networks and multiple cell-types required to orchestrate inflammatory responses have made it difficult to pinpoint specific cytokines and immune cell-types which drive IMDs.In this study, we developed an analytical framework which integrates Mendelian randomisation (MR) and multiple-trait colocalization (moloc) analyses to determine putative cell-specific drivers of IMDs. We used MR to determine the likelihood of causal associations between the levels of 10 circulating cytokines/cytokine receptors and 9 IMDs within human populations of European descent. Conservative (single SNP) and liberal (multiple SNP) MR analysis supported a causal role for IL-18 in inflammatory bowel disease (P = 1.17 × 10−4) and eczema/dermatitis (P = 2.81 × 10−3), as well as roles for IL-2rα and IL-6R in several IMDs.Where associations between cytokines/cytokine receptors and IMDs were discovered using MR, we undertook moloc analyses. This was to assess the likelihood that cytokine/cytokine receptor protein quantitative trait loci (pQTL) and IMD-associated loci share a causal genetic variant along with expression QTL (eQTL) using data from 3 immune cell-types: monocytes, neutrophils and T cells. We found a monocyte and neutrophil-driven role for IL-18 in IBD pathogenesis, amongst evidence supporting several other cell-specific inflammatory drivers of IMDs. Our study helps to elucidate causal pathways for the pathogeneses of IMDs which, together with other studies, highlights possible therapeutic targets for their treatment.
Nuclear Tau modulates VGluT1 expression: a new function for Tau
Authors: Siano Giacomo , Varisco Martina , Caiazza Maria Claudia , Quercioli Valentina , Mainardi Marco , Ippolito Chiara , Cattaneo Antonino , Primio Cristina Di 
Published: August 2018

SummaryTau displacement from microtubules is the first step in the onset of tauopathies, and is followed by toxic protein aggregation. However, other non-canonical functions of Tau might have a role in these pathologies. Here, we demonstrate that a small amount of Tau localizes in the nuclear compartment and accumulates in both the soluble and DNA-bound fractions. We show that nuclear Tau regulates the expression of VGluT1, a disease-relevant gene directly involved in glutamatergic synaptic transmission. Impeding Tau/tubulin interaction in the cytosol favours its nuclear translocation and increases VGluT1 expression. Remarkably, the P301L mutation impairs this mechanism leading to a loss of function. Altogether, our results provide the demonstration of a direct physiological role of Tau on gene expression. Alterations of this mechanism may be at the basis of the onset of neurodegeneration.
Bacterial community dynamics during embryonic and larval development of three confamilial echinoids
Authors: Carrier Tyler J. , Reitzel Adam M. 
Published: August 2018

ABSTRACTDevelopment of some animals is influenced by and, in some cases, dependent on the associated microbiota. The timing of when associated bacterial communities are established during the development of marine invertebrates and their subsequent dynamics across stages are known for only a few species. Here, we compare the bacterial communities of three confamilial echinoids from egg to juvenile using sequence-based approaches. Bacterial communities are established on unfertilized eggs and change gradually during embryonic and larval development. Despite the differences amongst these pre-metamorphic stages, approximately thirty-percent of OTUs identified in association with unfertilized egg were present in the juveniles. During embryonic development, host-associated communities diverged from the environmental microbiota but later converged following the onset of larval feeding. Taken together, the data presented here support the hypothesis that bacterial communities are established prior to fertilization and community composition shifts gradually thereafter, all while remaining distinct from the environment. Future work will need to determine the relative influence of the host and bacteria-bacteria interactions in shaping the associated bacterial community to determine the potential functional importance of bacteria during the development of larval sea urchins and benthic marine invertebrates more broadly.
A Data-driven Individual-based Model of Infectious Disease in Livestock Operation: A Validation Study for Paratuberculosis
Authors: Al-Mamun Mohammad. A. , Smith Rebecca. L. , Nigsch Annette. , Schukken Ynte. H. , Gröhn Yrjo.T. 
Published: August 2018

AbstractChronic livestock diseases cause large financial loss and affect the animal health and welfare. Controlling these diseases mostly requires precise information on both individual animal and population dynamics to inform farmer’s decision. Mathematical models provide opportunities to test different control and elimination options rather implementing them in real herds, but these models require valid parameter estimation and validation. Fitting these models to data is a difficult task due to heterogeneities in livestock processes. In this paper, we develop an infectious disease modeling framework for a livestock disease (paratuberculosis) that is caused by Mycobacterium avium subsp. paratuberculosis (MAP). Infection with MAP leads to reduced milk production, pregnancy rates, and slaughter value and increased culling rates in cattle and causes significant economic losses to the dairy industry in the US. These economic effects are particularly important motivations in the control and elimination of MAP. In this framework, an individual-based model (IBM) of a dairy herd was built and a MAP infection was integrated on top of it. Once the model produced realistic dynamics of MAP infection, we implemented an evaluation method by fitting it to data from three dairy herds from the Northeast region of the US. The model fitting exercises used least-squares and parameter space searching methods to obtain the best-fitted values of selected parameters. The best set of parameters were used to model the effect of interventions. The results show that the presented model can complement real herd statistics where the intervention strategies suggested a reduction in MAP but no elimination was observed. Overall, this research not only provides a complete model for MAP infection dynamics in a cattle herd, but also offers a method for estimating parameter by fitting IBM models.
Fluctuating environments select for short-term phenotypic variation leading to long-term exploration
Authors: Canino-Koning Rosangela , Wiser Michael J. , Ofria Charles 
Published: August 2018

AbstractGenetic spaces are often described in terms of fitness landscapes or genotype-to-phenotype maps, where each genetic sequence is associated with phenotypic properties and linked to other genotypes that are a single mutational step away. The positions close to a genotype make up its “mutational landscape” and, in aggregate, determine the short-term evolutionary potential of a population. Populations with wider ranges of phenotypes in their mutational neighborhood are known to be more evolvable. Likewise, those with fewer phenotypic changes available in their local neighborhoods are more mutationally robust. Here, we examine whether forces that change the distribution of phenotypes available by mutation profoundly alter subsequent evolutionary dynamics.We compare evolved populations of digital organisms that were subject to either static or cyclically-changing environments. For each of these, we examine diversity of the phenotypes that are produced through mutations in order to characterize the local genotype-phenotype map. We demonstrate that environmental change can push populations toward more evolvable mutational landscapes where many alternate phenotypes are available, though purely deleterious mutations remain suppressed. Further, we show that populations in environments with harsh changes switch phenotypes more readily than those in environments with more benign changes. We trace this effect to repeated population bottlenecks in the harsh environments, which result in shorter coalescence times and keep populations in regions of the mutational landscape where the phenotypic shifts in question are more likely to occur. Typically, static environments select solely for immediate optimization, at the expensive of long-term evolvability. In contrast, we show that with changing environments, short-term pressures to deal with immediate challenges can align with long-term pressures to explore a more productive portion of the mutational landscape.
SOL1 and SOL2 Regulate Fate Transition and Cell Divisions in the Arabidopsis Stomatal Lineage
Authors: Simmons Abigail R. , Davies Kelli A. , Wang Wanpeng , Liu Zhongchi , Bergmann Dominique C. 
Published: August 2018

AbstractIn the stomatal lineage, cells make fate transitions from asymmetrically dividing and self-renewing meristemoids, to commitment to the guard mother cell identity, and finally though a single division to create mature, post-mitotic stomatal guard cells. Flexibility in the stomatal lineage allows plants to alter leaf size and stomatal density in response to environmental conditions; however, transitions must be clean and unidirectional in order to produce functional and correctly patterned stomata. Among direct transcriptional targets of the stomatal initiating factor, SPEECHLESS, we found a pair of genes,SOL1andSOL2, required for effective transitions in the lineage. Here we show that these two genes, which are homologues of the LIN54 DNA-binding components of the mammalian DREAM complex, are expressed in a cell cycle dependent manner and regulate cell fate and division properties in the self-renewing early lineage. In the terminal division of the stomatal lineage, however, these two proteins appear to act in opposition to their closest paralogue,TSO1, revealing complexity in the gene family may enable customization of cell divisions in coordination with development.
Japanese–French tastes in simulated women’s sportswear t-shirts
Authors: Marsac Eva , Kim KyoungOk , Takatera Masayuki 
Published: August 2018

Purpose
The purpose of this paper is to investigate differences in taste in women’s sportswear t-shirts, between Japanese and French people.

Design/methodology/approach
A questionnaire survey on the impression of the appearance of t-shirts was conducted using three-dimensional simulations that the authors created. A sensory test was carried out for 24 designs (having varying types of sleeves, bodice length and fitting) on 51 examinees (26 Japanese and 25 French) who voluntarily participated.

Findings
Results show that both Japanese and French people most appreciated very short t-shirts and considered sleeveless and tank top shirts to be the most appropriated for exercise. Participants liked a cool, modern, showy, short, special, elaborate and feminine design. Additionally, Japanese people considered that casual clothes that are suitable for exercise are not suitable for wearing outside the gym, whereas this was not notable for French people.

Originality/value
The results of the present study will allow the sportswear industry to better target clients.
Performance investigation of micro-pocketed textured pad thrust bearing
Authors: Aggarwal Shipra , Pandey R.K. 
Published: August 2018

Purpose
The purpose of this paper is to conceive a new surface texture incorporating a tiny shape among the micro-pockets (with circular, rectangular, trapezoidal and triangular cross-sections) and dimples (cylindrical, hemispherical and ellipsoidal) for exploring to enhance the maximum possible performance behaviors of sector shape pad thrust bearing.

Design/methodology/approach
Numerical simulation of hydrodynamically lubricated sector shape textured pad thrust bearing has been presented incorporating thermal and cavitation effects. The coupled solution of governing equations (Reynolds equation, film thickness expression, viscosity–temperature relation, energy equation and Laplace equation) has been achieved using finite difference method and Gauss–Seidel iterative scheme.

Findings
With new textured pads, higher load-carrying capacity and lower coefficient of friction are obtained in comparison to plain sector shape pad. Texture pattern comprising square cross-sectional pockets yields higher load-carrying capacity and lower coefficient of friction in comparison to other cross-sectional shapes (circular, trapezoidal and triangular) of pockets considered herein.

Originality/value
This study reports a new texture, which involves micro-pockets of square cross-sectional shapes to improve the performance behavior of sector shape pad thrust bearing. About 75 per cent increase in load carrying capacity and 42 per cent reduction in coefficient of friction have been achieved with pad having new texture in comparison to conventional pad.
Pain points of cultural institutions in search visibility: the case of Serbia
Authors: Krstić Nataša , Masliković Dejan 
Published: August 2018

Purpose
The purpose of this paper is to identify the common issues affecting the cultural institutions’ websites in terms of organic search visibility and to detect if there are some category specifics for the national libraries, archives and museums.

Design/methodology/approach
In the first phase, an online survey was conducted involving the cultural institutions of national importance, aiming to map the current state of their websites in organizational and functional terms, to collect the information about the used domains, their social media activity and the use of analytical tools to monitor the visitor behavior and online traffic. In the second phase, the cultural institutions’ websites were analyzed using the “White Hat SEO” technics of optimization on Google.

Findings
From the category perspective, the historical archives have the best Technical search engine optimization (SEO) position due to the low coding errors and fair site speed, the libraries are leading in content generation and the museums have a very good total SEO index due to their strong social media activities. Common issues are detected in the description of web images, non-existence of sitemaps and low website mobile friendliness.

Research limitations/implications
The data were collected from the personnel of the national cultural institutions based on their pre-assumed knowledge and understanding of website management.

Practical implications
The research methodology can be used to analyze the organic visibility of any national culture on search engines.

Originality/value
A research gap in addressing the cultural institutions’ websites from the search engine perspective was identified and addressed within the paper.
Preparation of amphiphilic block copolymers (polyethylene adipate-block-polyethylene glycol) and its application in rotogravure ink formulations
Authors: Assem Yasser , Mohamed Heba A. , Said Rana , El-Masry Ahmed 
Published: August 2018

PurposeThe purpose of this paper is to prepare amphiphilic block copolymers polyethylene adipate-block-polyethylene glycol (PEA-b-PEG)s and study their performance as plasticizers in rotogravure ink formulations.Design/methodology/approachSeries of amphiphilic block copolymers (PEA-b-PEG1), (PEA-b-PEG2), (PEA-b-PEG3), (PEA-b-PEG4) and (PEA-b-PEG5) were prepared by the reaction of adipic acid, ethylene glycol and polyethylene glycol of different molecular weights (300, 1,000, 2,000, 10,000 and 20,000 g/mol), respectively. Full characterization of the prepared copolymers was achieved using Fourier Transfer Infrared Spectroscopy (FTIR), 1H NMR, thermal gravimetric analysis (TGA) and differential scanning calorimetry (DSC). The performance of the prepared copolymers as plasticizers for neat nitrocellulose resin were studied in different formulations, namely, R1, R2, R3, R4 and R5 containing copolymers (PEA-b-PEG1), (PEA-b-PEG2), (PEA-b-PEG3), (PEA-b-PEG4) and (PEA-b-PEG5), respectively. In addition to formula R0 that contains acetyl tributyl citrate (ATBC) as a commercial plasticizer. The mechanical properties, thermal analysis (DSC, TGA) and optical properties of the prepared formulations films were investigated. Theses amphiphilic block copolymers were then applied as plasticizers in different rotogravure ink formulations (F1, F2, F3, F4 and F5) and compared with commercial rotogravure ink formula (F0). The color measurements and optical properties of all formulations were achieved.FindingsIt was found that the performance of the prepared copolymers as plasticizers in different formulations based on nitro cellulose resin gives better gloss, adhesion for R1 compared with the other samples and color strength for F1 compared with F0. Finally, all the samples gave excellent plasticizing effect.Research limitations/implicationsThe authors believe that type of these materials open the way for a new class of plasticizers that upon application or even degradation gives small ecofriendly molecules (adipic acid and or ethylene glycol moieties) taking into consideration the simplicity of the rout of the synthesis process.Practical implicationsThe prepared ecofriendly (PEA-b-PEG)s could be successfully used as plasticizers instead of commercial plasticizer ATBC.Originality/valueThe research provides that the prepared (PEA-b-PEG)s with different molecular weights can act as plasticizers in rotogravure ink formulations, and their performance was acceptable and available.
Electrochemical noise assessment of effect of sol parameters on the performance of an eco-friendly silane sol-gel coating on 304L stainless steel
Authors: Ansari Fahimeh , Naderi Reza , Rafiaei Fahimeh 
Published: August 2018

ProposeThis paper aims to access the protective function of hybrid sol-gel coatings deposited on 304L stainless steel substrate in silane solutions containing a mixture of tetraethoxysilane, methyltriethoxysilane and glycidyloxypropyltrimethoxysilane with different pH values during various immersion periods.Design/methodology/approachThe 304L stainless steels coated through 10 and 30 s of immersion in the silane solutions with pH values of 2.1 and 2.8 were exposed to NaCl solution. The corrosion resistance of the coated substrates was studied through taking advantage of electrochemical noise method as well as atomic force microscopy (AFM), water contact angle and field emission-type scanning electron microscopy (FESEM) surface analysis.FindingsThe electrochemical current noise, PSD (I) plot, noise resistance and characteristic charge as parameters extracted from electrochemical noise method indicated the superiority of eco-friendly silane coating deposited on the substrate surface during 10 s exposure to the solution, due to the film uniformity and homogeneity as confirmed by FESEM and AFM. Moreover, immersion of the stainless steel in the silane solution with pH 2.1, characterized by higher hydrolysis ratio, led to more effective corrosion control in the NaCl electrolyte according to the results of electrochemical noise and FTIR measurements.Research limitations/implicationsThe noise resistance and characteristic charge as electrochemical noise parameters were only used in this research to evaluate the protective behavior of the water-based silane sol-gel coatings. Future studies should examine the correlation between electrochemical noise data and the parameters extracted from other electrochemical methods, e.g. electrochemical impedance spectroscopy.Practical implicationsThe data obtained in this research may provide an effective approach based on electrochemical noise method to screen the silane sol-gel coatings for protection of metallic substrates against corrosion.Originality/valueAccording to the literature, no report can be found studying the effect of immersion time on a silane solution, including glycidyloxypropyltrimethoxysilane, tetraethoxysilane and methyltriethoxysilane, as well as the silane solution pH on the corrosion resistance of 304L stainless steel in NaCl solution through electrochemical noise method.
Development of a diagnostic system for detection of specific antibodies and antigens against Middle East respiratory syndrome coronavirus
Authors: Lee Kunse , Ko Hae Li , Lee Eun‐Young , Park Hyo‐Jung , Kim Young Seok , Kim Yeon‐Sook , Cho Nam‐Hyuk , Park Man‐Seong , Lee Sang‐Myeong , Kim Jihye , Kim Hun , Seong Baik Lin , Nam Jae‐Hwan 
Published: August 2018

ABSTRACTMiddle East respiratory syndrome coronavirus (MERS‐CoV) is a single‐stranded RNA virus that causes severe respiratory disease in humans with a high fatality rate. Binding of the receptor binding domain (RBD) of the spike (S) glycoprotein to dipeptidyl peptidase 4 is the critical step in MERS‐CoV infection of a host cell. No vaccines or clinically applicable treatments are currently available for MERS‐CoV. Therefore, rapid diagnosis is important for improving patient outcomes through prompt treatment and protection against viral outbreaks. In this study, the aim was to establish two ELISA systems for detecting antigens and antibodies against MERS‐CoV. Using a recombinant full‐length S protein, an indirect ELISA was developed and found to detect MERS‐CoV‐specific antibodies in animal sera and sera of patient with MERS. Moreover, MAbs were induced with the recombinant S protein and RBD and used for sandwich ELISA to detect the MERS‐CoV S protein. Neither ELISA system exhibited significant intra‐assay or inter‐assay variation, indicating good reproducibility. Moreover, the inter‐day precision and sensitivity were adequate for use as a diagnostic kit. Thus, these ELISAs can be used clinically to diagnose MERS‐CoV.