bluuebunny/crossref_metadata_2025_split huggingface dataset:
M2IA: a Web Server for Microbiome and Metabolome Integrative Analysis
Authors: Ni Yan , Yu Gang , Chen Huan , Deng Yongqiong , Wells Philippa M , Steves Claire J , Ju Feng , Fu Junfen 
Published: June 2019

AbstractBackgroundIn the last decade, integrative studies of microbiome and metabolome have experienced exponential growth in understanding their impact on human health and diseases. However, analyzing the resulting multi-omics data and their correlations remains a significant challenge in current studies due to the lack of a comprehensive computational tool to facilitate data integration and interpretation. In this study, we have developed a microbiome and metabolome integrative analysis pipeline (M2IA) to meet the urgent needs for tools that effectively integrate microbiome and metabolome data to derive biological insights.ResultsM2IA streamlines the integrative data analysis between metabolome and microbiome, including both univariate analysis and multivariate modeling methods. KEGG-based functional analysis of microbiome and metabolome are provided to explore their biological interactions within specific metabolic pathways. The functionality of M2IA was demonstrated using TwinsUK cohort data with 1116 fecal metabolites and 16s rRNA microbiome from 786 individuals. As a result, we identified two important pathways, i.e., the benzoate degradation and phosphotransferase system, were closely associated with obesity from both metabolome and microbiome.ConclusionsM2IA is a public available web server (http://m2ia.met-bioinformatics.cn) with the capability to investigate the complex interplay between microbiome and metabolome, and help users to develop mechanistic hypothesis for nutritional and personalized therapies of diseases.
The common message of constraint-based optimization approaches: overflow metabolism is caused by two growth-limiting constraints
Authors: de Groot Daan H. , Lischke Julia , Muolo Riccardo , Planqué Robert , Bruggeman Frank J. , Teusink Bas 
Published: June 2019

AbstractLiving cells can express different metabolic pathways that support growth. The criteria that determine which pathways are selected in which environment remain unclear. One recurrent selection is overflow metabolism: the simultaneous usage of an ATP-efficient and -inefficient pathway, shown for example inEscherichia coli,Saccharomyces cerevisiaeand cancer cells. Many models, based on different assumptions, can reproduce this observation. Therefore, they provide no conclusive evidence which mechanism is causing overflow metabolism. We compare the mathematical structure of these models. Although ranging from Flux Balance Analyses to self-fabricating Metabolism and Expression models, we can rewrite all models into one standard form. We conclude that all models predict overflow metabolism when two, model-specific, growth-limiting constraints are hit. This is consistent with recent theory. Thus, identifying these two constraints is essential for understanding overflow metabolism. We list all imposed constraints by these models, so that they can hopefully be tested in future experiments.
Mismatch of the morphology model is mostly unproblematic in total-evidence dating: insights from an extensive simulation study
Authors: Klopfstein Seraina , Ryer Remo , Coiro Mario , Spasojevic Tamara 
Published: June 2019

AbstractCalibrating the molecular clock is the most contentious step in every dating analysis, but the emerging total-evidence dating approach promises increased objectivity. It combines molecular and morphological data of extant and fossil taxa in a Bayesian framework. Information about absolute node ages stems from the inferred fossil placements and associated branch lengths, under the assumption of a morphological clock. We here use computer simulations to assess the impact of mismatch of the morphology model, such as misspecification of character states and transition rates, non-stationarity of the evolutionary process, and extensive variation of evolutionary rates among branches. Comparisons with published datasets suggest that, at least for evolutionary rates typically observed in discrete morphological characters, the total-evidence dating framework is surprisingly robust to these factors. We show that even with relatively low numbers of morphological characters sampled, extensive model mismatch is mostly irrelevant for the performance of the method. The only exception we found are cases of highly asymmetric state frequencies and thus transition rates, but these can be accounted for by appropriate morphology models. In contrast, we find that the temporal scope of fossil sampling has a major impact on divergence time estimates, with the time signal quickly eroding if only rather young fossils are included in an analysis. Our results suggest that total-evidence dating might work even without a good understanding of morphological evolution and that study design should instead focus on an adequate sampling of all relevant fossils, even those with highly incomplete preservation.
Cryo-EM structure of the complete and ligand-saturated insulin receptor ectodomain
Authors: Gutmann Theresia , Schäfer Ingmar , Poojari Chetan , Brankatschk Beate , Vattulainen Ilpo , Strauss Mike , Coskun Ünal 
Published: June 2019

AbstractGlucose homeostasis and growth essentially depend on the peptide hormone insulin engaging its receptor. Despite biochemical and structural advances, a fundamental contradiction has persisted in the current understanding of insulin ligand–receptor interactions. While biochemistry predicts two distinct insulin binding sites, 1 and 2, recent structural analyses have only resolved site 1. Using a combined approach of cryo-EM and atomistic molecular dynamics simulation, we determined the structure of the entire dimeric insulin receptor ectodomain saturated with four insulin molecules. Complementing the previously described insulin–site 1 interaction, we present the first view of insulin bound to the discrete insulin receptor site 2. Insulin binding stabilizes the receptor ectodomain in a T-shaped conformation wherein the membrane-proximal domains converge and contact each other. These findings expand the current models of insulin binding to its receptor and of its regulation. In summary, we provide the structural basis enabling a comprehensive description of ligand–receptor interactions that ultimately will inform new approaches to structure-based drug design.In briefA cryo-EM structure of the complete insulin receptor ectodomain saturated with four insulin ligands is reported. The structural model of the insulin–insulin receptor complex adopts a T-shaped conformation, reveals two additional insulin-binding sites potentially involved in the initial interaction of insulin with its receptor, and resolves the membrane proximal region.
Salivary sex hormone levels following oxytocin administration in autistic and typical women
Authors: Procyshyn Tanya L. , Lombardo Michael V. , Lai Meng-Chuan , Auyeung Bonnie , Crockford Sarah K. , Deakin Julia , Soubramanian Sentil , Sule Akeem , Baron-Cohen Simon , Bethlehem Richard A. I. 
Published: June 2019

AbstractOxytocin administration, which may be of therapeutic value for social disabilities, likely influences endogenous levels of other socially-relevant hormones. However, to date, the effects of oxytocin administration on endogenous hormones have only been examined in typical males. The need to consider multi-hormone interactions is particularly warranted in oxytocin trials for autism due to evidence of irregularities in both oxytocin and sex steroid systems. Here, as part of a larger trial with a double-blind cross-over design, we assessed salivary testosterone and oestradiol levels in 16 autistic and 29 typical women before and after intranasal administration of 24IU oxytocin or placebo. Distinct patterns of change in testosterone and oestradiol across time were observed between groups, with autistic women showing increases in both hormones 90 min post-administration and typical women showing small decreases (mean %change oestradiol: +12% Autism, −10% Typical, 95%CI of difference: 5.0–39.4%, p=0.01; mean %change testosterone: +8% Autism, −14% Typical, 95%CI of difference: 7.8–35.6%, p=0.002). Under the oxytocin condition, the group difference in %change testosterone was amplified (+14.4% Autism, −15.2% Typical, p=0.018). Although baseline hormone levels did not differ between groups, greater baseline oestradiol relative to testosterone was negatively correlated with autistic-like traits (r= −0.36, p=0.019) and positively correlated (r=0.35, p=0.02) with self-reported empathy in the overall sample. These results provide further evidence that oxytocin influences endogenous testosterone, with autistic women showing increases similar to previous reports in typical men. These findings may help to identify autistic people expected to benefit most from interventions involving oxytocin.
Amyloid pathology disrupts gliotransmitter release in astrocytes
Authors: Pillai Anup G. , Nadkarni Suhita 
Published: June 2019

AbstractAccumulation of amyloid-β peptide (Aβ), a hallmark of Alzheimer’s disease (AD), is associated with synchronous hyperactivity and dysregulated Ca2+ signaling in hippocampal astrocytes. However, the consequences of altered Ca2+ signaling on the temporal dynamics of Ca2+ and gliotransmitter release events at astrocytic microdomains are not known. We have developed a detailed biophysical model of microdomain signaling at a single astrocytic process that accurately describes key temporal features of Ca2+ events and Ca2+-mediated kiss-and-run and full fusion exocytosis. Using this model, we ask how aberrant plasma-membrane Ca2+ pumps and mGluR activity, molecular hallmarks of Aβ toxicity that are also critically involved in Ca2+ signaling, modify astrocytic feedback at a tripartite synapse. We show that AD related molecular pathologies increase the rate and synchrony of Ca2+ and exocytotic events triggered by neuronal activity. Moreover, temporal precision between Ca2+ and release events, a mechanism indispensable for rapid modulation of synaptic transmission by astrocytes, is lost in AD astrocytic processes. Our results provide important evidence on the link between AD-related molecular pathology, dysregulated calcium signaling and gliotransmitter release at an astrocytic process.
A bacterial regulatory uORF senses multiple classes of ribosome-targeting antibiotics
Authors: Baniulyte Gabriele , Wade Joseph T. 
Published: June 2019

ABSTRACTExpression of many bacterial genes is regulated bycis- andtrans-acting elements in their 5’ upstream regions (URs).Cis-acting regulatory elements in URs include upstream ORFs (uORF), short ORFs that sense translation stress that manifests as ribosomes stalling at specific codons within the uORF. Here, we show that the transcript encoding theEscherichia coliTopAI-YjhQ toxin-antitoxin system is regulated by a uORF that we name “toiL”. We propose that in the absence of translation stress, a secondary structure in the UR represses translation of thetopAItranscript by occluding the ribosome-binding site. Translation repression oftopAIleads to premature Rho-dependent transcription termination within thetopAIORF. At least five different classes of ribosome-targeting antibiotics relieve repression oftopAI. Our data suggest that these antibiotics function by stalling ribosomes at different positions withintoiL, thereby altering the RNA secondary structure around thetopAIribosome-binding site. Thus,toiLis a multipurpose uORF that can respond to a wide variety of translation stresses.
Social isolation: development and validation of measures
Authors: Ranjan Sushant , Yadav Rama Shankar 
Published: June 2019

Purpose
The purpose of this paper is to develop and empirically validate items on social isolation. The comprehensive literature review of existing studies on the measures of social isolation, loneliness and the related construct was conducted. The paper seeks to conceptualize, validate and present items to measure social isolation.

Design/methodology/approach
The paper is based on theoretical and empirical investigation of the measures of social isolation, loneliness and related constructs such as social others, social loneliness and feeling of sociability. The items were generated through theoretical exploration of previous literature and later modified. The author examined the items through exploratory factor analysis, confirmatory factor analysis and further checked for external criterion validity. Data collected from 128 individuals, in India, were examined to design and validate the scale.

Findings
The finding of the paper is a ten-item social isolation scale. Using structural equation modeling, we have found extraversion and well-being significantly associated with final items in the present study, confirming the external quality of the scale.

Practical implications
Organizations may benefit by close examination of the presence of social isolation in employees along with providing support and assistance to employees so as to reduce negative consequences of social isolation and can address the well-being of the employee.

Originality/value
There is a dearth of developed and validated measures of social isolation in the literature. The study reveals the conceptualization and empirical validation of measures of social isolation in the Indian context so that researchers can move forward to develop theories on social isolation.
Numerical assessment of miniaturized cold spray nozzle for additive manufacturing
Authors: Nasif Gus , Barron R.M. , Balachandar Ram , Villafuerte Julio 
Published: June 2019

Purpose
Application of cold spray technology may exhibit significant benefits for the additive manufacturing process, particularly for producing intricate objects. To ascertain the feasibility of such an application, this paper aims to present a numerical investigation of the effect of scaling down a convergent-divergent (de Laval) nozzle, which is typically used in the cold spray industry, on the compressible flow parameters and thermal characteristics.

Design/methodology/approach
The Navier–Stokes equations and energy equation governing compressible flow are numerically solved using a finite volume method with a coupled solver. The conjugate heat transfer technique is used to couple fluid and solid heat transfer domains and predict the local heat transfer coefficient between the solid and fluid. The use of various RANS turbulence models has also been investigated to quantify the effect of the turbulence model on the simulation.

Findings
The numerical results reveal that the flow and thermal characteristics are altered as the convergent-divergent nozzle is scaled down. The static pressure and temperature profiles at any section in the nozzle are shifted toward higher values, while the Mach number profile at any section in the nozzle is shifted toward a lower Mach number. The turbulent kinetic energy at the nozzle exit increases with the scaling down of the nozzle geometry. This study also provides convincing evidence that the adiabatic approach is still suitable even though the temperature of the nozzle wall is extremely high, as required for industrial application. Results indicate that it is feasible to use the available capabilities of the cold spray technology for additive manufacturing after scaling down the nozzle.

Originality/value
The idea of adopting cold spray technology for additive manufacturing is new and innovative. To develop this idea into a viable commercial product, a thorough understanding of the flow physics within a cold spray nozzle is required. The simulation results discussed in this paper demonstrate the effect that scaling down of a convergent-divergent nozzle has on the flow characteristics in the nozzle.
Free convection analysis in a Γ-shaped heat exchanger using lattice Boltzmann method employing second law analysis and heatline visualization
Authors: KhakRah HamidReza , Mohammaei Mehdi , Hooshmand Payam , Bagheri Navid , Hasani Malekshah Emad 
Published: June 2019

Purpose
The nanofluid flow and heat transfer within a heat exchanger, with different thermal arrangements of internal active bodies, are investigated.

Design/methodology/approach
For the numerical simulations, the lattice Boltzmann method is utilized. The KKL model is used to predict the dynamic viscosity of CuO-water nanofluid. Furthermore, the Brownian method is taken account using this model. The influence of shapes of nanoparticles on the heat transfer performance is considered.

Findings
The results show that the platelet nanoparticles render higher average Nusselt number showing better heat transfer performance. In order to perform comprehensive analysis, the heatline visualization, local and total entropy generation, local and average Nusselt variation are employed.

Originality/value
The originality of this work is carrying out a comprehensive investigation of nanofluid flow and heat transfer during natural convection using lattice Boltzmann method and employing second law analysis and heatline visualization.
Behavioral intentions of different religions
Authors: Jumani Zulfiqar Ali , Sukhabot Sasiwemon 
Published: June 2019

Purpose
The demand for halal products is growing and attracting the attention of producers. In recent years, the importance of halal logo and popularity of halal products has increased. The purpose of this paper was to identify the behavioral intentions among people of different religion in respect of purchasing products bearing halal logo (halal logo products) at convenience stores in Hatyai. 7-Eleven store chain was targeted to collect data in this research because it serves people of different religions.

Design/methodology/approach
The conceptual model adopted for this research work was the theory of reasoned action (TRA). The response of consumers was collected through a structured survey, using the convenience sampling technique. A total of 215 respondents submitted their responses, consisting of 92.8 per cent local respondents and 8.2 per cent international respondents. The purposive sample technique was used to select the locations for collecting data, who was purchasing items from 7-Eleven stores and lives in Hatyai.

Findings
The findings indicate that Muslims strictly follow the halal logo and their attitude is positive in selecting halal logo products. The influence of their subjective norms is stronger because of their families and culture, as they are Muslim which influence their intentions. For non-Muslims, there is no obligation requiring them to select halal logo products, but even so, around 80 per cent of non-Muslims showed a positive attitude toward the halal logo, 54 per cent showed were interest and indicated that they may select products with halal logo in future.

Research limitations/implications
This study was conducted in Hatyai and the results were based on three independent variables, namely, attitude, subjective norms and intention, with religion as the demographic variable. The findings offer an insight into the importance of the halal logo for different religions at convenience stores in Hatyai.

Practical implications
This study is initially beneficial for 7-Eleven stores, other convenience stores, businesses and halal institutes. It offers an insight into the importance of the halal logo and the motives of consumers in choosing halal logo products.

Originality/value
This paper seeks to explicate consumers’ intentions to buy halal logo products in convenience stores.
Categories in emergency decision-making: prototype-based classification
Authors: Cai Mei , Wei Guo , Cao Jie 
Published: June 2019

PurposeThis paper aims to demonstrate how to make emergency decision when decision makers face a complex and turbulent environment that needs quite different decision-making processes from conventional ones. Traditional decision techniques cannot meet the demands of today’s social stability and security.Design/methodology/approachThe main work is to develop an instance-driven classifier for the emergency categories based upon three fuzzy measures: features for an instance, solution for the instance and effect evaluation of the outcome. First, the information collected from the past emergency events is encodes into a prototype model. Second, a three-dimensional space that describes the locations and mutual distance relationships of the emergency events in different emergency prototypes is formulated. Third, for any new emergency event to be classified, the nearest emergency prototype is identified in the three-dimensional space and is classified into that category.FindingsAn instance-driven classifier based on prototype theory helps decision makers to describe emergency concept more clearly. The maximizing deviation model is constructed to determine the optimal relative weights of features according to the characteristics of the new instance, such that every customized feature space maximizes the influence of features shared by members of the category. Comparisons and discusses of the proposed method with other existing methods are given.Practical implicationsTo reduce the affection to economic development, more and more countries have recognized the importance of emergency response solutions as an indispensable activity. In a new emergency instance, it is very challengeable for a decision maker to form a rational and feasible humanitarian aids scheme under the time pressure. After selecting a most suitable prototype, decision makers can learn most relevant experience and lessons in the emergency profile database and generate plan for the new instance. The proposed approach is to effectively make full use of inhomogeneous information in different types of resources and optimize resource allocation.Originality/valueThe combination of instances can reflect different aspects of a prototype. This feature solves the problem of insufficient learning data, which is a significant characteristic of emergency decision-making. It can be seen as a customized classification mechanism, while the previous classifiers always assume key features of a category.
The impact of corruption on travelers’ perceptions and preferences
Authors: Papathanassis Alexis 
Published: June 2019

Purpose
This paper aims to explore and model tourists’ perceptions of corruption-related holiday incidents and their impact on travel preferences and behavior.

Design/methodology/approach
This research methodology reflects an exploratory-sequential, mixed-method design, comprising a content analysis of 205 online reviews, followed by a survey of 268 respondents.

Findings
According to the data collected and analyzed, exposure to corruption appears to be more than an exception for holidaymakers. Moreover, tourists often associate corruption with a wide spectrum of incident types; those ranging from personal integrity threats to service delivery failures and heritage/attraction mismanagement. The impact of such incidents on travel preferences and behavior of tourists is highly dependent on the perceived competence, effectiveness and professionalism of local (destination) public services and authorities.

Practical implications
Recommendations for destination stakeholders include the need to enable and take ownership of tourists’ complaints and the importance of recognizing the role of heritage attractions as corruption-related symbols and destination image carriers.

Originality/value
This paper attempts to establish the connection between corruption and tourism externalities within the context of the recent “over-tourism” debate. In exploring tourism-corruption, the authors adopt a “micro-behavioral” perspective, which represents a novelty in the related macro/systemic-level approach, characterizing the predominant research in this area. Moreover, in terms of research methodology, both qualitative and quantitative methods are combined. This is an ambitious and challenging research design, demonstrating the synergies between the two paradigms and contributing to the completeness of the paper.