bluuebunny/crossref_metadata_2025_split huggingface dataset:
A causal inference framework for estimating genetic variance and pleiotropy from GWAS summary data
Authors: Park Yongjin , He Liang , Kellis Manolis 
Published: January 2019

MotivationMuch of research in genome-wide association studies has only searched for significantly associated signals without explicitly removing unwanted source of variation. Confounder correction is a necessary step to reveal causal effects, but often skipped in a summary-based analysis.ResultsWe present a novel causal inference algorithm that controls unwanted sources in genetic variance and covariance estimation tasks. We demonstrate substantially improved statistical power and accuracy in extensive simulations. In real-world applications on the UK biobank summary statistics data, our method recapitulates well-known pleiotropic modules, suggesting new insights into biobank-scale GWAS analysis.ContactYP (ypp@mit.edu) and MK (manoli@mit.edu)
High prevalence of class 1 integrase and characterization of class 1 integron gene cassettes in multiresistant bacteria isolated from the gut microbiota of extended antibiotic treated Salmo salar fish farms
Authors: Vásquez-Ponce Felipe , Higuera-Llantén Sebastián , Cortés Jimena , Zimin-Veselkoff Natalia , Marshall Sergio H. , Mardones Fernando O. , Olivares-Pacheco Jorge 
Published: January 2019

AbstractThe use of antimicrobials in aquaculture is a common practice. Chile is second larger producer of salmon worldwide, but unfortunately is the first consumer of antibiotics. Tonnes of florfenicol and oxytetracycline yearly are used in the Chilean salmoniculture to control the pathogens that threaten the sustainability of the industry. This excessive use of antibiotics have selected populations of resistant bacteria from the sediments and the water column that sorround the fish farms. In a recent work, our lab described the high prevalence of multiresistant bacteria and Antibiotic Resistance Genes (ARGs) in the gut microbiota of Antlactic salmon (Salmo salar) treated with high doses of antibiotics. In this work, we revisited the analysis of the previously described gut multiresistant bacteria grouped in banks of florfenicol resistant isolates (FB) and oxytetracycline resistant isolates (OB) looking for the presence of integron-integrase elements. These elements have been described as an important players in the Antimicrobial Resistance (AMR) phenomenon and they are considered a good markers of the anthopogenic activities pollution. The results showed that the 100% of the multiresistant isolates present the class 1 intagrase. Despite this result, no isolate from FB showed the typical structure of class 1 integrons: the presence in 3’-CS of qacEΔ1/sul1 genes. While in OB, only 23% of the isolates showed this characteristic structure. Additionally, only four isolates of OB and none of FB showed recognisable gene cassettes and no genes of resistance to florfenicol and oxytetacycline appeared in them. Of these four isolates, three of them showed a single gene cassette containing the dfrA-14 gene, which confers resistance to trimethoprim. Whilst the other isolate showed the aac(6’)31-qacH-blaoxa2 genes, which confers resistance to aminoglycosides, quaternary ammonium compounds and beta-lactams, respectively. Finally, it was possible to demonstrate that the described integrons probably come from anthropogenic activities like clinical settings and/or industrial animal husbandry, since they show integrases proteins identical to those carried by human pathogens.
Rosiglitazone in the thawing medium improves mitochondrial function in stallion spermatozoa through Akt phosphorylation and reduction of caspase 3
Authors: Ortiz-Rodriguez JM , Balao da Silva C , Masot J , Redondo E , Gazquez A , Gil MC , Ortega Ferrusola C , Peña FJ 
Published: January 2019

ABSTRACTBackgroundThe population of stallion spermatozoa surviving thawing, experience, among other changes, compromised mitochondrial functionality and accelerated senescence. It is known that the stallion spermatozoa show very active oxidative phosphorylation that may accelerate sperm senescence through increased production of reactive oxygen species. Rosiglitazone has proven to enhance the glycolytic capability of stallion spermatozoa maintained in refrigeration.ObjectivesThus, we hypothesized that thawed sperm may also benefit from rosiglitazone supplementation.Material and MethodsThawed sperm doses were washed and re-suspended in Tyrodes media, split sampled and supplemented with 0 or 75 μM rosiglitazone. After 1 and two hours of incubation, mitochondrial functionality, Akt phosphorylation and caspase 3 activity were evaluated. Further samples were incubated in presence of the Akt1/2 inhibitor, compound C (AMPK inhibitor) and GW9662 (antagonist of the PPARγ receptor).ResultsRosiglitazone maintained Akt phosphorylated and reduced caspase 3 activation (p<0.01) that was prevented by incubation in presence of the three inhibitors. Rosiglitazone also enhanced mitochondrial functionality (p<0.01).ConclusionWe provide, for the first time, evidences that the functionality of frozen stallion spermatozoa can be potentially improved after thawing through the activation pro survival pathways, opening new clues to improve current sperm biotechnologies.
Diagnosed and undiagnosed Diabetes mellitus among urban adults: a population based cross-sectional study
Authors: Ayele Behailu Hawulte , Shore Hirbo , Shunu Addisu , Mengesha Melkamu Merid 
Published: January 2019

AbstractBackgroundGlobally, diabetes mellitus (DM) accounts for 8.8% (424.9 million) morbidity and 4 million deaths. In 2017, more than 79% of people with diabetes live in low- and middle- income countries. To this end, locally available evidence can identify target groups for intervention. However, in resource-poor settings, population-based evidence on diabetes prevalence and on its risk factors is lacking. This study, therefore, assessed prevalence of Diabetes mellitus and associated factors among adults living in Dire Dawa town, Eastern Ethiopia.MethodsA total of 782 data points were analyzed from a random sample of the adult population aged 25-64 years who lived in Dire Dawa. World health organization STEPwise approach to non-communicable disease risk factors surveillance (WHO NCD STEPS) instrument was used to collect data. We estimated undiagnosed DM, uncontrolled DM among existing cases and the overall prevalence of DM. Hierarchical logistic regression models were run to identify correlates of diabetes mellitus, and STATA v 14.2 was used for data management and analysis. All statistical tests were declared significant at p-value<0.05.ResultsThe prevalence of DM among adults aged 25-64 was 8.95% (95% confidence interval (CI): 7.1, 11.2) and the magnitude of undiagnosed DM was 3.3% (95% CI: 2.3, 4.8). The magnitude of uncontrolled DM among those taking DM medications during the survey was 1.4% (95% CI: 0.8, 2.5). The prevalence of DM was 2.3 times more likely among the age group of 55-64 years (Adjusted Odds Ratio (AOR) 95% CI: 1.1, 5.0). Similarly, consuming two or less serving of vegetables/week increased the risk of DM, (AOR=2.1, 95% CI: 1.1, 2.9). Maintaining normal body mass index level was negatively correlated with the risk of DM, (AOR=0.6, 95% CI: 0.3, 0.8).ConclusionThe overall prevalence of diabetes mellitus was relatively high, and the magnitude of undiagnosed DM was a great concern. Therefore, creating community awareness, regular blood sugar checking, appropriate weight control and, increased consumption of vegetables would be helpful in preventing incident cases of DM.
A review of machine efficiency in mass customization
Authors: James C.D. , Mondal Sandeep 
Published: January 2019

Purpose
The purpose of this paper is to address the gap between definition and practical aspects of production efficiency in mass customization (MC). The paper summarizes all major issues impacting efficiency in MC. Also, the paper reviews metrics, relationship between various parameters and provides a best practices benchmark toolkit to achieve higher machine efficiencies.

Design/methodology/approach
The paper identified and categorized multiple challenges impacting machine efficiency in MC through a literature review spanning over three decades, and also ranked the identified issue-based parameters. Top issues were found varying across different types of industries identified through the review. Metrics pertaining to efficiency and degree of MC are reviewed in the paper. A chronological review of issues is presented, and a chain diagram is built in the paper. Toolkit of best practices created with solution strategies and tools are summarized through the review.

Findings
The paper found that MC reasonably impacts machine efficiency which needs to be addressed. Major issues through literature review-based ranking are uncovered, and worldwide research trend and comparison are presented. Active research in this area is observed to be at its peak since 2010. The extensive use of strategies and benchmark toolkit for improving efficiency are summarized.

Research limitations/implications
Ranking of issues has been done through a literature review; hence, there can be skewness depending on the frequency of issues researched by various authors in various areas of industries.

Practical implications
This paper is useful for manufacturing managers and companies willing to increase the size of their product portfolio and choices within their available resources without compromising machine efficiencies and, thereby, the cost. The identified issues help in providing a comprehensive issue list to the academia.

Originality/value
This paper describes what is believed to be the first study that explicitly examines the issues faced in achieving machine efficiency while manufacturing in an MC environment.
Employee optimism in India: validation of the POSO-E
Authors: Bharti Teena , Rangnekar Santosh 
Published: January 2019

PurposeThe purpose of this paper was to validate the short version of personal optimism and self-efficacy optimism scale developed by Gavrilov-Jerkovicet al.(2014) on a sample of 398 employees working in private and public sector organizations in India.Design/methodology/approachThe study needs to test the psychometric properties of the Indian version of scale by using exploratory factor analysis, convergent validity, discriminant validity and confirmatory factor analysis.FindingsThe results supported for the two-dimensional factor-structure of optimism in consonance with Gavrilov-Jerkovicet al.(2014).Research limitations/implicationsThe findings will benefit both the management and the employees. Also, the study expands the existing literature on the variable in the Indian context.Originality/valueThe work validates and provides a unique instrument to measure the employee optimism that can help the management and the employees to focus on themselves to increase the positivity to provide an innovative and creative environment. Also, the work supplements the existing literature on positive attitude or outcome expectancies and helps in establishing the bi-dimensional nature of the construct of optimism.
Antecedents, mediators and consequences of sustainable operations
Authors: De Guimarães Julio Cesar Ferro , Dorion Eric Charles Henri , Severo Eliana Andréa 
Published: January 2019

PurposeThe purpose of this paper is to propose a framework for analyzing the relationships between the antecedent factors, mediators and consequences of sustainable operations (SO), which can be applied for empirical studies in the manufacturing industry.Design/methodology/approachBased on the importance of identifying the determinants of SO, a qualitative and exploratory research was developed through an extensive review of the literature.FindingsThe main theoretical contribution of this research on organizational studies is the SO analysis proposition framework, which allows the elaboration of scales, based on observable variables of each factor, as well as evaluating the influence intensity of the relations between the constructs.Research limitations/implicationsThe proposed framework of this research was developed to analyze companies of the manufacturing industry. In order to use the proposed framework in other industries (commerce, services), it will be necessary to make adaptations and adjustments on the observable variables and constructs.Originality/valueThe paper has an important theoretical value in proposing scales for the SO factors and can be useful for future quantitative approach and surveys. Consequently, the researcher will be able to evaluate the scales of the factors and the intensity of the relations between observable variables in the formation of the constructs, as well as the intensity of influence among the constructs.
TQM, games design and the implications of integration in Industry 4.0 systems
Authors: Beard-Gunter Alison , Ellis David Geraint , Found Pauline Anne 
Published: January 2019

PurposeVoluntary participation, feedback loops, rules and goals are key elements of total quality management (TQM). The purpose of this paper is to determine if these four elements which make TQM successful are the same elements that make computer games successful. If this is the case, what are the implications for developers of Human Computer Interfaces (HCI) in Industry 4.0.Design/methodology/approachThis paper is a systematic literature review of recent literature on engagement in games and user experiences and HCI design for industry followed by interpretation of the literature. The findings from the literature review are analysed and compared to TQM.FindingsGood game design and TQM share four key components: goals, rules, a feedback system (including rewards) and voluntary participation. There is an opportunity for HCI developers to use a user experience lens inherent in games evolution and to expand on the design and motivational elements that have made games and TQM successful at motivating and engaging. Kuutti’s (1995) proposal of activity theory puts forward a promising framework for making systems engaging. There are positive implications merging good games design and TQM in socio-technic systems which could improve engagement and quality in companies implementing in Industy 4.0.Research limitations/implicationsThe implications of achieving increased engagement in HCI systems similar to those seen in companies that have successfully implemented TQM could lead to greater productivity in companies operating in the highly technical environments of Industry 4.0.Originality/valueThe originality of this paper is threefold: first, a description of the origins in industry of voluntary participation, feedback loops, rules and goals and their relationship to TQM; second, a systematic literature review of the same elements in computer games design; and third, the implications for developers of HCI systems in Industry 4.0.
The magnetotelluric impedance tensor through Clifford algebras: part I — theory
Authors: Romero‐Ruiz Ivan , Pous Jaume 
Published: January 2019

ABSTRACTThe magnetotelluric impedance tensor is analysed in the context of Clifford algebras. In this framework, the tensor is broken down into different parts, each one with a particular geometric algebra meaning, the simplicity of which allows us to deduce a number of known properties and opens up many other possibilities. As examples to show its capabilities, some of the algebraic relationships involving the impedance tensor, such as rotations, Mohr diagrams and phase tensor, are shown under this theory. Rotations are analysed in Clifford algebra and Mohr diagrams, and phase tensor are expressed in Clifford algebra . The galvanic distortion matrix and its transformations are also seen in Clifford algebra , where a number of relationships allow us to recognize the galvanic distortion in a measured two‐dimensional/three‐dimensional impedance tensor. These relationships are useful as constraints to determine the galvanic distortion parameters.
Resource overlap and dilution effects shape host plant use in a myrmecophilous butterfly
Authors: Valdés Alicia , Ehrlén Johan 
Published: January 2019

Abstract

The effects of consumers on fitness of resource organisms are a complex function of the spatio‐temporal distribution of the resources, consumer functional responses and trait preferences, and availability of other resources.

The ubiquitous variation in the intensity of species interactions has important consequences for the ecological and evolutionary dynamics of natural populations. Nevertheless, little is known about the processes causing this variation and their operational scales. Here, we examine how variation in the intensity of a consumer–resource interaction is related to resource timing, resource density and abundance of other resources.

Using the butterfly consumer Phengaris alcon and its two sequential resources, the host plant Gentiana pneumonanthe and the host ants Myrmica spp., we investigated how butterfly egg‐laying depended on focal host plant phenology, density and phenology of neighbouring host plants and host ant abundance.

Butterflies preferred plants that simultaneously maximized the availability of both larval resources in time and space, that is, they chose early‐flowering plants that were of higher nutritional quality for larvae where host ants were abundant. Both the probability of oviposition and the number of eggs were lower in plant individuals with a high neighbour density than in more isolated plants, and this dilution effect was stronger when neighbours flowered early.

Our results show that plant–herbivore interactions simultaneously depend on the spatio‐temporal distribution of a focal resource and on the small‐scale spatial variation in the abundance of other herbivore resources. Given that consumers have negative effects on fitness and prefer certain timing of the resource organisms, this implies that processes acting at the levels of individuals, populations and communities simultaneously contribute to variation in consumer‐mediated natural selection.
Tree species diversity promotes litterfall productivity through crown complementarity in subtropical forests
Authors: Zheng Li‐Ting , Chen Han Y. H. , Yan En‐Rong 
Published: January 2019

AbstractThe role of niche complementarity for driving the positive biodiversity–ecosystem productivity relationship has been widely recognized, but there is scant evidence regarding the role of tree canopy structure on this relationship. Litterfall productivity is proportional to forest net primary productivity in natural forests, and we hypothesized that litterfall productivity would increase with tree species diversity via increased tree crown complementarity.We investigated annual litterfall productivity, species diversity, tree crown architecture, soil moisture content, soil carbon content and stand age across 28 subtropical forest plots in eastern Zhejiang province, China. Simple linear regression was used to examine bivariate relationships among rarified species richness, crown complementarity, total crown volume, soil moisture content, soil carbon content, stand age and litterfall productivity. Structural equation modelling was employed to quantify the direct and indirect effects of species richness on litterfall productivity through tree crown complementarity.Litterfall productivity increased with rarefied species richness via increasing crown complementarity rather than total crown volume. Species richness, crown complementarity and litterfall productivity increased with soil moisture content, while crown complementarity and litterfall productivity increased with soil carbon content. Neither species richness nor crown complementarity increased with stand age, even though litterfall productivity increased with stand age.Synthesis. Our study provides evidence for the strong role of tree crown assembly in shaping ecosystem functions in complex natural forests. Our findings suggest that crown spatial complementarity among trees operates mechanistically to drive the positive tree species diversity–litterfall productivity relationship in subtropical forests. We argue that community and/or ecosystem ecology would benefit from more attention to crown variability among coexisting tree species.
A novel method for elimination of aflatoxin M1 in milk using Lactobacillus rhamnosus GG biofilm
Authors: Assaf Jean Claude , Khoury André El , Chokr Ali , Louka Nicolas , Atoui Ali 
Published: January 2019

This study aimed to develop a new method for detoxification of milk from aflatoxin M1 (AFM1) by using Lactobacillus rhamnosus GG biofilm. After inoculation of milk contaminated with AFM1 into L. rhamnosus GG biofilm, the unbound AFM1 was extracted and quantified by HPLC. The stability of the formed AFM1/biofilm complex using different AFM1 contamination levels of milk was also studied. We found that the percentages of bound AFM1 by L. rhamnosus GG biofilm reached up to 60.74%. While no significant difference in milk proteins content was observed after AFM1 binding, some changes in total dry matter and fat content were noticed.
CRISPR/Cas9‐mediated ebony knockout results in puparium melanism in Spodoptera litura
Authors: Bi Hong‐Lun , Xu Jun , He Lin , Zhang Yong , Li Kai , Huang Yong‐Ping 
Published: January 2019

AbstractInsect body pigmentation and coloration are critical to adaption to the environment. To explore the mechanisms that drive pigmentation, we used the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR‐associated protein 9 (Cas9) genome editing system to target the ebony gene in the non‐model insect Spodoptera litura. Ebony is crucial to melanin synthesis in insects. By directly injecting Cas9 messenger RNA and ebony‐specific guide RNAs into S. litura embryos, we successfully induced a typical ebony‐deficient phenotype of deep coloration of the puparium and induction of melanin formation during the pupal stage. Polymerase chain reaction‐based genotype analysis demonstrated that various mutations had occurred at the sites targeted in ebony. Our study clearly demonstrates the function of ebony in the puparium coloration and also provides a potentially useful marker gene for functional studies in S. litura as well as other lepidopteran pests.
Determination of Antifungal Effect of Edible Coatings Containing Williopsis saturnus var. saturnus Against Yeast and Mold Growth on Kashar Cheese
Authors: Civelek Ilknur , Cagri‐Mehmetoglu Arzu 
Published: January 2019

AbstractOne of the most important problems of Kashar cheese producers is mold and yeast spoilage during storage. Williopsis saturnus var. saturnus killer yeast has been reported to have an antagonistic effect on mold and yeast reproduction. In this study, the antifungal effect of a whey protein concentrate (WPC) coating containing W. saturnus was investigated in Kashar cheese. WPC with or without W. saturnus (7 log CFU/g) or W. saturnus without coating was applied on the surface of Kashar cheese samples and stored at 4 °C for 56 days. Microbiological, chemical, physical and sensory properties of cheese samples were assessed. After 56 days of storage, the numbers of lactic acid bacteria were not affected by WPC containing W. saturnus; however, the population of W. saturnus increased by 1 log CFU/g. Application of W. saturnus reduced the growth of other yeasts and molds (P < 0.05). Chemical, physical and sensory properties of all coated cheeses remained unchanged. In a conclusion, use of WPC coatings containing W. saturnus can potentially minimize mold and yeast spoilage of cheese during storage.