bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Evolutionary History and Impact of Bacterial tRNA Modifications
Authors: Diwan Gaurav D , Agashe Deepa 
Published: January 2018

ABSTRACTAlong with tRNAs, enzymes that modify anticodon bases are a key aspect of translation across the tree of life. tRNA modifications extend wobble pairing, allowing specific (“target”) tRNAs to recognize multiple codons and cover for other (“non-target”) tRNAs, often improving translation efficiency and accuracy. However, the detailed evolutionary history and impact of tRNA modifying enzymes has not been analyzed. Using ancestral reconstruction of five tRNA modifications across 1093 bacteria, we show that most modifications were ancestral to eubacteria, but were repeatedly lost in many lineages. Most modification losses coincided with evolutionary shifts in non-target tRNAs, often driven by increased bias in genomic GC and associated codon use, or by genome reduction. In turn, the loss of tRNA modifications stabilized otherwise highly dynamic tRNA gene repertoires. Our work thus traces the complex history of bacterial tRNA modifications, providing the first clear evidence for their role in the evolution of bacterial translation.
Including phenotypic causal networks in genome-wide association studies using mixed effects structural equation models
Authors: Momen Mehdi , Mehrgardi Ahmad Ayatollahi , Roudbar Mahmoud Amiri , Kranis Andreas , Pinto Renan Mercuri , Valente Bruno D. , Morota Gota , Rosa Guilherme J. M. , Gianola Daniel 
Published: January 2018

AbstractBackgroundPhenotypic networks describing putative causal relationships among multiple phenotypes can be used to infer single-nucleotide polymorphism (SNP) effects in genome-wide association studies (GWAS). In GWAS with multiple phenotypes, reconstructing underlying causal structures among traits and SNPs using a single statistical framework is essential for understanding the entirety of genotype-phenotype maps. A structural equation model (SEM) can be used for such purposes.MethodsWe applied SEM to GWAS (SEM-GWAS) in chickens, taking into account putative causal relationships among body weight (BW), breast meat (BM), hen-house production (HHP), and SNPs. We assessed the performance of SEM-GWAS by comparing the model results with those obtained from traditional multi-trait association analyses (MTM-GWAS).ResultsThree different putative causal path diagrams were inferred from highest posterior density (HPD) intervals of 0.75, 0.85, and 0.95 using the inductive causation algorithm. A positive path coefficient was estimated for BM→BW, and negative values were obtained for BM→HHP and BW→HHP in all implemented scenarios. Further, the application of SEM-GWAS enabled the decomposition of SNP effects into direct, indirect, and total effects, identifying whether a SNP effect is acting directly or indirectly on a given trait. In contrast, MTM-GWAS only captured overall genetic effects on traits, which is equivalent to combining the direct and indirect SNP effects from SEMGWAS.ConclusionsAlthough MTM-GWAS and SEM-GWAS use the same probabilistic models, we provide evidence that SEM-GWAS captures complex relationships and delivers a more comprehensive understanding of SNP effects compared to MTM-GWAS. Our results showed that SEM-GWAS provides important insight regarding the mechanism by which identified SNPs control traits by partitioning them into direct, indirect, and total SNP effects.
Autometa: Automated extraction of microbial genomes from individual shotgun metagenomes
Authors: Miller Ian J. , Rees Evan R. , Ross Jennifer , Miller Izaak , Baxa Jared , Lopera Juan , Kerby Robert L. , Rey Federico E. , Kwan Jason C. 
Published: January 2018

AbstractMotivationShotgun metagenomics is a powerful, high-resolution technique enabling the study of microbial communitiesin situ.However, species-level resolution is only achieved after a process of “binning” where contigs predicted to originate from the same genome are clustered. Such culture-independent sequencing frequently unearths novel microbes, and so various methods have been devised for reference-free binning. Existing methods, however, suffer from: (1) reliance on human pattern recognition, which is inherently unscalable; (2) requirement for multiple co-assembled metagenomes, which degrades assembly quality due to strain variance; and (3) assumption of prior host genome removal not feasible for non-model hosts. We therefore devised a fully-automated pipeline, termed “Autometa,” to address these issues. Results: Autometa implements a method for taxonomic partitioning of contigs based on predicted protein homology, and this was shown to vastly improve binning in host-associated and complex metagenomes. Autometa’s method of automated clustering, based on Barnes-Hut Stochastic Neighbor Embedding (BH-tSNE) and DBSCAN, was shown to be highly scalable, outperforming other binning pipelines in complex simulated datasets.Availability and implementationAutometa is freely available athttps://bitbucket.org/jasonckwan/autometaand as a docker image athttps://hub.docker.com/r/jasonkwan/autometaunder the GNU Affero General Public License 3 (AGPL 3).Contactjason.kwan@wisc.eduSupplementary informationSupplementary data are available attached to this article athttps://biorxiv.org
Staphylococcus aureustoxin LukSF dissociates from its membrane receptor target to enable renewed ligand sequestration
Authors: Haapasalo Karita , Wollman Adam J. M. , Haas Carla de , Kessel Kok van , Strijp Jos van , Leake Mark C. 
Published: January 2018

ABSTRACTbackgroundStaphylococcus aureusPanton Valentine Leukocidin (PVL) is a pore-forming toxin targeting the human C5a receptor (hC5aR), enabling this pathogen to battle the immune response by destroying phagocytes through targeted lysis. The mechanisms that contribute to rapid cell lysis are largely unexplored.ResultsHere we show that cell lysis may be enabled by a process of toxins targeting receptor clusters and receptor ‘recycling’ which allows multiple toxin pores to be formed close together. Using live cell single-molecule super-resolution imaging, Förster resonance energy transfer (FRET) and nanoscale total internal reflection fluorescence (TIRF) colocalization microscopy we visualized toxin pore formation in the presence of its natural docking ligand.ConclusionsWe demonstrate disassociation of hC5aR from toxin complexes and simultaneous binding of new ligands. This effect may free mobile receptors to amplify hyper inflammatory reactions in early stages of microbial infections and have implications for several other similar bi-component toxins and the design of new antibiotics.
Is reading automatic? Are the ERP correlates of masked priming really lexical?
Authors: Norris Dennis , Kinoshita Sachiko , Hall Jane , Henson Richard 
Published: January 2018

AbstractHumans have an almost unbounded ability to adapt their behaviour to perform different tasks. In the laboratory, this flexibility is sometimes viewed as a nuisance factor that prevents access to the underlying cognitive mechanisms of interest. For example, in order to study “automatic” lexical processing, psycholinguists have used masked priming or evoked potentials to measure “automatic” lexical processing. However, the pattern of masked priming can be radically altered by changing the task. In lexical decision, priming is observed for words but not for nonwords, yet in a same-different matching task, priming is observed for same responses but not for different responses, regardless of whether the target is a word or a nonword (Norris & Kinoshita, 2008). Here we show that evoked potentials are equally sensitive to the nature of required decision, with the neural activity normally associated with lexical processing being seen for both words and nonwords on same trials, and for neither on different trials. (150)
A meta-analysis of Planarian: an animal model useful to understand the effect of magnetic field Planarian and magnetic field researches
Authors: Gomez Luna Liliana María , Puente López Vivian de la 
Published: January 2018

AbstractThe planarians research since the first description until nowadays has a broad spectrum of topics. The present paper deals on a meta-analysis which identified as a problem the lack of consolidate information and data analysis about the use of planarian as animal model, and specifically the use of magnetic field in regeneration experiments. To conduct the meta-analysis 1255 papers published since 1955 to 2017 were analysed, identifying the Stem cell biology and regeneration as the most published topic, with 276 papers, followed by molecular and cellular analyses (238), genetics (175), inter and transdisciplinary research (107), ecotoxicological evaluations (102), animal model (67), ecological and biological studies (56), magnetic field (57), developmental biology (32) and RNA regulation (31).Other statistics and metrics indicators were taken in to account like total of papers and distribution per year, distribution of paper by journals and selection of main journals according to the number of published papers, most cited papers, authors and countries and distribution of papers by countries. Finally, were analysed those papers with Planarians research using magnetic field, all of them published during the last three years. It was an evidence that this topic is becoming a trending with rising interest, being the most reported species to study the magnetic field effects Dugesia spp. and Girardia sp.Summary statementThis work presents a meta-analysis which allows consolidating information and a better understanding of trends in Planarian researches, emphasizing in the use of magnetic field.
High-resolution wide-field human brain tumor margin detection and in vivo murine neuroimaging
Authors: Yecies Derek , Liba Orly , SoRelle Elliott , Dutta Rebecca , Yuan Edwin , Vogel Hannes , Grant Gerald A. , de la Zerda Adam 
Published: January 2018

AbstractCurrentin vivoneuroimaging techniques provide limited field of view or spatial resolution and often require exogenous contrast. These limitations prohibit detailed structural imaging across wide fields of view and hinder intraoperative tumor margin detection. Here we present a novel neuroimaging technique, speckle-modulating optical coherence tomography (SM-OCT), which allows us to image the brains of live mice andex vivohuman samples with unprecedented resolution and wide field of view using only endogenous contrast. The increased effective resolution provided by speckle elimination reveals white matter fascicles and cortical layer architecture in the brains of live mice. To our knowledge, the data reported herein represents the highest resolution imaging of murine white matter structure achievedin vivoacross a wide field of view of several millimeters. When applied to an orthotopic murine glioblastoma xenograft model, SM-OCT readily identifies brain tumor margins with near single-cell resolution. SM-OCT ofex vivohuman temporal lobe tissue reveals fine structures including cortical layers and myelinated axons. Finally, when applied to anex vivosample of a low-grade glioma resection margin, SM-OCT is able to resolve the brain tumor margin. Based on these findings, SM-OCT represents a novel approach for intraoperative tumor margin detection andin vivoneuroimaging.
Growth equity and sectoral decompositions of aggregate poverty changes in Cameroon
Authors: Atemnkeng Johannes Tabi , Tambi Daniel Mbu 
Published: January 2018

Purpose
The purpose of this paper is to provide insight to policy-makers into a framework for action, which is needed to effectively reduce poverty in its monetary and non-monetary dimensions.

Design/methodology/approach
Specifically, an exact decomposition analysis is conducted that is based on the Shapley value method, and investigated the growth and redistribution effects as well as changes due to mobility and sector-specific effects of the variation in both income/expenditure and non-income poverty dimensions.

Findings
Growth in mean consumption and household assets accounted for the bulk of the improvement in poverty reduction and the results complement the evidence obtained from the “sectoral decomposition” of poverty in Cameroon which may indeed have a strong bearing on the sectoral shares of poverty. The temptation is resisted, however, not to deny that redistribution also has an important role to play, yet there must be severe limits to what can be achieved by growth neutral redistribution. The redistribution effect had an ameliorating tendency in household asset deprivation among farming households.

Originality/value
This paper is a well-written piece using quite rigorous and interesting methodological approach. To obtain a measure of non-income dimensions of well-being, the authors constructed composite indices on household assets reflecting household access to a range of physical assets and services including human capital by polychoric principal component analysis method.
Applying data mining for online CRM marketing strategy
Authors: Chiang Wen-Yu 
Published: January 2018

Purpose
The purpose of this paper is to propose a data mining approach for mining valuable markets for online customer relationship management (CRM) marketing strategy. The industry of coffee shops in Taiwan is employed as an empirical case study in this research.

Design/methodology/approach
Via a proposed data mining approach, the study used fuzzy clustering algorithm and Apriori algorithm to analyze customers for obtaining more marketing and purchasing knowledge of online CRM systems.

Findings
The research found three hard markets and one fuzzy market. Furthermore, the study discovered two association rules and two fuzzy association rules.

Originality/value
However, industry of coffee shops has been always a fast-growing and competitive business around the world. Thus, marketing strategy is important for this industry. The results and the proposed data mining approach of this research can be used in the industry of coffee shop or other retailers for their online CRM marketing systems.
Adolescents’ sources for food safety knowledge and trust
Authors: Lange Marie , Göranzon Helen , Fleig Lena , Marklinder Ingela 
Published: January 2018

Purpose
The purpose of this paper is to investigate where students in a Swedish compulsory school acquire their knowledge of food safety and how trustworthy they deem them to be.

Design/methodology/approach
A survey of students’ self-reported sources of and trust in food safety knowledge was performed. A student response system was used for data collection, and the students were asked to answer questions presented on a PowerPoint presentation using a small wireless handheld device: a clicker. A questionnaire with 24 questions was used, and the responses were collected at 18 different schools with a total of 529 participants attending school Year 9.

Findings
Mothers were reported as being the most important source of food safety knowledge (38 per cent), especially among girls, and were also given high credibility (36 per cent). Boys reported trusting home and consumer studies (HCS), fathers and media to a higher extent. Girls reported cooking at home more often but, for all students, it was more common to rarely or never cook at home, which is why HCS teaching can be seen as valuable for many students. HCS teaching needs to be improved in order to raise its credibility. About half of the students (51 per cent) reported to have the highest trust for their source of knowledge.

Research limitations/implications
The students could only choose one source of knowledge and trust, although it is usual to learn from many different sources.

Practical implications
HCS teaching needs to get higher credibility among students as a counterweight against other sources.

Social implications
Educated consumers could influence their health.

Originality/value
Limited research has been performed on food safety knowledge among adolescents.
Food safety practices of future food handlers and their teachers, observed during practical lessons
Authors: Ovca Andrej , Jevšnik Mojca , Raspor Peter 
Published: January 2018

Purpose
The purpose of this paper is to investigate future food handlers’ practices during practical lessons close to the end of their formal vocational education, and to record teachers’ behaviour and to evaluate classrooms that were intended for practical lessons.

Design/methodology/approach
A total of 90 students between 17 and 19 years of age, 12 teachers, and 12 training classrooms intended for practical lessons, which were divided into six observation sessions in the field of catering and six observation sessions in the field of food processing (bakery, confectionery, and butchery), were observed.

Findings
Both proper and inappropriate food-handling practices were observed among teachers and students. Comparing the hygienic-technical conditions of the training classrooms with teachers’ and students’ behaviour revealed several interconnected situations increasing the risk of food contamination during the production process.

Research limitations/implications
Data were collected by one observer who was not part of the class. The sample size was small, limiting the generalisability of the results.

Practical implications
The results indicate the weaknesses in the formal vocational education of future professional food handlers.

Social implications
Good food safety practices among food handlers reduce societal costs related to health-care systems and food industry economic losses.

Originality/value
The study provides an insight into the education and training of future professional food handlers in a controlled environment in educational institutions.
Tackling the challenges of reducing and managing food waste in Mumbai restaurants
Authors: Bharucha Jehangir 
Published: January 2018

Purpose
Around 67 million tons of food is wasted in India every year, which has a value of more than US$14 billion (Haq, 2016). The purpose of this paper is to concentrate on one major source to which the current massive proportion of wastage can be attributed: restaurants. It investigates the statistics, the problem at large, how the restaurants are handling it and recommends ways to better manage the issue.

Design/methodology/approach
A qualitative inquiry has been used. The research population for this study consisted of 63 restaurant owners across Mumbai city and its suburbs. In-depth discussions were held with these restaurant owners/managers in various matters of interest to this study.

Findings
The group of restaurateurs opined that the solution to Mumbai’s restaurants waste management lies in micro management rather than large scale plans. In total, 75 percent of the restaurants have 10-20 percent extra preparation. High-end fine-dining restaurants make even more additional preparations and are the ones more receptive to participating and also sensitive toward importance of waste management. Several of the restaurant owners claim that they can estimate the requirements on specific days of the week. In all, 18 percent of the restaurants surveyed claimed to have a complete dispose of policy. Majority of the restaurants have a clear policy to distribute the surplus food among their staff. Several other innovative strategies were shared.

Research limitations/implications
The restaurant owners/mangers may not have truthfully answered all questions. The participants might have the fear that the authorities would take cognizance of some of the practices that they are following and would have been guarded in their responses. There would always be a fear that the identities would not be kept confidential.

Practical implications
India as a country has been agriculture based for centuries and characterized by massive food production. Yet, people face rampant starvation and malnourishment. This arises to a large extent due to the colossal amounts of food wasted at marriages, restaurants and even by destruction of crops.

Originality/value
The restaurant industry is of critical importance to the Indian economy and while research in India has focused on overall food wastage, studies on restaurant food waste are lacking.
Cooking skills and socio-demographics among Portuguese university students
Authors: Kowalkowska Joanna , Poínhos Rui , Rodrigues Sara 
Published: January 2018

Purpose
The purpose of this paper is to assess the reliability of a Portuguese version of the cooking skills scale (CSS) and to evaluate the association between cooking skills and socio-demographic, psychological and other cooking-related variables.

Design/methodology/approach
The study was conducted as an online survey among 730 Portuguese university students. Translation and back-translation of the CSS were performed. Data were assessed in two stages (test and retest) and the psychometric properties of the CSS were analyzed. The effect of socio-demographic variables was assessed by binary logistic regression analysis. The odds ratios for upper tertile of the CSS score were calculated using the lower tertile as reference.

Findings
Cronbach’s α for the CSS was 0.90. In the analysis of test-retest reliability, Spearman’s rank correlation coefficient was 0.79 and Cohen’s κ (for tertiles) was 0.49. Cooking skills were higher in respondents cooking more often, feeling more confident, enjoying more and indicating the personal interest as the main motivation to learn how to cook. Cooking skills were significantly better in females, older students and those with more independent place of residence.

Originality/value
Very good psychometric properties of the Portuguese version of the CSS were found among university students, providing a proper and simple tool to measure cooking skills in future studies with similar populations. The interventions encouraging to acquire and improve cooking skills as part of promoting healthy eating should be targeted especially toward men and young adults.