bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative glycoproteomics reveals cellular substrate selectivity of the ER protein quality control sensors UGGT1 and UGGT2
Authors: Adams Benjamin M. , Canniff Nathan P. , Guay Kevin P. , Larsen Ida Signe Bohse , Hebert Daniel N. 
Published: October 2020

ABSTRACTUDP-glucose: glycoprotein glucosyltransferase (UGGT) 1 and 2 are central hubs in the chaperone network of the endoplasmic reticulum (ER), acting as gatekeepers to the early secretory pathway yet little is known about their cellular clients. These two quality control sensors control lectin chaperone binding and glycoprotein egress from ER. A quantitative glycoproteomics strategy was deployed to identify cellular substrates of the UGGTs at endogenous levels in CRISPR-edited HEK293 cells. The seventy-one UGGT substrates identified were mainly large multidomain and heavily glycosylated proteins when compared to the general N-glycome. UGGT1 was the dominant glucosyltransferase with a preference towards large plasma membrane proteins whereas UGGT2 favored the modification of smaller, soluble lysosomal proteins. This study sheds light on differential specificities and roles of UGGT1 and UGGT2 and provides insight into the cellular reliance on carbohydrate-dependent chaperone intervention by UGGT1 and UGGT2 to facilitate proper folding and maturation of the cellular N-glycome.
Functional repertoire convergence of distantly related eukaryotic plankton lineages revealed by genome-resolved metagenomics
Authors: Delmont Tom O. , Gaia Morgan , Hinsinger Damien D. , Fremont Paul , Vanni Chiara , Guerra Antonio Fernandez , Eren A. Murat , Kourlaiev Artem , d’Agata Leo , Clayssen Quentin , Villar Emilie , Labadie Karine , Cruaud Corinne , Poulain Julie , Da Silva Corinne , Wessner Marc , Noel Benjamin , Aury Jean-Marc ,   Tara Oceans Coordinators, de Vargas Colomban , Bowler Chris , Karsenti Eric , Pelletier Eric , Wincker Patrick , Jaillon Olivier 
Published: October 2020

AbstractMarine planktonic eukaryotes play a critical role in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billionTaraOceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years.CoverNavigating on the map of plankton genomics withTaraOceans and anvi’o: a comprehensive genome-resolved metagenomic survey dedicated to eukaryotic plankton.
Mosaic changes to the global transcriptome in response to inhibiting ribosome formation versus inhibition of ribosome function
Authors: Shamsuzzaman Md , Rahman Nusrat , Gregory Brian , Bruno Vincent M , Lindahl Lasse 
Published: October 2020

AbstractCell fate is susceptible to several internal and external stresses. Stress resulting from mutations in genes for ribosomal proteins and assembly factors leads to many congenital diseases, collectively called ribosomopathies. Even though such mutations all depress the cell’s protein synthesis capacity, they are manifested in many different phenotypes. This prompted us to useSaccharomyces cerevisiaeto explore whether reducing the protein synthesis capacity by different mechanisms result in the same or different changes to the global transcriptome. We have compared the transcriptome after abolishing the assembly of new ribosomes and inhibiting the translocation of ribosomes on the mRNA. Our results show that these alternate obstructions generate different mosaics of expression for several classes of genes, including genes for ribosomal proteins, mitotic cell cycle, cell wall synthesis, and protein transport.
Computational and experimental analyses of mitotic chromosome formation pathways in fission yeast
Authors: Gerguri Tereza , Fu Xiao , Kakui Yasutaka , Khatri Bhavin S. , Barrington Christopher , Bates Paul A. , Uhlmann Frank 
Published: October 2020

AbstractUnderlying higher order chromatin organization are Structural Maintenance of Chromosomes (SMC) complexes, large protein rings that entrap DNA. The molecular mechanism by which SMC complexes organize chromatin is as yet incompletely understood. Two prominent models posit that SMC complexes actively extrude DNA loops (loop extrusion), or that they sequentially entrap two DNAs that come into proximity by Brownian motion (diffusion capture). To explore the implications of these two mechanisms, we perform biophysical simulations of a 3.76 Mb-long chromatin chain, the size of the longS. pombechromosome I left arm. On it, the SMC complex condensin is modeled to perform loop extrusion or diffusion capture. We then compare computational to experimental observations of mitotic chromosome formation. Both loop extrusion and diffusion capture can result in native-like contact probability distributions. In addition, the diffusion capture model more readily recapitulates mitotic chromosome axis shortening and chromatin density enrichment. Diffusion capture can also explain why mitotic chromatin shows reduced, as well as more anisotropic, movements, features that lack support from loop extrusion. The condensin distribution within mitotic chromosomes, visualized by stochastic optical reconstruction microscopy (STORM), shows clustering predicted from diffusion capture. Our results inform the evaluation of current models of mitotic chromosome formation.
Coping with darkness: The adaptive response of marine picocyanobacteria to repeated light energy deprivation
Authors: Coe Allison , Biller Steven J. , Thomas Elaina , Boulias Konstantinos , Bliem Christina , Arellano Aldo , Dooley Keven , Rasmussen Anna N. , LeGault Kristen , O’Keefe Tyler J. , Greer Eric L. , Chisholm Sallie W. 
Published: October 2020

AbstractThe picocyanobacteriaProchlorococcusandSynechococcusare found throughout the ocean’s euphotic zone, where the daily light:dark cycle drives their physiology. Periodic deep mixing events can, however, move cells below this zone, depriving them of light for extended periods of time. Here we demonstrate thatProchlorococcusandSynechococcuscan adapt to tolerate repeated periods of light energy deprivation. Cyanobacterial cultures kept in the dark for 3 days and then returned to the light initially required 18-26 days to resume growth, but after multiple rounds of dark exposure the strains began to regrow after only 1-2 days. This dark-tolerant phenotype was stable and heritable; cultures retained the trait across at least 18-21 generations even when grown in a standard 13:11 light:dark cycle. We found no genetic differences between the dark-tolerant and parental strains ofProchlorococcusNATL2A, indicating that an epigenetic change is responsible for the adaptation. To begin to explore this possibility, we asked whether DNA methylation – an epigenetic mechanism in bacteria – occurs inProchlorococcus. LC-MS/MS analysis showed that while DNA methylations, including 6mA and 5mC, are found in some otherProchlorococcusstrains, no methylations were detected in either the parental or dark-tolerant strain used in our experiments –i.e. the NATL2A strain. These findings suggest thatProchlorococcusutilizes a yet-to-be-determined epigenetic mechanism to adapt to the stress of extended light energy deprivation.
Behavioral and genomic sensory adaptations underlying the pest activity ofDrosophila suzukii
Authors: Durkin Sylvia M. , Chakraborty Mahul , Abrieux Antoine , Lewald Kyle M. , Gadau Alice , Svetec Nicolas , Peng Junhui , Kopyto Miriam , Langer Christopher B. , Chiu Joanna C. , Emerson J.J. , Zhao Li 
Published: October 2020

ABSTRACTStudying how novel phenotypes originate and evolve is fundamental to the field of evolutionary biology as it allows us to understand how organismal diversity is generated and maintained. However, determining the basis of novel phenotypes is challenging as it involves orchestrated changes at multiple biological levels. Here, we aim to overcome this challenge by using a comparative species framework combining behavioral, gene expression, and genomic analyses to understand the evolutionary novel egg-laying substrate-choice behavior of the invasive pest speciesDrosophila suzukii. First, we used egg-laying behavioral assays to understand the evolution of ripe fruit oviposition preference inD. suzukiias compared to closely related speciesD. subpulchrellaandD. biarmipes, as well asD. melanogaster. We show thatD. subpulchrellaandD. biarmipeslay eggs on both ripe and rotten fruits, suggesting that the transition to ripe fruit preference was gradual. Secondly, using two-choice oviposition assays, we studied howD. suzukii, D. subpulchrella, D. biarmipesandD. melanogasterdifferentially process key sensory cues distinguishing ripe from rotten fruit during egg-laying. We found thatD. suzukii’s preference for ripe fruit is in part mediated through a species-specific preference for stiff substrates. Lastly, we sequenced and annotated a high-quality genome forD. subpulchrella. Using comparative genomic approaches, we identified candidate genes involved inD. suzukii’s ability to seek out and target ripe fruits. Our results provide detail to the stepwise evolution of pest activity inD. suzukii, indicating important cues used by this species when finding a host, and the molecular mechanisms potentially underlying their adaptation to a new ecological niche.
Influences of time of day on generalization
Authors: Tandoc Marlie C. , Bayda Mollie , Poskanzer Craig , Cho Eileen , Cox Roy , Stickgold Robert , Schapiro Anna C. 
Published: October 2020

AbstractExtracting shared structure across our experiences allows us to generalize our knowledge to novel contexts. How do different brain states influence this ability to generalize? Using a novel category learning paradigm, we assess the effect of both sleep and time of day on generalization that depends on the flexible integration of recent information. Counter to our expectations, we found no evidence that this form of generalization is better after a night of sleep relative to a day awake. Instead, we observed an effect of time of day, with better generalization in the morning than the evening. This effect also manifested as increased false memory for generalized information. In a nap experiment, we found that generalization did not benefit from having slept recently, suggesting a role for circadian rhythms apart from sleep. We found, however, that this time of day effect appears to be sensitive to category structure and to task engagement more generally. We propose that a state of lowered inhibition in the morning may facilitate spreading activation between otherwise separate memories, promoting this form of generalization.
Press xenobiotic disturbance favors deterministic assembly with a shift in function and structure of bacterial communities in sludge bioreactors
Authors: Santillan Ezequiel , Seshan Hari , Wuertz Stefan 
Published: October 2020

AbstractDisturbance is thought to affect community assembly mechanisms, which in turn shape community structure and the overall function of the ecosystem. Here, we tested the effect of a continuous (press) xenobiotic disturbance on the function, structure, and assembly of bacterial communities within a wastewater treatment system. Two sets of four-liter sequencing batch reactors were operated in triplicate with and without the addition of 3-chloroaniline for a period of 132 days, following 58 days of acclimation after inoculation with sludge from a full-scale treatment plant. Temporal dynamics of bacterial community structure were derived from 16S rRNA gene amplicon sequencing. Community function, structure and assembly differed between press disturbed and undisturbed reactors. Temporal partitioning of assembly mechanisms via phylogenetic and non-phylogenetic null modelling analysis revealed that deterministic assembly prevailed for disturbed bioreactors, while the role of stochastic assembly was stronger for undisturbed reactors. Our findings are relevant because research spanning various disturbance types, environments and spatiotemporal scales is needed for a comprehensive understanding of the effects of press disturbances on assembly mechanisms, structure, and function of microbial communities.Graphical abstract
Optimization design of building isolation structure based on sustainable benefit analysis
Authors: Wu Jia 
Published: October 2020

PurposeThe study shows that with the progress of building technologies and building materials, the scale of buildings has increased. But in earthquake-prone areas, large-scale buildings mean higher risks; therefore improving the seismic capacity of buildings is an important measure to reduce the risk of buildings.Design/methodology/approachIn this study, the isolation structure of buildings was introduced briefly, and the cost-benefit based optimization model of the isolation structure was constructed. The optimization of the isolation structure was carried out from the perspective of benefit analysis. Then, two buildings with the same structure were analyzed as examples. One kept the original isolation structure, and the other optimized the isolation structure with the optimization model.FindingsThe final results showed that the optimized isolation structure had a lower input cost ratio, i.e. it had a higher benefit in the same whole life cycle, and the expected loss cost of the structure produced in the same life cycle was lower.Originality/valueIn conclusion, the optimization model of the isolated structure based on benefit analysis can effectively improve the benefit of building isolation structure produced in the whole life cycle.
Study on the tearing behaviour of woven shirting fabrics – the effect of yarn and fabric properties
Authors: Safari Gorjan Elnaz , Ezazshahabi Nazanin , Mousazadegan Fatemeh 
Published: October 2020

PurposeOccurrence of fabric rupture is a problem that can influence fabric performance during wear. In this regard, fabric tearing resistance is considered by manufacturers and consumers and enhancing tear resistance through optimization of related parameters is beneficial.Design/methodology/approachIn this study, the tearing resistance of a series of shirting fabrics with various weave patterns and weft densities were investigated by both static and dynamic tear test methods. Moreover, the constituent yarn's frictional and tensile behaviour was evaluated and their relation with tear resistance was analysis.FindingsAccording to the outcomes, the fabric firmness and density and friction of yarns affect the tear resistance, reversely. However an improvement in yarn's tenacity can raise the tear resistance.Originality/valueIn this study it was aimed to not only consider influence of both static and dynamic tear test approach on the tearing performance of fabrics regarding their structural parameters, the impact of the constituent's yarn properties include tensile behaviour and friction coefficient on the tearing performance of fabric considered, as well.
Power relations in the production of historical context in disaster inquiry reporting
Authors: Furey Mary A. , Corrigan Lawrence T. , Helms Mills Jean 
Published: October 2020

PurposeThis study aims to examine the textual performance of the Ocean Ranger Disaster inquiry, thus responding to recent calls to “practice context” in historical writing. This study goes beyond the epistemological assumptions about the grounds for knowing about the past as the authors explore how history is produced in the context of power relations.Design/methodology/approachThis paper imagines history-making as a storytelling performance. The authors combine critical historiography and critical sensemaking because these qualitative perspectives help us to understand the composition of the Ocean Ranger Royal Commission Report.FindingsThis case study makes a contribution within the genre of disaster inquiry reporting. The study explains how a formal historical record (the public inquiry report) may be created and how the report is related to aspects of power embedded in a writer’s sense of reality.Social implicationsThe Ocean Ranger Disaster continues to be of tremendous importance to the people of Newfoundland, Canada. There have been numerous studies of the disaster, but these have been overwhelmingly focused on technical matters. To authors’ knowledge, this study is the first to consider the inquiry from an historical context perspective.Originality/valueThe study site enables reflection on a question not often asked in the management history literature: How can we critically understand the composition of an official disaster inquiry report in the context of its power relations?
Paramedicine and mental health: a qualitative analysis of limitations to education and practice in Ontario
Authors: Ford-Jones Polly Christine , Daly Tamara 
Published: October 2020

Purpose
Paramedics increasingly attend to mental health-related emergencies; however, there has been little evaluation of the mental health training for paramedics. This study aims to analyze the fit between paramedicine pedagogy, patient needs and the conditions for paramedics’ skill development.

Design/methodology/approach
Data were collected in a single, qualitative, critical ethnographic case study of pre-hospital mental health and psychosocial care in paramedicine in Ontario, Canada. Transcripts from interviews (n = 46), observation (n ∼ 90h) and document analysis were thematically analyzed using a constant comparative method. The study is theoretically grounded in a feminist political economy framework.

Findings
Tensions are explored in relation to the pedagogy of paramedicine and the conditions of work faced by paramedics. The paper presents challenges and insufficiencies with existing training, the ways in which certain work and training are valued and prioritized, increased emergency care and training needs and the limitations of training to improving care.

Research limitations/implications
Recommendations include more comprehensive didactic training, including the social determinants of health; scenario training; practicum placements in mental health or social services; collaboration with mental health and social services to further develop relevant curriculum and potential inclusion of service users.

Originality/value
This paper addresses the lack of mental health pedagogy in Ontario and internationally and the need for further training pre-certification and while in the workforce. It presents promising practices to ameliorate mental health training and education for paramedics.
Constructing definition of smart cities from systems thinking view
Authors: Singh Anita , Singla A.R. 
Published: October 2020

PurposeOn review of literature on “Smart Cities”, it can be asserted that there are multiple definitions of the term “Smart Cities”; however, a universally accepted definition of “Smart Cities” has not been adopted till date. In these circumstances of uncertainty, this paper aims to propose a conclusive definition of “Smart Cities” from systems thinking view.Design/methodology/approachThe key properties, components and dimensions of “Smart Cities” were identified through text analysis of existing definitions of smart cities in literature using tools such as word cloud, network graph, bubble chart, mind map and web chart of top keywords. The definitions were further subjected to principal component analysis to identify the key components such as characteristics and enablers of “Smart Cities”. The concept of “Smart Cities” was then examined from systems thinking view, to arrive at a systemic understanding of the concept, as it examines the key elements of Government, Citizens and Business using the Golden Circle tool (Why, What and How). Thereon, the interactions between these elements were scrutinized by drawing a Systemigram, which aided in constructing the definition of “Smart Cities”. Thereafter, the validity of the definition was empirically tested by applying it to a set of cities and testing the efficiency of cities through data envelopment analysis.FindingsThe Literature Review and definition analysis of “Smart Cities” have not only facilitated in identifying elements of widely accepted constructs of “Smart Cities” also helps in advancing a formal conceptual definition of “Smart Cities”. A formal definition, which is commonly accepted, would enable researchers in advancing theory and building measurement instruments for “Smart Cities”.Originality/valueGiven the fact that there is no uniform definition of “Smart Cities” leading to varying standards for conceptualization or construction of a “Smart City”, this paper attempts to propose a formal conceptual definition of “Smart Cities” from systems thinking view. Thus, this paper shall not only attempt to advance theory building of the concept of “Smart Cities” but shall also provide a reference to researchers and practitioners, to enable them to build appropriate measures for Smart Cities.
How does nutrition education contribute to the consumers’ use and attitudes towards food labels?
Authors: Ayaz Aylin , Dedebayraktar Damla , Inan-Eroglu Elif , Besler Halit Tanju , Buyuktuncer Zehra 
Published: October 2020

Purpose
This study aims to determine the effects of nutrition knowledge on the use of nutrition facts labels in emerging adults by defining the nutrition education status.

Design/methodology/approach
For this cross-sectional study, 919 young adults, aged 18–24 years, were recruited. Participants trained by dietetic professional at least 2 h per week during the period of at least one education period were considered as having nutrition education. Food label use, specific circumstances and different food products were recorded. The participants were also asked about their attitudes regarding food label use with a questionnaire including 15 products.

Findings
Nutrition facts label is mainly used when buying a product for the first time, a product of an unknown brand or comparing different companies’ similar products, regardless of nutrition education status. Participants with nutrition education had a higher nutrition facts label use and they use the score for specific food products including breakfast cereal (p = 0.003), snacks (p < 0.001), beverages (p = 0.004), ready to eat soups (p = 0.004) and diet products for special occasions (p < 0.001). Mean total score of attitudes regarding food label use for participants who had nutrition education was found as 58.9 ± 6.1 and who did not have nutrition education was found as 51.7 ± 9.2 (p < 0.01).

Originality/value
Nutrition education, which is related to the nutrition facts label use, would be especially useful in helping people for the selection of healthier foods. As habits acquired from childhood will last for a lifetime, more effective nutrition education programs and nutrition label reading education programs should be designed. The findings need to be considered for promoting nutrition facts label use by developing nutrition education.