bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated Design of D.D.I., Filament Winding and Curing Processes for Manufacturing the High Pressure Vessel (Type II)
Authors: Kwak Hyoseo , Park Gunyoung , Seong Hansaem , Kim Chul 
Published: October 2019

Abstract
As energy crisis and environment pollution all around the world threaten the widespread use of fossil fuels, compressed natural gas (CNG) vehicles are explored as an alternative to the conventional gasoline powered vehicles. Because of the limited space available for the car, the composite pressure vessel (Type II) has been applied to the CNG vehicles to reach large capacity and weight lightening vehicles. High pressure vessel (Type II) is composed of a composite layer and a metal liner. The metal liner is formed by the deep drawing and ironing (D.D.I.) process, which is a complex process of deep drawing and ironing. The cylinder part is reinforced by composite layer wrapped through the filament winding process and is bonded to the liner by the curing process. In this study, an integrated design method was presented by establishing the techniques for FE analysis of entire processes (D.D.I., filament winding and curing processes) to manufacture the CNG composite pressure vessel (Type II). Dimensions of the dies and the punches of the 1st (cup drawing), 2nd (redrawing-ironing 1-ironing 2) and 3rd (redrawing-ironing) stages were calculated theoretically, and shape of tractrix die to be satisfied with the minimum forming load was suggested for life improvement and manufacturing costs in the D.D.I. process. Thickness of the composite material was determined in the filament winding process, finally, conditions of the curing process (number of heating stage, curing temperature, heating rate and time) were proposed to reinforce adhesive strength between the composite layers.
Cuttlebone morphometrics and sex identification of Sepia bertheloti (d’Orbigny, 1835) from the central-east Atlantic
Authors: Guerra-Marrero Airam , Jiménez-Alvarado David , Hernández-García Vicente , Curbelo-Muñoz Leticia , Castro-Hernández José Juan 
Published: October 2019

Abstract
Analysis of 322 cuttlebones of Sepia bertheloti caught in the waters of the Northwest Africa showed significant differences in growth between males and females. Morphometric analysis revealed a relatively different cuttlebone growth pattern between sexes, with males presenting faster growth in length to reach larger sizes and females displaying greater growth in width. This difference in cuttlebone growth is related to female gonadal development and the subsequent increase of the paleal cavity, providing more support and space to accommodate a higher number of oocytes.
Incorporating genetic networks into case-control association studies with high-dimensional DNA methylation data
Authors: Kim Kipoong , Sun Hokeun 
Published: October 2019

Abstract

Background
In human genetic association studies with high-dimensional gene expression data, it has been well known that statistical selection methods utilizing prior biological network knowledge such as genetic pathways and signaling pathways can outperform other methods that ignore genetic network structures in terms of true positive selection. In recent epigenetic research on case-control association studies, relatively many statistical methods have been proposed to identify cancer-related CpG sites and their corresponding genes from high-dimensional DNA methylation array data. However, most of existing methods are not designed to utilize genetic network information although methylation levels between linked genes in the genetic networks tend to be highly correlated with each other.

Results
We propose new approach that combines data dimension reduction techniques with network-based regularization to identify outcome-related genes for analysis of high-dimensional DNA methylation data. In simulation studies, we demonstrated that the proposed approach overwhelms other statistical methods that do not utilize genetic network information in terms of true positive selection. We also applied it to the 450K DNA methylation array data of the four breast invasive carcinoma cancer subtypes from The Cancer Genome Atlas (TCGA) project.

Conclusions
The proposed variable selection approach can utilize prior biological network information for analysis of high-dimensional DNA methylation array data. It first captures gene level signals from multiple CpG sites using data a dimension reduction technique and then performs network-based regularization based on biological network graph information. It can select potentially cancer-related genes and genetic pathways that were missed by the existing methods.
Construction of strains to identify novel factors for regulation of centromeric cohesion protection (CCP) and sister kinetochore mono-orientation (SKM)
Authors: Bharati Akhilendra Pratap , Ghosh Santanu Kumar 
Published: October 2019

AbstractBackgroundMeiosis-I is a unique type of chromosome segregation where each chromosome aligns and segregates from its homolog. The mechanism of meiosis I homolog separation in different eukaryotes depends on their centromere and kinetochore architecture which in turn relies mainly on two processes, first on a specialized four protein complex known as monopolin and second, the centromeric cohesion protection (CCP). However, in mammals the complex has not been identified. Furthermore, in budding yeast, there could be additional factors in this process which includes some meiosis specific and some non meiosis specific factors.ResultWe constructed two strains. In the first strain we expressed Mam1 and Cdc5 which leads to sister kinetochore monoorientation (SKM) and in the second case we expressed Rec8 and Spo13 which enhanced CCP even in mitosis. The expression of these proteins in mitotically dividing cells caused co-orientation of the chromosomes, which lead to the cell death followed by miss-segregation of chromosomes. Then we utilized these strains to screen the cDNA libraries from yeast and mammals to identify the novel factors which participate in CCP and SKM. Finally, SGY4119 strain expressing Spo13 and Rec8 was transformed with pRS316 gal cDNA library and transformants were screened for lethality on galactose. We screened ~ 105transformants colonies. Out of these ~ 3000 colonies were able to survive on galactose plate which was narrow down to 6 on the basis of desired phenotype.ConclusionSo far, meiosis specific kinetochore proteins have been identified only in two yeasts. Recently, in mammals a meiosis specific kinetochore protein (MEIKIN) has been identified with similar function. Till now a single protein in mammals and four proteins monopolin complex in budding yeast has been identified to coorient the centromere. Many more novel factors have to be identified yet. That is why we wished to device genetic screen using a functional genomics approach. Since the list of proteins already identified in yeast is not exhaustive as the circumstantial evidence suggests, we wish to use the same yeast strains to identify additional novel yeast proteins that may be involved in the execution of meiosis.
A genomic analysis and transcriptomic atlas of gene expression in Psoroptes ovis reveals feeding- and stage-specific patterns of allergen expression
Authors: Burgess Stewart T. G. , Marr Edward J. , Bartley Kathryn , Nunn Francesca G. , Down Rachel E. , Weaver Robert J. , Prickett Jessica C. , Dunn Jackie , Rombauts Stephane , Van Leeuwen Thomas , Van de Peer Yves , Nisbet Alasdair J. 
Published: October 2019

AbstractBackgroundPsoroptic mange, caused by infestation with the ectoparasitic mite,Psoroptes ovis, is highly contagious, resulting in intense pruritus and represents a major welfare and economic concern for the livestock industry Worldwide. Control relies on injectable endectocides and organophosphate dips, but concerns over residues, environmental contamination, and the development of resistance threaten the sustainability of this approach, highlighting interest in alternative control methods. However, development of vaccines and identification of chemotherapeutic targets is hampered by the lack ofP. ovistranscriptomic and genomic resources.ResultsBuilding on the recent publication of theP. ovisdraft genome, here we present a genomic analysis and transcriptomic atlas of gene expression inP. ovisrevealing feeding- and stage-specific patterns of gene expression, including novel multigene families and allergens. Network-based clustering revealed 14 gene clusters demonstrating either single- or multi-stage specific gene expression patterns, with 3075 female-specific, 890 male-specific and 112, 217 and 526 transcripts showing larval, protonymph and tritonymph specific-expression, respectively. Detailed analysis ofP. ovisallergens revealed stage-specific patterns of allergen gene expression, many of which were also enriched in “fed” mites and tritonymphs, highlighting an important feeding-related allergenicity in this developmental stage. Pair-wise analysis of differential expression between life-cycle stages identified patterns of sex-biased gene expression and also identified novelP. ovismultigene families including known allergens and novel genes with high levels of stage-specific expression.ConclusionsThe genomic and transcriptomic atlas described here represents a unique resource for the acarid-research community, whilst the OrcAE platform makes this freely available, facilitating further community-led curation of the draftP. ovisgenome.
Comparative genomic analysis of the Hafnia genus reveals an explicit evolutionary relationship between the species alvei and paralvei and provides insights into pathogenicity
Authors: Yin Zhiqiu , Yuan Chao , Du Yuhui , Yang Pan , Qian Chengqian , Wei Yi , Zhang Si , Huang Di , Liu Bin 
Published: October 2019

Abstract

Background
The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also uncertain. Here, we used comparative genomic analysis to define the taxonomy of Hafnia, identify species-specific genes that may be the result of ecological and pathogenic specialization, and reveal virulence-related genetic profiles that may contribute to pathogenesis.

Results
One complete genome sequence and 19 draft genome sequences for Hafnia strains were generated and combined with 27 publicly available genomes. We provided high-resolution typing methods by constructing phylogeny and population structure based on single-copy core genes in combination with whole genome average nucleotide identity to identify two distant Hafnia species (alvei and paralvei) and one mislabeled strain. The open pan-genome and the presence of numerous mobile genetic elements reveal that Hafnia has undergone massive gene rearrangements. Presence of species-specific core genomes associated with metabolism and transport suggests the putative niche differentiation between alvei and paralvei. We also identified possession of diverse virulence-related profiles in both Hafnia species., including the macromolecular secretion system, virulence, and antimicrobial resistance. In the macromolecular system, T1SS, Flagellum 1, Tad pilus and T6SS-1 were conserved in Hafnia, whereas T4SS, T5SS, and other T6SSs exhibited the evolution of diversity. The virulence factors in Hafnia are related to adherence, toxin, iron uptake, stress adaptation, and efflux pump. The identified resistance genes are associated with aminoglycoside, beta-lactam, bacitracin, cationic antimicrobial peptide, fluoroquinolone, and rifampin. These virulence-related profiles identified at the genomic level provide insights into Hafnia pathogenesis and the differentiation between alvei and paralvei.

Conclusions
Our research using core genome phylogeny and comparative genomics analysis of a larger collection of strains provides a comprehensive view of the taxonomy and species-specific traits between Hafnia species. Deciphering the genome of Hafnia strains possessing a reservoir of macromolecular secretion systems, virulence factors, and resistance genes related to pathogenicity may provide insights into addressing its numerous infections and devising strategies to combat the pathogen.
Genome rearrangements induce biofilm formation in Escherichia coli C – an old model organism with a new application in biofilm research
Authors: Król Jarosław E. , Hall Donald C. , Balashov Sergey , Pastor Steven , Sibert Justin , McCaffrey Jennifer , Lang Steven , Ehrlich Rachel L. , Earl Joshua , Mell Joshua C. , Xiao Ming , Ehrlich Garth D. 
Published: October 2019

AbstractBackgroundEscherichia coliC forms more robust biofilms than other laboratory strains. Biofilm formation and cell aggregation under a high shear force depend on temperature and salt concentrations. It is the last of fiveE. colistrains (C, K12, B, W, Crooks) designated as safe for laboratory purposes whose genome has not been sequenced.ResultsHere we present the complete genomic sequence of this strain in which we utilized both long-read PacBio-based sequencing and high resolution optical mapping to confirm a large inversion in comparison to the other laboratory strains. Notably, DNA sequence comparison revealed the absence of several genes thought to be involved in biofilm formation, including antigen 43,waaSBOJYZULfor lipopolysaccharide (LPS) synthesis, andcpsBfor curli synthesis. The first main difference we identified that likely affects biofilm formation is the presence of an IS3-like insertion sequence in front of the carbon storage regulatorcsrAgene. This insertion is located 86 bp upstream of thecsrAstart codon inside the − 35 region of P4 promoter and blocks the transcription from the sigma32and sigma70promoters P1-P3 located further upstream. The second is the presence of an IS5/IS1182 in front of thecsgDgene. And finally,E. coliC encodes an additional sigma70subunit driven by the same IS3-like insertion sequence. Promoter analyses using GFP gene fusions provided insights into understanding this regulatory pathway inE. coli.ConclusionsBiofilms are crucial for bacterial survival, adaptation, and dissemination in natural, industrial, and medical environments. Most laboratory strains ofE. coligrown for decades in vitro have evolved and lost their ability to form biofilm, while environmental isolates that can cause infections and diseases are not safe to work with. Here, we show that the historic laboratory strain ofE. coliC produces a robust biofilm and can be used as a model organism for multicellular bacterial research. Furthermore, we ascertained the full genomic sequence of this classic strain, which provides for a base level of characterization and makes it useful for many biofilm-based applications.
Cohabitation is associated with a greater resemblance in gut microbiota which can impact cardiometabolic and inflammatory risk
Authors: Finnicum Casey T. , Beck Jeffrey J. , Dolan Conor V. , Davis Christel , Willemsen Gonneke , Ehli Erik A. , Boomsma Dorret I. , Davies Gareth E. , de Geus Eco J. C. 
Published: October 2019

Abstract

Background
The gut microbiota composition is known to be influenced by a myriad of factors including the host genetic profile and a number of environmental influences. Here, we focus on the environmental influence of cohabitation on the gut microbiota as well as whether these environmentally influenced microorganisms are associated with cardiometabolic and inflammatory burden. We perform this by investigating the gut microbiota composition of various groups of related individuals including cohabitating monozygotic (MZ) twin pairs, non-cohabitating MZ twin pairs and spouse pairs.

Results
A stronger correlation between alpha diversity was found in cohabitating MZ twins (45 pairs, r = 0.64, p = 2.21 × 10− 06) than in non-cohabitating MZ twin pairs (121 pairs, r = 0.42, p = 1.35 × 10− 06). Although the correlation of alpha diversity did not attain significance between spouse pairs (42 pairs, r = 0.23, p = 0.15), the correlation was still higher than those in the 209 unrelated pairs (r = − 0.015, p = 0.832). Bray-Curtis (BC) dissimilarity metrics showed cohabitating MZ twin pairs had the most similar gut microbiota communities which were more similar than the BC values of non-cohabitating MZ twins (empirical p-value = 0.0103), cohabitating spouses (empirical p-value = 0.0194), and pairs of unrelated non-cohabitating individuals (empirical p-value< 0.00001). There was also a significant difference between the BC measures from the spouse pairs and those from the unrelated non-cohabitating individuals (empirical p-value< 0.00001). Intraclass correlation coefficients were calculated between the various groups of interest and the results indicate the presence of OTUs with an environmental influence and one OTU that appeared to demonstrate genetic influences. One of the OTUs (Otu0190) was observed to have a significant association with both the cardiometabolic and inflammatory burden scores (p’s < 0.05).

Conclusions
Through the comparison of the microbiota contents of MZ twins with varying cohabitation status and spousal pairs, we showed evidence of environmentally influenced OTUs, one of which had a significant association with cardiometabolic and inflammatory burden scores.
Silencing of one copy of the translation initiation factor eIFiso4G in Japanese plum (Prunus salicina) impacts susceptibility to Plum pox virus (PPV) and small RNA production
Authors: Rubio Julia , Sánchez Evelyn , Tricon David , Montes Christian , Eyquard Jean-Philippe , Chague Aurélie , Aguirre Carlos , Prieto Humberto , Decroocq Véronique 
Published: October 2019

AbstractBackgroundIn plants, host factors encoded by susceptibility (S) genes are indispensable for viral infection. Resistance is achieved through the impairment or the absence of those susceptibility factors. ManySgenes have been cloned from model and crop species and a majority of them are coding for members of the eukaryotic translation initiation complex, mainly eIF4E, eIF4G and their isoforms. The aim of this study was to investigate the role of those translation initiation factors in susceptibility of stone fruit species to sharka, a viral disease due toPlum pox virus(PPV).ResultsFor this purpose, hairpin-inducing silencing constructs based onPrunus persicaorthologs were used to generatePrunus salicina(Japanese plum) 4E and 4G silenced plants byAgrobacterium tumefaciens-mediated transformation and challenged with PPV. While down-regulatedeIFiso4Etransgenic Japanese plums were not regenerated in our conditions,eIFiso4G11-, but not theeIFiso4G10-, silenced plants displayed durable and stable resistance to PPV. We also investigated the alteration of the si- and mi-RNA profiles in transgenic and wild-type Japanese plums upon PPV infection and confirmed that the newly generated small interfering (si) RNAs, which are derived from the engineered inverted repeat construct, are the major contributor of resistance to sharka.ConclusionsOur results indicate thatSgene function of the translation initiation complex isoform is conserved inPrunusspecies. We discuss the possibilities of using RNAi silencing or loss-of-function mutations of the different isoforms of proteins involved in this complex to breed for resistance to sharka in fruit trees.
Diversification and genetic structure of the western-to-eastern progression of European Phaseolus vulgaris L. germplasm
Authors: Pipan Barbara , Meglič Vladimir 
Published: October 2019

Abstract

Background
Common bean (Phaseolus vulgaris L.) is the most important food legume for direct human consumption around the world, as it represents a valuable source of components with nutritional and health benefits.

Results
We conducted a study to define and explain the genetic relatedness and diversification level of common bean (Phaseolus vulgaris L.) germplasm from Portugal to Ukraine, along a western-to-eastern line of southern European countries, including Poland. This was based on the P. vulgaris genetic structure, and was designed to better describe its distribution and domestication pathways in Europe. Using the multi-crop passport descriptors that include geographic origin and different phaseolin types (corresponding to the Mesoamerican and Andean gene pools), 782 accessions were obtained from nine gene banks and 12 geographic origins. We selected 33 genome/ gene-related/ gene-pool-related nuclear simple sequence repeat markers that covered the genetic diversity across the P. vulgaris genome. The overall polymorphic information content was 0.800. Without specifying geographic origin, global structure cluster analysis generated 10 genetic clusters. Among the PvSHP1 markers, the most informative for gene pool assignment of the European P. vulgaris germplasm was PvSHP1-B. Results of AMOVA show that 89% of the molecular variability is shared within the 782 accessions, with 4% molecular variability among the different geographic origins along this western-to-eastern line of southern Europe (including Poland).

Conclusions
This study shows that the diversification line of the European P. vulgaris germplasm followed from the western areas of southern Europe (Portugal, Spain, Italy, Slovenia) to the more eastern areas of southern Europe. This progression defines three geographically separated subgroups, as the northern (Poland, Ukraine, Romania), southern (Albania, Bulgaria), and central (Bosnia and Herzegovina, Serbia, Hungary) areas of eastern Europe.
Accepting new patients who require opioids into family practice: results from the MAAP-NS census survey study
Authors: Marshall Emily Gard , Burge Frederick , Gibson Richard J. , Lawson Beverley , O’Connell Colleen 
Published: October 2019

Abstract

Background
Acceptance to a family practice is key to access and continuity of care. While Canadian patients increasingly report not being able to acquire acceptance to a family practice, little is known about the association between requiring opioids and acceptance. We aim to determine the proportion of family physicians who would accept new patients who require opioids and describe physician and practice characteristics associated with willingness to accept these patients.

Methods
Census telephone survey of family physicians’ practices in Nova Scotia, Canada. Measures: physician (i.e., age, sex, years in practice) and practice (i.e., number/type of provider in the practice, care hours/week) characteristics and practice-reported willingness to accept new patients who require opioids.

Results
The survey was completed for 587 family physicians (83.7% response rate). 354 (60.3%) were taking new patients unconditionally or with conditions; 326 provided a response to whether they would accept new patients who require opioids; 91 (27.9%) reported they would not accept a new patient who requires opioids. Compared to family physicians who would not accept patients who require opioids, in bivariate analysis, those who would, tended to work in larger practices; had fewer years in practice; are female; and provided more patient care. The relationship to number of providers in the practice, having a nurse, and experience persisted in multivariate analysis.

Conclusions
The strongest predictors of willingness to accept patients who require opioids are fewer years in practice (OR = 0.96 [95% CI 0.93, 0.99]) and variables indicating a family physician has support of a larger (OR = 1.19 [95% CI 1.00, 1.42]), interdisciplinary team (e.g., nurses, mental health professionals) (OR = 1.15 [95% CI 1.11, 5.05]). Almost three-quarters (72.1%) of surveyed family physicians would accept patients requiring opioids.