bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of litter and additional enrichment elements on the occurrence of feather pecking in pullets and laying hens – A focused review
Authors: Schreiter Ruben , Damme Klaus , von Borell Eberhard , Vogt Isabelle , Klunker Michael , Freick Markus 
Published: July 2019

AbstractSevere feather pecking (SFP) is a serious problem in the egg production industry with regard to animal welfare and performance. The multifactorial causes of SFP are discussed in the areas of genetics, feeding, husbandry, stable climate and management. Several studies on the influence of manipulable material on the incidence of SFP in different environments and housing systems have been performed. This review presents current knowledge on the effects of litter and additional enrichment elements on the occurrence of SFP in pullets and laying hens. Because SFP is associated with foraging and feed intake behaviour, the provision of manipulable material in the husbandry environment is an approach that is intended to reduce the occurrence of SFP by adequate exercise of these behaviours. As shown in the literature, the positive effect of enrichment and litter substrate on SFP in a low‐complexity cage environment is evident. On the other hand, consistent results have not been reported on the influence of additional enrichment material in housing systems with litter substrate, which represent the most common type of husbandry in Northwestern Europe. Thus, further research is recommended.
d‐Xylose consumption by nonrecombinant Saccharomyces cerevisiae: A review
Authors: Patiño Margareth Andrea , Ortiz Juan Pablo , Velásquez Mario , Stambuk Boris U. 
Published: June 2019

AbstractXylose is the second most abundant sugar in nature. Its efficient fermentation has been considered as a critical factor for a feasible conversion of renewable biomass resources into biofuels and other chemicals. The yeast Saccharomyces cerevisiae is of exceptional industrial importance due to its excellent capability to ferment sugars. However, although S. cerevisiae is able to ferment xylulose, it is considered unable to metabolize xylose, and thus, a lot of research has been directed to engineer this yeast with heterologous genes to allow xylose consumption and fermentation. The analysis of the natural genetic diversity of this yeast has also revealed some nonrecombinant S. cerevisiae strains that consume or even grow (modestly) on xylose. The genome of this yeast has all the genes required for xylose transport and metabolism through the xylose reductase, xylitol dehydrogenase, and xylulokinase pathway, but there seems to be problems in their kinetic properties and/or required expression. Self‐cloning industrial S. cerevisiae strains overexpressing some of the endogenous genes have shown interesting results, and new strategies and approaches designed to improve these S. cerevisiae strains for ethanol production from xylose will also be presented in this review.
Children’s Magical Realism for New Spatial Interactions: Augmented Reality and the David Almond Archives
Authors: Reynolds Kimberley , Schofield Tom , Trujillo-Pisanty Diego 
Published: June 2019

Abstract
This article draws on a multi-disciplinary project based on the David Almond archives at Seven Stories, the National Centre for Children’s Books in Newcastle upon Tyne, UK. The project combined archival research, augmented reality (AR) technology, Almond’s magical realist writing and experimental workshops to explore whether AR can enhance young people’s engagement with archives and literature. In the process it highlighted the extent to which Almond’s fiction is itself a form of augmentation that represents a particular geographical location—the North East of England—in ways that challenge official accounts of that place. This aspect of Almond’s writing corresponds to what Michel de Certeau describes as tactical spatial practice and is closely associated with some forms of AR.
Evolution of Fine‐Scale Segmentation at Intermediate‐Spreading Rate Ridges
Authors: Le Saout M. , Clague D.A. , Paduan J.B. 
Published: July 2019

AbstractMid‐ocean ridge axes are marked by segmentation of the axes and underlying magmatic systems. Fine‐scale segmentation has mainly been studied along fast‐spreading ridges. Here we offer insight into the third‐ and fourth‐order segmentation of intermediate‐spreading ridges and their temporal evolution. The Alarcón Rise and the Endeavour Segment have similar spreading rates (49 and 52.5 mm/year, respectively) but contrasting morphologies that vary from an axial high with a relatively narrow axial summit trough to an axial valley. One‐meter resolution bathymetry acquired by autonomous underwater vehicles, lava geochemistry, and ages from sediment cores is combined with available seismic reflection profiles to analyze variations in (1) geometry and orientation of the axial summit trough or valley, (2) seafloor depth near the axis, and (3) distribution of hydrothermal vents, (4) lava chemistry, and (5) flow ages between contiguous axes. Along both intermediate‐spreading segments, third‐ and fourth‐order discontinuities and associated segments are similar in dimension to what has been observed along fast‐spreading ridges. The Alarcón Rise and the Endeavour Segment also allow the study of the evolution of fine‐scale segmentation over periods of 300 to 4,000 years. Comparison between old and young axes reveals that the evolution of fine‐scale segmentation depends on the intensity of the magmatic activity. High magmatic periods are associated with rapid evolution of third‐order segments, while low magmatic activity periods, dominated by tectonic deformation and/or hydrothermal activity, are associated with little to no change in segmentation.
Characterization of Submesoscale Turbulence in the East/Japan Sea Using Geostationary Ocean Color Satellite Images
Authors: Choi J. , Park Y.‐G. , Kim W. , Kim Y. H. 
Published: July 2019

AbstractSubmesoscale processes are key in understanding physical and biological phenomena near the surface, but there remains a lack of observational evidence over large areas. We used hourly images from a geostationary satellite that can resolve variation in surface ocean color over an area of few hundred kilometers. The temporal variation in the surface chlorophyll a distribution captured by the satellite images was first used to generate a submesoscale‐permitting velocity field, from which we calculated the turbulence statistics such as kinetic energy spectra, velocity structure functions, and energy flux. Application to the April scenes in the East/Japan Sea showed that the kinetic energy spectra had a transition scale at 50 km that suggested two spectral regimes following k−3 and k−5/3, implying the coexistence of quasi‐geostrophic turbulence and surface quasi‐geostrophic turbulence. The chlorophyll a scalar spectrum suggested two spectral regimes of k−5/3 and k−1 with a transition at 3 km.
Association of SP1 rs1353058818 and STAT3 rs1053004 gene polymorphisms with human tongue squamous cell carcinoma
Authors: Lai Heqing , Xu Guochao , Meng Haifeng , Zhu Haiying 
Published: July 2019

Abstract
Objective: To study the association between SP1 rs1353058818 and STAT3 rs1053004 gene polymorphisms and risk of human tongue squamous cell carcinoma (TSCC).
Methods: Sanger sequencing was used to determine the genotypes of SP1 rs1353058818 and STAT3 rs1053004 loci in 240 TSCC patients and 240 controls. Levels of hsa-miR-149-5p and hsa-miR-21-5p and expression levels of SP1 and STAT3 proteins in tumor tissues and adjacent normal tissues of TSCC patients were ascertained.
Results: Carrying the SP1 rs1353058818 locus deletion allele was a high risk factor for TSCC (OR = 2.997, 95% CI: 1.389–6.466, P = 0.003). The STAT3 rs1053004 locus A allele was a protective factor for TSCC (OR = 0.604, 95% CI: 0.460-0.793, P &lt; 0.001). There was a negative correlation between SP1 mRNA and hsa-miR-149-5p in tumor and adjacent normal tissues (r = −0.81, −0.77). The expression of SP1 protein in tumor tissues of the SP1 rs1353058818 locus DD genotype was significantly higher than in tissues of the ID type, and in tissues of type II it was the lowest. STAT3 mRNA was positively correlated with hsa-miR-21-5p in tumor and adjacent normal tissues (r = 0.75, 0.78). The expression level of STAT3 protein in tumor tissues of patients with STAT3 rs1053004 locus GG genotype was significantly higher than in patients with type GA, and it was the lowest in patients with type AA.
Conclusion: Polymorphisms in the SP1 rs1353058818 and STAT3 rs1053004 loci are associated with the risk of human TSCC.
Powertrain EV synchronous reluctance motor design with redundant topology with novel control
Authors: Herrera Danilo , Villegas Javier , Galván Eduardo , Carrasco Juan Manuel 
Published: June 2019

A doubly three‐phase fed synchronous reluctance machine (SynRM) is designed for electrical vehicle powertrain application. SynRM aims to deliver instant power and high power density, high torque at low speeds and high power at high speeds, wide speed range, high efficiency throughout its range of operation, ruggedness, high safety at a reasonable cost. Under these requirements, a 60 kW, 9000 rpm and 400 Nm SynRM has been designed. The main objective is to demonstrate the SynRM powertrain operation behaviour and determinate the operation points electrically and thermally. To reach the proposed SynRM goal, a new direct torque control algorithm based on output regulation subspace theory control is presented. The winding motor topology is galvanic isolated, so it is possible to operate with the six phases directly to the load and because of that, the combination with a back‐to‐back (B2B) converter becomes so profitable. To validate the system, two B2B full‐converters and two motors (SynRM and induction machine) were used in a real test bench. Finally, a simulated and real efficiency map is obtained covering different drive cycles range. Some remarks about normal and failure mode of operation are presented.
Elevated Complement C3 and C4 Levels are Associated with Postnatal Pregnancy-Related Venous Thrombosis
Authors: Dahm Anders E. A. , Jacobsen Eva Marie , Wik Hilde Skuterud , Jacobsen Anne Flem , Mollnes Tom Eirik , Kanse Sandip M. , Sandset Per Morten 
Published: June 2019

AbstractHigh levels of complement C3 are associated with venous thrombosis (VT) in the general population. We investigated if high C3 and C4 levels were associated with pregnancy-related VT. We undertook the Norwegian VIP study, a case–control study of VT in pregnancy or within 3 months postpartum (cases, n = 313) and women without pregnancy-related VT (controls, n = 353). Determinants of C3 and C4 in the control women were investigated with linear regression and the odds ratio (OR) for pregnancy-related VT was calculated with logistic regression. We found that levels of C3 and C4 were associated with body mass index (BMI), C-reactive protein (CRP); with the coagulation factors (F) fibrinogen, FVIII, and FIX; and with the coagulation inhibitors antithrombin, protein C, protein S, and tissue factor pathway inhibitor. These associations were influenced by CRP levels. The crude OR for pregnancy-related VT was 1.8 (95% confidence interval [CI], 1.1–3.0) for C3 above the 90th percentile and 2.0 (95% CI, 1.2–3.2) for C4 above the 90th percentile. Stratification in antenatal and postnatal VT showed that C3 and C4 were only associated with postnatal VT with an OR for high C3 of 3.0 (95% CI, 1.8–5.0), and for high C4 of 2.6 (95% CI, 1.5–4.6). Adjustment for high FIX and BMI reduced the ORs. We conclude that the association between postnatal VT and C3 and C4 suggests that there is clinically relevant crosstalk between the complement and the coagulation system.
Identification of 58 Mutations (26 Novel) in 94 of 109 Symptomatic Spanish Probands with Protein C Deficiency
Authors: Martos Laura , Fernández-Pardo Álvaro , López-Fernández María F. , Ibáñez Francisco , Herrero Sonia , Tàssies Dolors , González-Porras José R. , Solmoirago María J. , Costa María J. , Reverter Juan C. , Marco Pascual , Roldán Vanessa , Lecumberri Ramón , Velasco Francisco , Oto Julia , Iruin Gemma , Alonso María N. , Vayá Amparo , Bonanad Santiago , Ferrando Fernando , Martí Edelmira , Cid Ana R. , Plana Emma , Oña Francisca , Cuesta Isabel , González-López Tomás J. , España Francisco , Medina Pilar , Navarro Silvia ,   on behalf of the Working Group of the Spanish Society of Thrombosis Haemostasis (SETH)
Published: June 2019

AbstractPresently, no data on the molecular basis of hereditary protein C (PC) deficiency in Spain is available. We analyzed the PC gene (PROC) in 109 patients with symptomatic PC deficiency and in 342 relatives by sequencing the 9 PROC exons and their flanking intron regions. In 93 probands, we found 58 different mutations (26 novel). Thirty-seven consisted of a nucleotide change, mainly missense mutations, 1 was a 6-nucleotide insertion causing the duplication of 2 amino acids, and 4 were deletions of 1, 3, 4, and 16 nucleotides. Nine mutations caused type II deficiencies, with the presence of normal antigen levels but reduced anticoagulant activity. Using a PC level of 70% as lowest normal limit, we found no mutations in 16 probands and 25 relatives with PC levels ≤ 70%. On the contrary, 4 probands and 12 relatives with PC levels > 70% carried the mutation identified in the proband. The spectrum of recurrent mutations in Spain is different from that found in the Netherlands, where the most frequent mutations were p.Gln174* and p.Arg272Cys, and is more similar to that found in France, where the most frequent were p.Arg220Gln and p.Pro210Leu. In our study, p.Val339Met (9 families), p.Tyr166Cys (7), p.Arg220Gln (6), and p.Glu58Lys (5) were the most prevalent. This study confirms the considerable heterogeneity of the genetic abnormality in PC deficiencies, and allowed genetic counseling to those individuals whose PC levels were close to the lower limit of the normal reference range.
Platelet–Neutrophil Crosstalk in Atherothrombosis
Authors: Pircher Joachim , Engelmann Bernd , Massberg Steffen , Schulz Christian 
Published: June 2019

AbstractAtherothrombosis is a frequent cause of cardiovascular mortality. It is mostly triggered by plaque rupture and exposure of the thrombogenic subendothelial matrix, which initiates platelet aggregation and clot formation. Current antithrombotic strategies, however, target both thrombosis and physiological hemostasis and thereby increase bleeding risk. Thus, there is an unmet clinical need for optimized therapies. Neutrophil activation and consecutive interactions of neutrophils and platelets contribute mechanistically to thromboinflammation and arterial thrombosis, and thus present a potential therapeutic target. Platelet–neutrophil interactions are mediated through adhesion molecules such as P-selectin and P-selectin glycoprotein ligand 1 as well as glycoprotein Ib and macrophage-1 antigen, which mediate physical cell interactions and intracellular signaling. Release of soluble mediators as well as direct signaling between platelets and neutrophils lead to their reciprocal activation and neutrophil release of extracellular traps, scaffolds of condensed chromatin that play a prothrombotic role in atherothrombosis. In this article, we review the role of neutrophils and neutrophil-derived prothrombotic molecules in platelet activation and atherothrombosis, and highlight potential therapeutic targets.
ValTrendsDB: bringing Protein Data Bank validation information closer to the user
Authors: Horský Vladimír , Bendová Veronika , Toušek Dominik , Koča Jaroslav , Svobodová Radka 
Published: June 2019

Abstract

Summary
Structures in PDB tend to contain errors. This is a very serious issue for authors that rely on such potentially problematic data. The community of structural biologists develops validation methods as countermeasures, which are also included in the PDB deposition system. But how are these validation efforts influencing the structure quality of subsequently published data? Which quality aspects are improving, and which remain problematic? We developed ValTrendsDB, a database that provides the results of an extensive exploratory analysis of relationships between quality criteria, size and metadata of biomacromolecules. Key input data are sourced from PDB. The discovered trends are presented via precomputed information-rich plots. ValTrendsDB also supports the visualization of a set of user-defined structures on top of general quality trends. Therefore, ValTrendsDB enables users to see the quality of structures published by selected author, laboratory or journal, discover quality outliers, etc. ValTrendsDB is updated weekly.

Availability and implementation
Freely accessible at http://ncbr.muni.cz/ValTrendsDB. The web interface was implemented in JavaScript. The database was implemented in C++.

Supplementary information
Supplementary data are available at Bioinformatics online.
A river runs through it: tree frog genomics supports the Dead Sea Rift as a rare phylogeographical break
Authors: Dufresnes Christophe , Mazepa Glib , Jablonski Daniel , Sadek Riyad A , Litvinchuk Spartak N 
Published: June 2019

AbstractPhylogeographical breaks can be viewed as regional hotspots of diversity where the genetic integrity of incipient species is put to the test. We focus on an understudied species transition from the Middle East, namely the Dead Sea Rift in the Levant region, which presumably divided the tree frogs Hyla savignyi and H. felixarabica. Combining multilocus genetic analyses (mitochondrial DNA and RAD-sequencing) with ecological niche modelling, we test whether the rift effectively acts as a biogeographical barrier preventing this pair from admixing and merging. The answer is yes: despite weak signs of introgression, all parapatric populations were assigned to either species without cyto-nuclear discordance. Yet, the projected distributions under present and glacial conditions largely overlapped in the area, meaning their current parapatric ranges do not represent an ecological transition. Instead, we hypothesize that H. savignyi and H. felixarabica are maintained apart by limited opportunities for dispersal across the barren Jordan Valley, combined with advanced reproductive isolation. Therefore, the Dead Sea Rift may represent a rare phylogeographical break, and we encourage international efforts to assess its contribution to the rich biodiversity of the Middle East.
How the Cluster-randomized Trial “Works”
Authors: Hurley James C 
Published: June 2019

AbstractCluster-randomized trials (CRTs) are able to address research questions that randomized controlled trials (RCTs) of individual patients cannot answer. Of great interest for infectious disease physicians and infection control practitioners are research questions relating to the impact of interventions on infectious disease dynamics at the whole-of-population level. However, there are important conceptual differences between CRTs and RCTs relating to design, analysis, and inference. These differences can be illustrated by the adage “peas in a pod.” Does the question of interest relate to the “peas” (the individual patients) or the “pods” (the clusters)? Several examples of recent CRTs of community and intensive care unit infection prevention interventions are used to illustrate these key concepts. Examples of differences between the results of RCTs and CRTs on the same topic are given.
Altered Intestinal Permeability and Fungal Translocation in Ugandan Children With Human Immunodeficiency Virus
Authors: Dirajlal-Fargo Sahera , El-Kamari Vanessa , Weiner Lukasz , Shan Lingpeng , Sattar Abdus , Kulkarni Manjusha , Funderburg Nicholas , Nazzinda Rashidah , Karungi Christine , Kityo Cissy , Musiime Victor , McComsey Grace A 
Published: June 2019

AbstractBackgroundChildren with perinatally acquired human immunodeficiency virus (HIV; PHIVs) face a lifelong cumulative exposure to HIV and antiretroviral therapy (ART). The relationship between gut integrity, microbial translocation, and inflammation in PHIV is poorly understood.MethodsThis is a cross-sectional study in 57 PHIVs, 59 HIV-exposed but uninfected children, and 56 HIV-unexposed and -uninfected children aged 2–10 years old in Uganda. PHIVs were on stable ART with HIV-1 RNA &lt;400 copies/mL. We measured markers of systemic inflammation, monocyte activation, and gut integrity. Kruskal-Wallis tests were used to compare markers by group and the Spearman correlation was used to assess correlations between biomarkers.ResultsThe mean age of all participants was 7 years and 55% were girls. Among PHIVs, the mean CD4 % was 34%, 93% had a viral load ≤20 copies/mL, and 79% were on a nonnucleoside reverse transcriptase inhibitor regimen. Soluble cluster of differentiation 14 (sCD14), beta-D-glucan (BDG), and zonulin were higher in the PHIV group (P ≤ .01). Intestinal fatty acid binding protein (I-FABP) and lipopolysaccharide binding protein (LBP) did not differ between groups (P &gt; .05). Among PHIVs who were breastfed, levels of sCD163 and interleukin 6 (IL6) were higher than levels in PHIV who were not breastfed (P &lt; .05). Additionally, in PHIVs with a history of breastfeeding, sCD14, BDG, LBP, zonulin, and I-FABP correlated with several markers of systemic inflammation, including high-sensitivity C-reactive protein, IL6, d-dimer, and systemic tumor necrosis factor receptors I and II (P ≤ .05).ConclusionsDespite viral suppression, PHIVs have evidence of altered gut permeability and fungal translocation. Intestinal damage and the resultant bacterial and fungal translocations in PHIVs may play a role in the persistent inflammation that leads to many end-organ diseases in adults.Despite viral suppression, children with perinatally acquired human immunodeficiency virus (HIV) in Uganda have evidence of alterations in intestinal permeability and fungal translocation, compared to HIV-exposed but uninfected and HIV-unexposed children, which may play a role in HIV-associated chronic inflammation.