bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transmission of ESBL-producing Escherichia coli between broilers and humans on broiler farms
Authors: van Hoek Angela H A M , Dierikx Cindy , Bosch Thijs , Schouls Leo , van Duijkeren Engeline , Visser Michael 
Published: November 2019

Abstract

Background
ESBL and AmpC β-lactamases are an increasing concern for public health. Studies suggest that ESBL/pAmpC-producing Escherichia coli and their plasmids carrying antibiotic resistance genes can spread from broilers to humans working or living on broiler farms. These studies used traditional typing methods, which may not have provided sufficient resolution to reliably assess the relatedness of these isolates.

Methods
Eleven suspected transmission events among broilers and humans living/working on eight broiler farms were investigated using whole-genome short-read (Illumina) and long-read sequencing (PacBio). Core genome MLST (cgMLST) was performed to investigate the occurrence of strain transmission. Horizontal plasmid and gene transfer were analysed using BLAST.

Results
Of eight suspected strain transmission events, six were confirmed. The isolate pairs had identical ESBL/AmpC genes and fewer than eight allelic differences according to the cgMLST, and five had an almost identical plasmid composition. On one of the farms, cgMLST revealed that the isolate pairs belonging to ST10 from a broiler and a household member of the farmer had 475 different alleles, but that the plasmids were identical, indicating horizontal transfer of mobile elements rather than strain transfer. Of three suspected horizontal plasmid transmission events, one was confirmed. In addition, gene transfer between plasmids was found.

Conclusions
The present study confirms transmission of strains as well as horizontal plasmid and gene transfer between broilers and farmers and household members on the same farm. WGS is an important tool to confirm suspected zoonotic strain and resistance gene transmission.
Zinc supplementation during in vitro embryo culture increases inner cell mass and total cell numbers in bovine blastocysts1
Authors: Wooldridge Lydia K , Nardi Madison E , Ealy Alan D 
Published: November 2019

Abstract
Deficiencies in current embryo culture media likely contribute to the poor blastocyst development rates and pregnancy retention rates for in vitro produced (IVP) bovine embryos. Of special concern is the lack of micronutrients in these media formulations. One micronutrient of interest is zinc, an essential trace element involved with various enzyme and transcription factor activities. The objective of this work was to describe whether zinc sulfate supplementation during in vitro embryo culture affects bovine embryo development and blastomere numbers. Either 0, 2, 20, or 40 µM zinc sulfate was supplemented to presumptive zygotes cultured in synthetic oviductal fluid containing AAs and bovine serum albumin for 8 d. None of the treatments affected cleavage rates. Percentage of blastocysts on days 7 and 8 postfertilization was not affected by supplementing 2 or 20 µM zinc but were reduced (P &lt; 0.05) with 40 µM zinc. In blastocysts harvested on day 8, inner cell mass (ICM) and total cell number were increased (P &lt; 0.05) with 2 µM zinc supplementation but not with the other zinc concentrations. Numbers of trophectoderm cells were not affected by zinc treatment. In conclusion, supplementing zinc during bovine embryo culture did not impact blastocyst development but improved ICM cell numbers. This improvement in ICM cell number may have implications for improved pregnancy retention rates after IVP embryo transfer as smaller ICM sizes are associated with poor pregnancy success in cattle.
Reaction of threonine synthase with the substrate analogue 2-amino-5-phosphonopentanoate: implications into the proton transfer at the active site
Authors: Machida Yasuhiro , Murakawa Takeshi , Sakai Akiko , Shoji Mitsuo , Shigeta Yasuteru , Hayashi Hideyuki 
Published: November 2019

AbstractThreonine synthase catalyses the conversion of O-phospho-l-homoserine and a water molecule to l-threonine and has the most complex catalytic mechanism among the pyridoxal 5′-phosphate-dependent enzymes. In order to study the less-characterized earlier stage of the catalytic reaction, we studied the reaction of threonine synthase with 2-amino-5-phosphonopentanoate, which stops the catalytic reaction at the enamine intermediate. The global kinetic analysis of the triphasic spectral changes showed that, in addition to the theoretically expected pathway, the carbanion is rapidly reprotonated at Cα to form an aldimine distinct from the external aldimine directly formed from the Michaelis complex. The Kd for the binding of inhibitor to the enzyme decreased with increasing pH, showing that the 2-amino-group-unprotonated form of the ligand binds to the enzyme. On the other hand, the rate constants for the proton migration steps within the active site are independent of the solvent pH, indicating that protons are shared by the active dissociative groups and are not exchanged with the solvent during the course of catalysis. This gives an insight into the role of the phosphate group of the substrate, which may increase the basicity of the ε-amino group of the catalytic lysine residue in the active site.
The internal anatomy of Sandersiella chilenica Stuardo & Vega, 2011 (Crustacea: Cephalocarida)
Authors: Valdovinos-Zarges Claudio 
Published: November 2019

AbstractThe gross internal anatomy of the cephalocarid crustacean Sandersiella chilenicaStuardo & Vega, 2011 is described based on light microscopy of histological sections of three specimens of the type series, all collected in coastal soft bottoms off central Chile. Observations mainly concern the nervous, digestive, and reproductive systems, heart, haemocoel, and skeleto-musculature. The main organ systems and musculature are similar to those previously described for Hutchinsoniella macracanthaSanders, 1955, Lightiella magdaleninaCarcupino, Floris, Addis, Castelli & Curini-Galletti, 2006, and Sandersiella sp.
TeV-peaked candidate BL Lac objects
Authors: Costamante L 
Published: November 2019

ABSTRACT
BL Lac objects can be extreme in two ways: with their synchrotron emission, peaking beyond 1 keV in their spectral energy distribution, or with their gamma-ray emission, peaking at multi-TeV energies up to and beyond 10–20 TeV, like 1ES 0229+200. This second type of extreme BL Lacs – which we can name TeV-peaked BL Lacs – is not well explained by the usual synchrotron self-Compton scenarios for BL Lacs. These sources are also important as probes for the intergalactic diffuse infrared background and cosmic magnetic fields, as well as possible sites of production of ultra-high-energy cosmic rays and neutrinos. However, all these studies are hindered by their still very limited number. Here I propose a new, simple criterium to select the best candidates for TeV observations, specifically aimed at this peculiar type of BL Lac objects by combining X-ray, gamma-ray, and infrared data. It is based on the observation of a clustering towards a high X-ray to GeV gamma-ray flux ratio, and it does not rely on the radio flux or X-ray spectrum. This makes it suitable to find TeV-peaked sources also with very faint radio emission. Taking advantage of the Fermi all-sky gamma-ray survey applied to the ROMA-BZCAT and Sedentary Survey samples, I produce an initial list of 47 TeV-peaked candidates for observations with present and future air-Cherenkov telescopes.
Direct Effects of the Environment on AGN Triggering in SDSS Spiral Galaxies: Merger-AGN connection
Authors: Kim Minbae , Choi Yun-Young , Kim Sungsoo S 
Published: November 2019

Abstract
We examine whether galaxy environments directly affect triggering nuclear activity in Sloan Digital Sky Survey (SDSS) local spiral galaxies using a volume-limited sample with the r-band absolute magnitude Mr < −19.0 and 0.02 < z < 0.055 selected from the SDSS Data Release 7. To avoid incompleteness of the central velocity dispersion σ of the volume-limited sample and to fix the black hole mass affecting AGN activity, we limit the sample to a narrow σ range of 130 < σ < 200 km s−1. We define a variety of environments as a combination of neighbour interactions and local density on a galaxy. After the central star formation rate (which is closely related to AGN activity level) is additionally restricted, the direct impact of the environment is unveiled. In the outskirts of rich clusters, red spiral galaxies show a significant excess of the AGN fraction despite the lack of central gas. We argue that they have been pre-processed before entering the rich clusters, and due to mergers or strong encounters in the in-fall region, their remaining gases efficiently lose angular momentum. Furthermore, we find many star-forming galaxies and only a few starburst-AGN composite hosts with the highest [OIII] luminosity. We claim that they are a gas-rich merger product in groups or are group galaxies in-falling into clusters, indicating that many AGN signatures may be obscured during the merger events.
Quantum mechanics at high redshift – Modelling Damped Lyman–α absorption systems
Authors: Lee C C , Webb J K , Carswell R F 
Published: November 2019

Abstract
For around 100 years, hydrogen spectral modelling has been based on Voigt profile fitting. The semi-classical Voigt profile is based on a 2-level atom approximation. Whilst the Voigt profile is excellent for many circumstances, the accuracy is insufficient for very high column density damped Lyman-α absorption systems. We have adapted the quantum-mechanical Kramers-Heisenberg model to include thermal broadening, producing a new profile, the KHT profile. Interactions involving multiple discrete atomic levels and continuum terms, not accounted for in the Voigt model, generate asymmetries in the Lyman line wings. If not modelled, this can lead to significant systematics in parameter estimation when modelling real data. There are important ramifications in particular for measurements of the primordial deuterium abundance. However, the KHT model is complicated. We therefore present a simplified formulation based on Taylor series expansions and look-up tables, quantifying the impact of the approximations made. The KHT profile has been implemented within the widely-used VPFIT code.
Mechanistic insight into the role of Poly(ADP-ribosyl)ation in DNA topology modulation and response to DNA damage
Authors: Matkarimov Bakhyt T , Zharkov Dmitry O , Saparbaev Murat K 
Published: November 2019

AbstractGenotoxic stress generates single- and double-strand DNA breaks either through direct damage by reactive oxygen species or as intermediates of DNA repair. Failure to detect and repair DNA strand breaks leads to deleterious consequences such as chromosomal aberrations, genomic instability and cell death. DNA strand breaks disrupt the superhelical state of cellular DNA, which further disturbs the chromatin architecture and gene activity regulation. Proteins from the poly(ADP-ribose) polymerase (PARP) family, such as PARP1 and PARP2, use NAD+ as a substrate to catalyse the synthesis of polymeric chains consisting of ADP-ribose units covalently attached to an acceptor molecule. PARP1 and PARP2 are regarded as DNA damage sensors that, upon activation by strand breaks, poly(ADP-ribosyl)ate themselves and nuclear acceptor proteins. Noteworthy, the regularly branched structure of poly(ADP-ribose) polymer suggests that the mechanism of its synthesis may involve circular movement of PARP1 around the DNA helix, with a branching point in PAR corresponding to one complete 360° turn. We propose that PARP1 stays bound to a DNA strand break end, but rotates around the helix displaced by the growing poly(ADP-ribose) chain, and that this rotation could introduce positive supercoils into damaged chromosomal DNA. This topology modulation would enable nucleosome displacement and chromatin decondensation around the lesion site, facilitating the access of DNA repair proteins or transcription factors. PARP1-mediated DNA supercoiling can be transmitted over long distances, resulting in changes in the high-order chromatin structures. The available structures of PARP1 are consistent with the strand break-induced PAR synthesis as a driving force for PARP1 rotation around the DNA axis.
Effects of valproic acid on histone deacetylase inhibition in vitro and in glioblastoma patient samples
Authors: Berendsen Sharon , Frijlink Elselien , Kroonen Jèrôme , Spliet Wim G M , van Hecke Wim , Seute Tatjana , Snijders Tom J , Robe Pierre A 
Published: November 2019

Abstract

Background
The antiepileptic drug valproic acid (VPA) inhibits histone deacetylase in glioblastoma cells in vitro, which influences several oncogenic pathways and decreases glioma cell proliferation. The clinical relevance of these observations remains unclear, as VPA does not seem to affect glioblastoma patient survival. In this study, we analyzed whether the in vitro effects of VPA treatment on histone acetylation are also observed in tumor tissues of glioblastoma patients.

Methods
The in vitro effects of VPA treatment on histone acetylation were assessed with immunofluorescence and western blotting. On tissue microarrays and in fresh-frozen glioblastoma tissues we investigated the histone acetylation patterns of patients who were either treated with VPA or did not receive antiepileptic drugs at the time of their surgery. We also performed mRNA expression-based and gene set enrichment analyses on these tissues.

Results
VPA increased the expression levels of acetylated histones H3 and H4 in vitro, in agreement with previous reports. In tumor samples obtained from glioblastoma patients, however, VPA treatment affected neither gene (set) expression nor histone acetylation.

Conclusions
The in vitro effects of VPA on histone acetylation status in glioblastoma cells could not be confirmed in clinical tumor samples of glioblastoma patients using antiepileptic doses of VPA, which reflects the lack of effect of VPA on the clinical outcome of glioblastoma patients.
Regulation of the Poly(A) Status of Mitochondrial mRNA by Poly(A)-Specific Ribonuclease Is Conserved among Land Plants
Authors: Kanazawa Mai , Ikeda Yoko , Nishihama Ryuichi , Yamaoka Shohei , Lee Nam-Hee , Yamato Katsuyuki T , Kohchi Takayuki , Hirayama Takashi 
Published: November 2019

Abstract
Regulation of the stability and the quality of mitochondrial RNA is essential for the maintenance of mitochondrial and cellular functions in eukaryotes. We have previously reported that the eukaryotic poly(A)-specific ribonuclease (PARN) and the prokaryotic poly(A) polymerase encoded by AHG2 and AGS1, respectively, coordinately regulate the poly(A) status and the stability of mitochondrial mRNA in Arabidopsis. Mitochondrial function of PARN has not been reported in any other eukaryotes. To know how much this PARN-based mitochondrial mRNA regulation is conserved among plants, we studied the AHG2 and AGS1 counterparts of the liverwort, Marchantia polymorpha, a member of basal land plant lineage. We found that M. polymorpha has one ortholog each for AHG2 and AGS1, named MpAHG2 and MpAGS1, respectively. Their Citrine-fused proteins were detected in mitochondria of the liverwort. Molecular genetic analysis showed that MpAHG2 is essential and functionally interacts with MpAGS1 as observed in Arabidopsis. A recombinant MpAHG2 protein had a deadenylase activity in vitro. Overexpression of MpAGS1 and the reduced expression of MpAHG2 caused an accumulation of polyadenylated Mpcox1 mRNA. Furthermore, MpAHG2 suppressed Arabidopsis ahg2-1 mutant phenotype. These results suggest that the PARN-based mitochondrial mRNA regulatory system is conserved in land plants.
Establishing a student-run free clinic in a major city in Northern Europe: a 1-year experience from Hamburg, Germany
Authors: Drexler Richard , Fröschle Felix , Predel Christopher , Sturm Berit , Ustorf Klara , Lehner Louisa , Janzen Jara , Valentin Lisa , Scheer Tristan , Lehnert Franziska , Tadzic Refmir , Oldhafer Karl Jürgen , Meyer Tobias N 
Published: November 2019

Abstract

Background
Student-Run Free Clinics (SRFCs) have been an integral part of US medical schools since the 1960s and provide health care to underserved populations. In 2018, we established an SRFC in Hamburg, Germany, a major city in Northern Europe. The aim of this study was to describe the central problems and to investigate the usefulness of an SRFC in a country with free access to medical care, such as Germany.

Methods
All consecutive patients treated at the SRFC Hamburg between February 2018 and March 2019 that consented to this study were analyzed regarding clinical characteristics, diagnosis, readmission rate and country of origin.

Results
Between February 2018 and March 2019, 229 patients were treated at the SRFC in Hamburg. The patients came from 33 different countries with a majority (n = 206, 90%) from countries inside the European Union. The most common reasons for visiting the SRFC were infections (23.2%), acute or chronic wounds (13.5%) and fractures (6.3%).

Conclusion
Our multicultural patients suffer mainly from infections and traumatological and dermatological diseases. We find similarities to published Canadian SRFC patient cohorts but differences in diseases and treatment modalities compared to US SRFCs. Importantly, we demonstrate the relevance and necessity of the SRFC in a major city in Northern Europe.
A comparative study of two porous sponge scaffolds prepared by collagen derived from porcine skin and fish scales as burn wound dressings in a rabbit model
Authors: Shi Yufei , Zhang Hongjian , Zhang Xin , Chen Zhan , Zhao Dan , Ma Jun 
Published: November 2019

Abstract
Collagen is widely used in biomedical applications due to its outstanding properties. In this study, highly porous sponge scaffolds were developed by using porcine skin-derived collagen (PSC) and fish scale-derived collagen (FSC), respectively. The morphology and composition of these PSC and FSC scaffolds were compared. The water uptake ratio of FSC scaffolds reached 47.8, which is 1.7 times of PSC scaffolds. The water vapour transmission rates (WVTR) of PSC and FSC scaffolds were 952.6 ± 55.5 and 1090.9 ± 77.1 g/m2/day, which could produce a moist healing environment for wounds. Both scaffolds show non-toxicity to L929 fibroblast cells. The burn wound healing efficiency of these two scaffolds was examined in vivo using rabbits. No scars around the wounds were observed after applying PSC and SFC scaffolds. Histopathological studies reveal that the wound treated with PSC and FSC scaffolds showed much better wound recovery than gauze and vaseline gauze groups. It was suggested that FSC scaffolds have great potential as same as PSC to be used as burn wound dressing materials.
Higher Social Rejection Sensitivity in Opioid-Dependent Patients Is Related to Smaller Insula Gray Matter Volume: A Voxel-Based Morphometric Study
Authors: Bach Patrick , Frischknecht Ulrich , Klinkowski Svenja , Bungert Melanie , Karl Damian , Vollmert Christian , Vollstädt-Klein Sabine , Lis Stefanie , Kiefer Falk , Hermann Derik 
Published: November 2019

Abstract
Opioid-dependent patients are highly sensitized to negative social feedback, and increased social rejection sensitivity was linked to adverse treatment outcome, but its neurobiological underpinnings have not been understood yet. The present study investigated gray matter (GM) volume differences between 19 opioid maintenance treatment (OMT) patients and 20 healthy controls using magnetic resonance imaging and voxel-based morphometry. Associations of GM volumes with subjective feelings of exclusion and inclusion during a social ostracism (Cyberball) paradigm, with rejection sensitivity, social interaction anxiety and social phobia were explored. OMT patients displayed smaller GM volume in the bilateral insula and inferior frontal gyri. Psychometric and task data showed that patients reported significantly higher rejection sensitivity, social anxiety and social phobia scores and felt more excluded and less included during the social ostracism paradigm. Smaller GM volume in the insula was associated with higher subjective exclusion, lower subjective inclusion and higher rejection sensitivity, social anxiety and social phobia scores. Findings indicate that structural deficits in emotion- and anxiety-processing brain regions in OMT patients are associated with increased social rejection sensitivity. As social rejection is a potential trigger for relapse, patients might benefit from therapeutic strategies that promote social integration.
Differences in Functional Connectivity Networks Related to the Midbrain Dopaminergic System-Related Area in Various Psychiatric Disorders
Authors: Nakamura Yuko , Okada Naohiro , Koshiyama Daisuke , Kamiya Kouhei , Abe Osamu , Kunimatsu Akira , Okanoya Kazuo , Kasai Kiyoto , Koike Shinsuke 
Published: November 2019

AbstractObjectiveDisruptions in the dopamine system have been observed in psychiatric disorders. Since dopamine is mainly produced in the ventral tegmental area (VTA), elucidating the differences in the VTA neural network across psychiatric disorders would facilitate a greater understanding of the pathophysiological mechanisms underlying these disorders. However, no study has compared VTA-seed-based functional connectivity across psychiatric disorders. Therefore, we conducted a resting-state functional magnetic resonance imaging (rs-fMRI) study to perform a seed-based fMRI analysis, using the VTA as a seed.MethodsWe included participants with major depressive disorder (MDD; n = 45), schizophrenia (n = 32), and bipolar disorder (BPD; n = 30), along with healthy control participants (n = 46) who were matched for age, gender, and handedness.ResultsThe results showed that patients with MDD and BPD had altered VTA-related connectivity in the superior frontal gyrus, frontal pole regions, hippocampus, cerebellum, and posterior cingulate cortex. Some of these differences in connectivity were also found between affective disorders and schizophrenia; however, there were no differences between the schizophrenia and control groups. Connectivity between the VTA and the hippocampus was correlated with positive symptoms in the schizophrenia group. The connectivity was not associated with medication dose, and the results remained significant after controlling for dose.ConclusionsThe results suggest that altered brain functional connectivity related to VTA networks could be associated with the distinctive pathophysiologies of psychiatric disorders, especially affective disorders.
The Wall Around EU Fundamental Freedoms: the Purely Internal Rule at the Forty-Year Mark
Authors: Arena Amedeo 
Published: November 2019

Abstract
‘Purely internal situations’ are sets of facts entirely confined within a single Member State. According to the ‘purely internal rule’, introduced by the European Court of Justice (ECJ) in 1979, purely internal situations lie outside the scope of the internal market fundamental freedoms and of other EU provisions having a cross-border scope. On the fortieth anniversary of the jurisprudential genesis of the purely internal rule, this article seeks to examine its origins, rationale, and evolution, by analyzing the most relevant patterns in the over 250 preliminary rulings handed down in disputes involving purely internal situations. This survey will enable an assessment of the systemic significance of the purely internal rule and of the consequences that abolishing that rule would have for the European integration process.