bluuebunny/crossref_metadata_2025_split huggingface dataset:
Indoxyl Sulphate is Associated with Atrial Fibrillation Recurrence after Catheter Ablation
Authors: Yamagami Fumi , Tajiri Kazuko , Doki Kosuke , Hattori Masayuki , Honda Junya , Aita Satoshi , Harunari Tomohiko , Yamasaki Hiro , Murakoshi Nobuyuki , Sekiguchi Yukio , Homma Masato , Takahashi Naohiko , Aonuma Kazutaka , Nogami Akihiko , Ieda Masaki 
Published: November 2018

AbstractRenal dysfunction results in the accumulation of various uremic toxins, including indoxyl sulphate (IS), and is a major risk factor for atrial fibrillation (AF). Experimental studies have demonstrated that IS exacerbates atrial remodelling via oxidative stress, inflammation, and fibrosis. However, its clinical impact on AF-promoting cardiac remodelling has not been described. Therefore, the purpose of this study was to clarify the relationship between basal IS levels and the 1-year outcomes after catheter ablation for the treatment of AF. Our prospective observational study included data from 125 patients with AF who underwent catheter ablation. Over a 1-year follow-up period, AF recurrence was identified in 21 patients. The 1-year AF-free survival was significantly lower in patients with high serum IS levels (≥0.65 μg/mL) than in those with low IS levels (60.1 ± 10.4% versus 85.2 ± 3.9%, P = 0.007). Univariable analysis identified that an IS concentration ≥ 0.65 μg/mL was associated with AF recurrence (hazard ratio [HR] = 3.10 [1.26–7.32], P = 0.015), and this association was maintained in multivariate analysis (HR = 3.67 [1.13–11.7], P = 0.031). Thus, in patients undergoing AF ablation, serum IS levels at baseline independently predict the recurrence of arrhythmia.
The prevalence and transcriptional activity of the mucosal microbiota of ulcerative colitis patients
Authors: Moen Aina E. Fossum , Lindstrøm Jonas Christoffer , Tannæs Tone Møller , Vatn Simen , Ricanek Petr , Vatn Morten H. , Jahnsen Jørgen ,   The IBD-Character Consortium, Frengen Anna B. , Dahl Fredrik A. , You Panpan , Sølvernes Janne , Ekeland Gunn S. , Detlie Trond E. , Olbjørn Christine , O’Leary Kate R. , Ventham Nicholas T. , Kennedy Nicholas A. , Kalla Rahul , Adams Alex , Drummond Hazel E. , Boyapati Ray , Nimmo Elaine R. , Wilson David C. , Satsangi Jack , Heath Simon C. , Gut Marta , Merkel Angelika , Bayes Monica , Gut Ivo G. , Keita Åsa V. , Söderholm Johan D. , Hjortswang Henrik , Carstens Adam , Bergemalm Daniel , Halfvarson Jonas , Andersson Erik , Lindqvist Mårten , Repsilber Dirk , Pierik Marieke , Jonkers Daisy , Gomollón Fernando , D’Amato Mauro , Törkvist Leif , Hjelm Fredrik , Gullberg Mats , Nordberg Niklas , Ocklind Anette , Pettersson Erik , Ekman Daniel , Sundell Mikael , Modig Eddie , Bonfiglio Ferdinando , Veillard Anne-Clémence , Schoemans Renaud , Poncelet Dominique , Sabatel Céline , Lindahl Torbjørn , Ciemniejewska Ewa , Casén Christina , Lees Charles , Noble Colin L. , Arnott Ian , Ho Gwo-Tzer , Shand Alan G. 
Published: November 2018

AbstractActive microbes likely have larger impact on gut health status compared to inactive or dormant microbes. We investigate the composition of active and total mucosal microbiota of treatment-naïve ulcerative colitis (UC) patients to determine the microbial picture at the start-up phase of disease, using both a 16S rRNA transcript and gene amplicon sequencing. DNA and RNA were isolated from the same mucosal colonic biopsies. Our aim was to identify active microbial members of the microbiota in early stages of disease and reveal which members are present, but do not act as major players. We demonstrated differences in active and total microbiota of UC patients when comparing inflamed to non-inflamed tissue. Several taxa, among them the Proteobacteria phyla and families therein, revealed lower transcriptional activity despite a high presence. The Bifidobacteriaceae family of the Actinobacteria phylum showed lower abundance in the active microbiota, although no difference in presence was detected. The most abundant microbiota members of the inflamed tissue in UC patients were not the most active. Knowledge of active members of microbiota in UC patients could enhance our understanding of disease etiology. The active microbial community composition did not deviate from the total when comparing UC patients to non-IBD controls.
The influence of surface chemistry on the kinetics and thermodynamics of bacterial adhesion
Authors: Oh Jun Kyun , Yegin Yagmur , Yang Fan , Zhang Ming , Li Jingyu , Huang Shifeng , Verkhoturov Stanislav V. , Schweikert Emile A. , Perez-Lewis Keila , Scholar Ethan A. , Taylor T. Matthew , Castillo Alejandro , Cisneros-Zevallos Luis , Min Younjin , Akbulut Mustafa 
Published: November 2018

AbstractThis work is concerned with investigating the effect of substrate hydrophobicity and zeta potential on the dynamics and kinetics of the initial stages of bacterial adhesion. For this purpose, bacterial pathogens Staphylococcus aureus and Escherichia coli O157:H7 were inoculated on the substrates coated with thin thiol layers (i.e., 1-octanethiol, 1-decanethiol, 1-octadecanethiol, 16-mercaptohexadecanoic acid, and 2-aminoethanethiol hydrochloride) with varying hydrophobicity and surface potential. The time-resolved adhesion data revealed a transformation from an exponential dependence to a square root dependence on time upon changing the substrate from hydrophobic or hydrophilic with a negative zeta potential value to hydrophilic with a negative zeta potential for both pathogens. The dewetting of extracellular polymeric substances (EPS) produced by E. coli O157:H7 was more noticeable on hydrophobic substrates, compared to that of S. aureus, which is attributed to the more amphiphilic nature of staphylococcal EPS. The interplay between the timescale of EPS dewetting and the inverse of the adhesion rate constant modulated the distribution of E. coli O157:H7 within microcolonies and the resultant microcolonial morphology on hydrophobic substrates. Observed trends in the formation of bacterial monolayers rather than multilayers and microcolonies rather than isolated and evenly spaced bacterial cells could be explained by a colloidal model considering van der Waals and electrostatic double-layer interactions only after introducing the contribution of elastic energy due to adhesion-induced deformations at intercellular and substrate-cell interfaces. The gained knowledge is significant in the context of identifying surfaces with greater risk of bacterial contamination and guiding the development of novel surfaces and coatings with superior bacterial antifouling characteristics.
In-depth validation of total HIV-1 DNA assays for quantification of various HIV-1 subtypes
Authors: Rutsaert Sofie , De Spiegelaere Ward , Van Hecke Clarissa , De Scheerder Marie-Angélique , Kiselinova Maja , Vervisch Karen , Trypsteen Wim , Vandekerckhove Linos 
Published: November 2018

AbstractHIV-1 DNA quantification serves as an important reservoir biomarker in HIV cure trials. However, the high genetic diversity of HIV-1 represented by different subtypes may bring inaccuracy in quantifying HIV-1 DNA and a sensitive and validated assay covering diverse HIV-1 subtypes is lacking. Therefore, we cross-validated total HIV-1 DNA assays described in literature using a three-step comparative analysis. First, a bioinformatics tool was developed in-house to perform an in silico evaluation of 67 HIV-1 DNA assays. Secondly, these selected assays were in vitro validated using a panel of different HIV-1 subtypes and, finally, ex vivo assessed on selected patient samples with different HIV-1 subtypes. Our results show that quantification of HIV-1 DNA substantially differs between assays and we advise five best performing HIV-1 DNA assays for ddPCR and qPCR (Schvachsa_2007, Viard_2004, Heeregrave_2009, Van_der_Sluis_2013, Yu_2008 and Yun_2002). This in-depth analysis of published HIV-1 DNA assays indicates that not all assays guarantee an optimal measurement of HIV-1 DNA, especially when looking across subtypes. Using an in-depth cross-validation, we were able to validate HIV-1 DNA assays that are suitable for quantification of HIV-1 DNA in a wide variety of HIV-1 infected patients.
Proximity-induced supercurrent through topological insulator based nanowires for quantum computation studies
Authors: Bhattacharyya Biplab , Awana V. P. S. , Senguttuvan T. D. , Ojha V. N. , Husale Sudhir 
Published: November 2018

AbstractProximity-induced superconducting energy gap in the surface states of topological insulators has been predicted to host the much wanted Majorana fermions for fault-tolerant quantum computation. Recent theoretically proposed architectures for topological quantum computation via Majoranas are based on large networks of Kitaev’s one-dimensional quantum wires, which pose a huge experimental challenge in terms of scalability of the current single nanowire based devices. Here, we address this problem by realizing robust superconductivity in junctions of fabricated topological insulator (Bi2Se3) nanowires proximity-coupled to conventional s-wave superconducting (W) electrodes. Milling technique possesses great potential in fabrication of any desired shapes and structures at nanoscale level, and therefore can be effectively utilized to scale-up the existing single nanowire based design into nanowire based network architectures. We demonstrate the dominant role of ballistic topological surface states in propagating the long-range proximity induced superconducting order with high IcRN product in long Bi2Se3 junctions. Large upper critical magnetic fields exceeding the Chandrasekhar-Clogston limit suggests the existence of robust superconducting order with spin-triplet cooper pairing. An unconventional inverse dependence of IcRN product on the width of the nanowire junction was also observed.
Identifying the region responsible for Brucella abortus MucR higher-order oligomer formation and examining its role in gene regulation
Authors: Pirone Luciano , Pitzer Joshua Edison , D’Abrosca Gianluca , Fattorusso Roberto , Malgieri Gaetano , Pedone Emilia Maria , Pedone Paolo Vincenzo , Roop Roy Martin , Baglivo Ilaria 
Published: November 2018

AbstractMucR is a member of the Ros/MucR family of prokaryotic zinc-finger proteins found in the α-proteobacteria which regulate the expression of genes required for the successful pathogenic and symbiotic interactions of these bacteria with the eukaryotic hosts. The structure and function of their distinctive zinc-finger domain has been well-studied, but only recently the quaternary structure of the full length proteins was investigated demonstrating their ability to form higher-order oligomers. The aim of this study was to identify the region of MucR involved in higher-order oligomer formation by analysing deletion and point mutants of this protein by Light Scattering, and to determine the role that MucR oligomerization plays in the regulatory function of this protein. Here we demonstrate that a conserved hydrophobic region at the N-terminus of MucR is responsible for higher-order oligomer formation and that MucR oligomerization is essential for its regulatory function in Brucella. All these features of MucR are shared by the histone-like nucleoid structuring protein, (H-NS), leading us to propose that the prokaryotic zinc-finger proteins in the MucR/Ros family control gene expression employing a mechanism similar to that used by the H-NS proteins, rather than working as classical transcriptional regulators.
The timing and widespread effects of the largest Holocene volcanic eruption in Antarctica
Authors: Antoniades Dermot , Giralt Santiago , Geyer Adelina , Álvarez-Valero Antonio M. , Pla-Rabes Sergi , Granados Ignacio , Liu Emma J. , Toro Manuel , Smellie John L. , Oliva Marc 
Published: November 2018

AbstractThe caldera collapse of Deception Island Volcano, Antarctica, was comparable in scale to some of the largest eruptions on Earth over the last several millennia. Despite its magnitude and potential for far-reaching environmental effects, the age of this event has never been established, with estimates ranging from the late Pleistocene to 3370 years before present. Here we analyse nearby lake sediments in which we identify a singular event produced by Deception Island’s caldera collapse that occurred 3980 ± 125 calibrated years before present. The erupted tephra record the distinct geochemical composition of ejecta from the caldera-forming eruption, whilst an extreme seismic episode is recorded by lake sediments immediately overlying the collapse tephra. The newly constrained caldera collapse is now the largest volcanic eruption confirmed in Antarctica during the Holocene. An examination of palaeorecords reveals evidence in marine and lacustrine sediments for contemporaneous seismicity around the Antarctic Peninsula; synchronous glaciochemical volcanic signatures also record the eruption in ice cores spread around Antarctica, reaching >4600 km from source. The widespread footprint suggests that this eruption would have had significant climatic and ecological effects across a vast area of the south polar region.
Non-contact Quantification of Jugular Venous Pulse Waveforms from Skin Displacements
Authors: Lam Po Tang Emily J. , HajiRassouliha Amir , Nash Martyn P. , Nielsen Poul M. F. , Taberner Andrew J. , Cakmak Yusuf O. 
Published: November 2018

AbstractThe jugular venous (JV) pressure waveform is a non-invasive, proven indicator of cardiovascular disease. Conventional clinical methods for assessing these waveforms are often overlooked because they require specialised expertise, and are invasive and expensive to implement. Recently, image-based methods have been used to quantify JV pulsation waveforms on the skin as an indirect way of estimating the pressure waveforms. However, these existing image-based methods cannot explicitly measure skin deformations and rely on the use of photoplethysmography (PPG) devices for identification of the pulsatile waveforms. As a result, they often have limited accuracy and robustness and are unsuitable in the clinical environment. Here, we propose a technique to directly measure skin deformations caused by the JV pulse using a very accurate subpixel registration algorithm. The method simply requires images obtained from the subject’s neck using a commodity camera. The results show that our measured waveforms contained all of the essential features of diagnostic JV waveforms in all of 19 healthy subjects tested in this study, indicating a significantly important capability for a potential future diagnostic device. The shape of our measured JV displacement waveforms was validated using waveforms measured with a laser displacement sensor, where the average correlation score between the two waveforms was 0.93 ± 0.05. In addition, synchronously recorded ECG signals were used to verify the timings of diagnostic features of the measured waveforms. To our knowledge, this is the first use of image registration for direct measurement of JV displacement waveforms. Significant advantages of our novel method include the high precision of our measurements, and the ability to use ordinary cameras, such as those in modern mobile phones. These advantages will enable the development of affordable and accessible devices to measure JV waveforms for cardiac diagnostics in the clinical environment. Future devices based on this technology may provide viable options for telemedicine applications, point of care diagnostics, and mobile-based cardiac health monitoring systems.
A high-density genetic linkage map and QTL mapping for growth and sex of yellow drum (Nibea albiflora)
Authors: Qiu Changliang , Han Zhaofang , Li Wanbo , Ye Kun , Xie Yangjie , Wang Zhiyong 
Published: November 2018

AbstractA high-density genetic linkage map is essential for the studies of comparative genomics and gene mapping, and can facilitate assembly of reference genome. Herein, we constructed a high-density genetic linkage map with 8,094 SNPs selected from 113 sequenced fish of a F1 family. Ultimately, the consensus map spanned 3818.24 cM and covered nearly the whole genome (99.4%) with a resolution of 0.47 cM. 1,457 scaffolds spanning 435.15 Mb were anchored onto 24 linkage groups, accounting for 80.7% of the draft genome assembly of the yellow drum. Comparative genomic analyses with medaka and zebrafish genomes showed superb chromosome-scale synteny between yellow drum and medaka. QTL mapping and association analysis congruously revealed 22 QTLs for growth-related traits and 13 QTLs for sex dimorphism. Some important candidate genes such as PLA2G4A, BRINP3 and P2RY1 were identified from these growth-related QTL regions. A gene family including DMRT1, DMRT2 and DMRT3 was identified from these sex-related QTL regions on the linkage group LG9. We demonstrate that this linkage map can facilitate the ongoing marker-assisted selection and genomic and genetic studies for yellow drum.
In-depth analysis of Bacillus subtilis proteome identifies new ORFs and traces the evolutionary history of modified proteins
Authors: Ravikumar Vaishnavi , Nalpas Nicolas C. , Anselm Viktoria , Krug Karsten , Lenuzzi Maša , Šestak Martin Sebastijan , Domazet-Lošo Tomislav , Mijakovic Ivan , Macek Boris 
Published: November 2018

AbstractBacillus subtilis is a sporulating Gram-positive bacterium widely used in basic research and biotechnology. Despite being one of the best-characterized bacterial model organism, recent proteomics studies identified only about 50% of its theoretical protein count. Here we combined several hundred MS measurements to obtain a comprehensive map of the proteome, phosphoproteome and acetylome of B. subtilis grown at 37 °C in minimal medium. We covered 75% of the theoretical proteome (3,159 proteins), detected 1,085 phosphorylation and 4,893 lysine acetylation sites and performed a systematic bioinformatic characterization of the obtained data. A subset of analyzed MS files allowed us to reconstruct a network of Hanks-type protein kinases, Ser/Thr/Tyr phosphatases and their substrates. We applied genomic phylostratigraphy to gauge the evolutionary age of B. subtilis protein classes and revealed that protein modifications were present on the oldest bacterial proteins. Finally, we performed a proteogenomic analysis by mapping all MS spectra onto a six-frame translation of B. subtilis genome and found evidence for 19 novel ORFs. We provide the most extensive overview of the proteome and post-translational modifications for B. subtilis to date, with insights into functional annotation and evolutionary aspects of the B. subtilis genome.
BET Inhibition Improves NASH and Liver Fibrosis
Authors: Middleton Sarah A. , Rajpal Neetu , Cutler Leanne , Mander Palwinder , Rioja Inmaculada , Prinjha Rab K. , Rajpal Deepak , Agarwal Pankaj , Kumar Vinod 
Published: November 2018

AbstractNon-alcoholic fatty liver disease (NAFLD) is a leading form of chronic liver disease with large unmet need. Non-alcoholic steatohepatitis (NASH), a progressive variant of NAFLD, can lead to fibrosis, cirrhosis, and hepatocellular carcinoma. To identify potential new therapeutics for NASH, we used a computational approach based on Connectivity Map (CMAP) analysis, which pointed us to bromodomain and extra-terminal motif (BET) inhibitors for treating NASH. To experimentally validate this hypothesis, we tested a small-molecule inhibitor of the BET family of proteins, GSK1210151A (I-BET151), in the STAM mouse NASH model at two different dosing timepoints (onset of NASH and progression to fibrosis). I-BET151 decreased the non-alcoholic fatty liver disease activity score (NAS), a clinical endpoint for assessing the severity of NASH, as well as progression of liver fibrosis and interferon-γ expression. Transcriptional characterization of these mice through RNA-sequencing was consistent with predictions from the CMAP analysis of a human NASH signature and pointed to alterations in molecular mechanisms related to interferon signaling and cholesterol biosynthesis, as well as reversal of gene expression patterns linked to fibrotic markers. Altogether, these results suggest that inhibition of BET proteins may present a novel therapeutic opportunity in the treatment of NASH and liver fibrosis.
Seabird-affected taluses are denitrification hotspots and potential N2O emitters in the High Arctic
Authors: Hayashi Kentaro , Tanabe Yukiko , Ono Keisuke , Loonen Maarten J. J. E. , Asano Maki , Fujitani Hirotsugu , Tokida Takeshi , Uchida Masaki , Hayatsu Masahito 
Published: November 2018

AbstractIn High Arctic tundra ecosystems, seabird colonies create nitrogen cycling hotspots because of bird-derived labile organic matter. However, knowledge about the nitrogen cycle in such ornithocoprophilous tundra is limited. Here, we determined denitrification potentials and in-situ nitrous oxide (N2O) emissions of surface soils on plant-covered taluses under piscivorous seabird cliffs at two sites (BL and ST) near Ny-Ålesund, Svalbard, in the European High Arctic. Talus soils at both locations had very high denitrification potentials at 10 °C (2.62–4.88 mg N kg−1 dry soil h−1), near the mean daily maximum air temperature in July in Ny-Ålesund, with positive temperature responses at 20 °C (Q10 values, 1.6–2.3). The talus soils contained abundant denitrification genes, suggesting that they are denitrification hotspots. However, high in-situ N2O emissions, indicating the presence of both active aerobic nitrification and anaerobic denitrification, were observed only at BL (max. 16.6 µg N m−2 h−1). Rapid nitrogen turnover at BL was supported by lower carbon-to-nitrogen ratios, higher nitrate content, and higher δ15N values in the soils at BL compared with those at ST. These are attributed to the 30-fold larger seabird density at BL than at ST, providing the larger organic matter input.
Urotensin-II gene rs228648 polymorphism associated with the risk of diabetes mellitus
Authors: Zhao Yawei , Fang Shuhua , Que Kerong , Xu Guangli , Zhang Heng , Qi Cong , Yang Nian 
Published: November 2018

Background: Urotensin-II (UII) rs228648 polymorphism has been reported to be associated with the risk of diabetes mellitus (DM) with inconsistent results. The present study sought to reassess the relationship between this polymorphism and susceptibility to DM by meta-analysis.
Methods: Relevant eligible studies and whole genome association study (GWAS) data electronically searched were pooled to evaluate the strength of the association with odds ratios (ORs) and 95% confidence intervals (CIs).
Results: Seven case–control studies involving 894 cases and 1186 controls were finally included in the meta-analysis. Overall analyses indicated that UII gene rs228648 variant was significantly associated with reduced risk of DM (allele, A vs. G: OR = 0.68, 95%CI = 0.56–0.82; dominant, AA+GA vs. GG: OR = 0.70, 95%CI = 0.53–0.91; homozygote, AA vs. GG: OR = 0.41, 95%CI = 0.28–0.61; recessive, AA vs. GA+GG: OR = 0.36, 95%CI = 0.19–0.71). In subgroup analyses based on ethnicity, the results showed a significant association of rs228648 polymorphism with decreased risk of DM in Chinese population under all five genetic models as well as in non-Chinese population under heterozygote and recessive models. Stratified analyses by specific type of DM also presented a significant association for common diabetes mellitus (CDM) under allele and homozygote as well as gestational diabetes mellitus (GDM) under all genetic models except for homozygote model. However, the synthetic analysis with GWAS data suggested an increased risk of DM with rs228648 effect allele in European population (OR = 1.01, 95%CI = 1.00–1.02).
Conclusion: The present meta-analysis preliminarily suggested a potentially opposite role of rs228648 polymorphism associated with DM risk in the Chinese and European population. Further studies are in great request to verify the results.