bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monomerization of the photoconvertible fluorescent protein SAASoti by rational mutagenesis of single amino acids
Authors: Solovyev Ilya D. , Gavshina Alexandra V. , Katti Aditya S. , Chizhik Alexey I. , Vinokurov Leonid M. , Lapshin Grigory D. , Ivashina Tatiana V. , Khrenova Maria G. , Kireev Igor I. , Gregor Ingo , Enderlein Jörg , Savitsky Alexander P. 
Published: October 2018

AbstractPhotoconvertible fluorescent proteins (PCFPs) are widely used as markers for the visualization of intracellular processes and for sub-diffraction single-molecule localization microscopy. Although wild type of a new photoconvertible fluorescent protein SAASoti tends to aggregate, we succeeded, via rational mutagenesis, to obtain variants that formed either tetramers or monomers. We compare two approaches: one is based on the structural similarity between SAASoti and Kaede, which helped us to identify a single point mutation (V127T) at the protein’s hydrophobic interface that leads to monomerization. The other is based on a chemical modification of amino groups of SAASoti with succinic anhydride, which converts the protein aggregates into monomers. Mass-spectrometric analysis helped us to identify that the modification of a single ε-amino group of lysine K145 in the strongly charged interface AB was sufficient to convert the protein into its tetrameric form. Furthermore, site-directed mutagenesis was used to generate mutants that proved to be either monomeric or tetrameric, both capable of rapid green-to-red photoconversion. This allows SAASoti to be used as a photoconvertible fluorescent marker for in vivo cell studies.
Change points, memory and epidemic spreading in temporal networks
Authors: P. Peixoto Tiago , Gauvin Laetitia 
Published: October 2018

AbstractDynamic networks exhibit temporal patterns that vary across different time scales, all of which can potentially affect processes that take place on the network. However, most data-driven approaches used to model time-varying networks attempt to capture only a single characteristic time scale in isolation — typically associated with the short-time memory of a Markov chain or with long-time abrupt changes caused by external or systemic events. Here we propose a unified approach to model both aspects simultaneously, detecting short and long-time behaviors of temporal networks. We do so by developing an arbitrary-order mixed Markov model with change points, and using a nonparametric Bayesian formulation that allows the Markov order and the position of change points to be determined from data without overfitting. In addition, we evaluate the quality of the multiscale model in its capacity to reproduce the spreading of epidemics on the temporal network, and we show that describing multiple time scales simultaneously has a synergistic effect, where statistically significant features are uncovered that otherwise would remain hidden by treating each time scale independently.
Relative positioning of Kv11.1 (hERG) K+ channel cytoplasmic domain-located fluorescent tags toward the plasma membrane
Authors: Barros Francisco , Domínguez Pedro , de la Peña Pilar 
Published: October 2018

AbstractRecent cryo-EM data have provided a view of the KCNH potassium channels molecular structures. However, some details about the cytoplasmic domains organization and specially their rearrangements associated to channel functionality are still lacking. Here we used the voltage-dependent dipicrylamine (DPA)-induced quench of fluorescent proteins (FPS) linked to different positions at the cytoplasmic domains of KCNH2 (hERG) to gain some insights about the coarse structure of these channel parts. Fast voltage-clamp fluorometry with HEK293 cells expressing membrane-anchored FPs under conditions in which only the plasma membrane potential is modified, demonstrated DPA voltage-dependent translocation and subsequent FRET-triggered FP quenching. Our data demonstrate for the first time that the distance between an amino-terminal FP tag and the intracellular plasma membrane surface is shorter than that between the membrane and a C-terminally-located tag. The distances varied when the FPs were attached to other positions along the channel cytoplasmic domains. In some cases, we also detected slower fluorometric responses following the fast voltage-dependent dye translocation, indicating subsequent label movements orthogonal to the plasma membrane. This finding suggests the existence of additional conformational rearrangements in the hERG cytoplasmic domains, although their association with specific aspects of channel operation remains to be established.
Functionalisation of Polydimethylsiloxane (PDMS)- Microfluidic Devices coated with Rock Minerals
Authors: Alzahid Yara A. , Mostaghimi Peyman , Gerami Alireza , Singh Ankita , Privat Karen , Amirian Tammy , Armstrong Ryan T. 
Published: October 2018

AbstractFluid flow in porous rocks is commonly capillary driven and thus, dependent on the surface characteristics of rock grains and in particular the connectivity of corners and crevices in which fluids reside. Traditional microfluidic fabrication techniques do not provide a connected pathway of crevices that are essential to mimic multiphase flow in rocks. Here, geo-material microfluidic devices with connected pathways of corners and crevices were created by functionalising Polydimethylsiloxane (PDMS) with rock minerals. A novel fabrication process that provides attachment of rock minerals onto PDMS was demonstrated. The geo-material microfluidic devices were compared to carbonate and sandstone rocks by using energy dispersive X-ray spectroscopy, scanning electron microscopy (SEM), contact angle measurements, and a surface profilometer. Based on SEM coupled with energy-dispersive X-ray spectrometry (SEM-EDS) analyses, roughness measurements, contact angle, wettability, and roughness were comparable to real rocks. In addition, semivariograms showed that mineral deposition across the different geo-material devices was nearly isotropic. Lastly, important multiphase flow phenomena, such as snap-off and corner flow mechanisms, equivalent to those occurring in reservoir rocks have been visualised. The presented approach can be used to visualise rock-fluid interactions that are relevant to subsurface engineering applications, such as hydrocarbon recovery and CO2 sequestration.
Skyrmion Lattice Topological Hall Effect near Room Temperature
Authors: Leroux Maxime , Stolt Matthew J. , Jin Song , Pete Douglas V. , Reichhardt Charles , Maiorov Boris 
Published: October 2018

AbstractMagnetic skyrmions are stable nanosized spin structures that can be displaced at low electrical current densities. Because of these properties, they have been proposed as building blocks of future electronic devices with unprecedentedly high information density and low energy consumption. The electrical detection of an ordered skyrmion lattice via the Topological Hall Effect (THE) in a bulk crystal, has so far been demonstrated only at cryogenic temperatures in the MnSi family of compounds. Here, we report the observation of a skyrmion lattice Topological Hall Effect near room temperature (276 K) in a mesoscopic lamella carved from a bulk crystal of FeGe. This region coincides with the skyrmion lattice location revealed by neutron scattering. We provide clear evidence of a re-entrant helicoid magnetic phase adjacent to the skyrmion phase, and discuss the large THE amplitude (5 nΩ.cm) in view of the ordinary Hall Effect.
Sulphur and carbon cycling in the subduction zone mélange
Authors: Schwarzenbach Esther M. , Caddick Mark J. , Petroff Matthew , Gill Benjamin C. , Cooperdock Emily H. G. , Barnes Jaime D. 
Published: October 2018

AbstractSubduction zones impose an important control on the geochemical cycling between the surficial and internal reservoirs of the Earth. Sulphur and carbon are transferred into Earth’s mantle by subduction of pelagic sediments and altered oceanic lithosphere. Release of oxidizing sulphate- and carbonate-bearing fluids modifies the redox state of the mantle and the chemical budget of subduction zones. Yet, the mechanisms of sulphur and carbon cycling within subduction zones are still unclear, in part because data are typically derived from arc volcanoes where fluid compositions are modified during transport through the mantle wedge. We determined the bulk rock elemental, and sulphur and carbon isotope compositions of exhumed ultramafic and metabasic rocks from Syros, Greece. Comparison of isotopic data with major and trace element compositions indicates seawater alteration and chemical exchange with sediment-derived fluids within the subduction zone channel. We show that small bodies of detached slab material are subject to metasomatic processes during exhumation, in contrast to large sequences of obducted ophiolitic sections that retain their seafloor alteration signatures. In particular, fluids circulating along the plate interface can cause sulphur mobilization during several stages of exhumation within high-pressure rocks. This takes place more pervasively in serpentinites compared to mafic rocks.
Itch induced by peripheral mu opioid receptors is dependent on TRPV1-expressing neurons and alleviated by channel activation
Authors: Melo Helvira , Basso Lilian , Iftinca Mircea , MacNaughton Wallace K. , Hollenberg Morley D. , McKay Derek M. , Altier Christophe 
Published: October 2018

AbstractOpioids remain the gold standard for the treatment of moderate to severe pain. However, their analgesic properties come with important side effects, including pruritus, which occurs frequently after systemic or neuraxial administration. Although part of the opioid-induced itch is mediated centrally, recent evidence shows that the opioid receptor system in the skin also modulates itch. The goal of our study was to identify the peripherally located transducer mechanisms involved in opioid-induced pruritus. Scratching behaviors in response to an intradermal injection of the mu-opioid receptor (MOR) agonist [D-Ala2, N-MePhe4, Gly-ol]-enkephalin (DAMGO) was quantified in mast cell-, PAR2- and TRPV1-deficient mice or following ablation of TRPV1+ sensory neurons. We found that mast cells−/−, PAR-2−/−, or TRPV1−/− mice still exhibit DAMGO-induced itch responses. However, we show that ablation of TRPV1+ neurons or acute TRPV1 activation by capsaicin abolishes DAMGO-induced itch. Overall, our work shows that peripheral DAMGO-induced itch is dependent on the presence of TRPV1-expressing pruriceptors, but not the TRPV1 channel itself. Activation of these fibers by capsaicin prevents the opioid-induced itch.
Soil Organic Carbon Increases in Semi-Arid Regions while it Decreases in Humid Regions Due to Woody-Plant Encroachment of Grasslands in South Africa
Authors: Mureva Admore , Ward David , Pillay Tiffany , Chivenge Pauline , Cramer Michael 
Published: October 2018

AbstractGrasslands and savannas are experiencing intensive land-cover change due to woody plant encroachment. This change in land cover is thought to alter soil carbon (C) and nitrogen (N) storage in these ecosystems. Some studies have reported a negative correlation between soil C and N and mean annual precipitation while others have indicated that there is no relationship with mean annual precipitation. We quantified the changes in C and N pools and δ13C and δ15N values to a depth of 1 m in pairs of encroached and adjacent open grassland sites along a precipitation gradient from 300 mm to 1500 mm per annum in South Africa. Our study showed a negative correlation between changes in soil organic C stocks in the 0–100 cm soil layer and mean annual precipitation (MAP). The most humid site (1500 mm MAP) had less C in shrub-encroached sites while the drier sites (300–350 mm MAP) had more C than their paired open grasslands. This study generally showed soil organic C gains in low precipitation areas, with a threshold value between 750 mm and 900 mm. Our threshold value was higher than that found in North America, suggesting that one cannot extrapolate across continents.
Structural and electronic effects of adatoms on metallic atomic chains in Si(111)5 × 2-Au
Authors: Do Eui Hwan , Kwon Se Gab , Kang Myung Ho , Yeom Han Woong 
Published: October 2018

AbstractWe investigate the effects of native Si adatoms on structural and electronic properties of the Si(111)5 × 2-Au surface, a representative one-dimensional metal-chain system, by means of scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. High-resolution STM images of relatively long adatom-free chain segments evidence directly the inherent ×2 reconstruction, which is the essential part of a recently proposed structural model based on a renewed Au coverage of 0.7 monolayer. On the other hand, STM images for chain segments of different lengths reveal that the structural distortion induced by Si adatoms is confined in neighboring unit cells, in good agreement with DFT calculations based on that model. Si adatoms greatly affect the metallic bands of Au chains, one of which becomes fully occupied and represents a tightly confined electronic state to the distortion around Si adatoms, potentially forming short insulating segments within metallic chains. This finding provides an atomic-scale understanding of the observed gradual metal-insulator transition and atomic-scale phase separation induced by Si adatoms.
Blood vessel imaging using radiofrequency-induced second harmonic acoustic response
Authors: Huang Yuanhui , Kellnberger Stephan , Sergiadis George , Ntziachristos Vasilis 
Published: October 2018

AbstractWe introduce a contrast mechanism for visualizing blood vessels based on radiofrequency-induced second harmonic acoustic (RISHA) signals sensing blood conductivity. We develop a novel imaging system using commonly available inexpensive components, and demonstrate in vivo RISHA visualization of blood vessels based on low-power quasi-continuous radiofrequency excitation of tissue at frequencies of a few MHz. We show how the novel approach also implicitly enables radiofrequency-induced passive ultrasound imaging and can be readily applied to non-invasive imaging of blood vessels ex vivo and in vivo. We discuss the implications of non-invasive conductivity measurements in the context of biomedical applications.
Chromatin accessibility landscape of articular knee cartilage reveals aberrant enhancer regulation in osteoarthritis
Authors: Liu Ye , Chang Jen-Chien , Hon Chung-Chau , Fukui Naoshi , Tanaka Nobuho , Zhang Zhenya , Lee Ming Ta Michael , Minoda Aki 
Published: October 2018

AbstractOsteoarthritis (OA) is a common joint disorder with increasing impact in an aging society. While genetic and transcriptomic analyses have revealed some genes and non-coding loci associated to OA, the pathogenesis remains incompletely understood. Chromatin profiling, which provides insight into gene regulation, has not been reported in OA mainly due to technical difficulties. Here, we employed Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) to map the accessible chromatin landscape in articular knee cartilage of OA patients. We identified 109,215 accessible chromatin regions for cartilages, of which 71% were annotated as enhancers. By overlaying them with genetic and DNA methylation data, we have determined potential OA-relevant enhancers and their putative target genes. Furthermore, through integration with RNA-seq data, we characterized genes that are altered both at epigenomic and transcriptomic levels in OA. These genes are enriched in pathways regulating ossification and mesenchymal stem cell (MSC) differentiation. Consistently, the differentially accessible regions in OA are enriched for MSC-specific enhancers and motifs of transcription factor families involved in osteoblast differentiation. In conclusion, we demonstrate how direct chromatin profiling of clinical tissues can provide comprehensive epigenetic information for a disease and suggest candidate genes and enhancers of translational potential.
Predictors for success in renal denervation–a single centre retrospective analysis
Authors: Reshetnik Alexander , Gohlisch Christopher , Scheurig-Münkler Christian , De Bucourt Maximilian , Zidek Walter , Tölle Markus , van der Giet Markus 
Published: October 2018

AbstractRenal denervation (RDN) is one of the most frequently used invasive methods for the treatment of arterial hypertension. However, recent randomized sham-controlled studies raised concern about the efficacy and predictability of response. We retrospectively analyzed outcomes of patients, who underwent RDN in our hypertension center between November 2010 and April 2014 and report here outcomes twelve months after procedure based on 24-hours ambulatory blood pressure monitoring. We defined ten-mm Hg decrease in office systolic blood pressure (SBP) as a cut-off for response and looked for possible predictors of this response using binary multiple regression analysis. 42 patients were included. Their mean age was 59.6 ± 9.2 years and 24% were female. Baseline office SBP and diastolic blood pressure (DBP) were 164.1 ± 20.3 and 91.8 ± 12.4 mm Hg respectively. Mean 24 h-SBP significantly decreased from 149.8 ± 13.3 mm Hg to 141.2 ± 14.6 mm Hg. Mean 24 h-DBP significantly decreased from 83.3 ± 11.7 mm Hg to 78.8 ± 11.2 mm Hg. A higher level of mean 24 h-DBP and office DBP was shown to be predictive for response in office BP and a higher level of mean 24 h-DBP for response in 24 h-SBP and 24 h-DBP. Further properly designed randomized trials are warranted to confirm this finding as well as further investigate the role of diabetes mellitus and arterial stiffness in RDN.
Limited congruence exhibited across microbial, meiofaunal and macrofaunal benthic assemblages in a heterogeneous coastal environment
Authors: Cronin-O’Reilly Sorcha , Taylor Joe D. , Jermyn Ian , Allcock A. Louise , Cunliffe Michael , Johnson Mark P. 
Published: October 2018

AbstractOne of the most common approaches for investigating the ecology of spatially complex environments is to examine a single biotic assemblage present, such as macroinvertebrates. Underlying this approach are assumptions that sampled and unsampled taxa respond similarly to environmental gradients and exhibit congruence across different sites. These assumptions were tested for five benthic groups of various sizes (archaea, bacteria, microbial eukaryotes/protists, meiofauna and macrofauna) in Plymouth Sound, a harbour with many different pollution sources. Sediments varied in granulometry, hydrocarbon and trace metal concentrations. Following variable reduction, canonical correspondence analysis did not identify any associations between sediment characteristics and assemblage composition of archaea or macrofauna. In contrast, variation in bacteria was associated with granulometry, trace metal variations and bioturbation (e.g. community bioturbation potential). Protists varied with granulometry, hydrocarbon and trace metal predictors. Meiofaunal variation was associated with hydrocarbon and bioturbation predictors. Taxon turnover between sites varied with only three out of 10 group pairs showing congruence (meiofauna-protists, meiofauna-macrofauna and protists-macrofauna). While our results support using eukaryotic taxa as proxies for others, the lack of congruence suggests caution should be applied to inferring wider indicator or functional interpretations from studies of a single biotic assemblage.
Tomography of the 2016 Kumamoto earthquake area and the Beppu-Shimabara graben
Authors: Zhao Dapeng , Yamashita Kei , Toyokuni Genti 
Published: October 2018

AbstractDetailed three-dimensional images of P and S wave velocity and Poisson’s ratio (σ) of the crust and upper mantle beneath Kyushu in SW Japan are determined, with a focus on the source area of the 2016 Kumamoto earthquake (M 7.3) that occurred in the Beppu-Shimabara graben (BSG) where four active volcanoes and many active faults exist. The 2016 Kumamoto earthquake took place in a high-velocity and low-σ zone in the upper crust, which is surrounded and underlain by low-velocity and high-σ anomalies in the upper mantle. This result suggests that, in and around the source zone of the 2016 Kumamoto earthquake, strong structural heterogeneities relating to active volcanoes and magmatic fluids exist, which may affect the seismogenesis. Along the BSG, low-velocity and high-σ anomalies do not exist everywhere in the upper mantle but mainly beneath the active volcanoes, suggesting that hot mantle upwelling is not the only cause of the graben. The BSG was most likely formed by joint effects of northward extension of the Okinawa Trough, westward extension of the Median Tectonic Line, and hot upwelling flow in the mantle wedge beneath the active volcanoes.
Increased transferrin saturation is associated with subgingival microbiota dysbiosis and severe periodontitis in genetic haemochromatosis
Authors: Boyer Emile , Le Gall-David Sandrine , Martin Bénédicte , Fong Shao Bing , Loréal Olivier , Deugnier Yves , Bonnaure-Mallet Martine , Meuric Vincent 
Published: October 2018

AbstractGenetic haemochromatosis (GH) is responsible for iron overload. Increased transferrin saturation (TSAT) has been associated with severe periodontitis, which is a chronic inflammatory disease affecting tissues surrounding the teeth and is related to dysbiosis of the subgingival microbiota. Because iron is essential for bacterial pathogens, alterations in iron homeostasis can drive dysbiosis. To unravel the relationships between serum iron biomarkers and the subgingival microbiota, we analysed samples from 66 GH patients. The co-occurrence analysis of the microbiota showed very different patterns according to TSAT. Healthy and periopathogenic bacterial clusters were found to compete in patients with normal TSAT (≤45%). However, significant correlations were found between TSAT and the proportions of Porphyromonas and Treponema, which are two genera that contain well-known periopathogenic species. In patients with high TSAT, the bacterial clusters exhibited no mutual exclusion. Increased iron bioavailability worsened periodontitis and promoted periopathogenic bacteria, such as Treponema. The radical changes in host-bacteria relationships and bacterial co-occurrence patterns according to the TSAT level also suggested a shift in the bacterial iron supply from transferrin to NTBI when TSAT exceeded 45%. Taken together, these results indicate that iron bioavailability in biological fluids is part of the equilibrium between the host and its microbiota.
Efficacy of tenofovir in preventing perinatal transmission of HBV infection in pregnant women with high viral loads
Authors: Lin Yayun , Liu Yan , Ding Guifeng , Touqui Lhousseine , Wang Weimin , Xu Na , Liu Keying , Zhang Lingyan , Chen Dunjin , Wu Yongzheng , Bai Guiqin 
Published: October 2018

AbstractMother-to-child transmission is the major cause of chronic hepatitis B virus (HBV) infection. This double-blind trial tested the effect of tenofovir disoproxil fumarate (TDF) in preventing vertical transmission. Pregnant women who were HBsAg/HBeAg-positive with a HBV DNA titer ≥ 2×106 IU/mL were randomly assigned to the control (n = 60) and TDF-treated (n = 60) groups. TDF treatment (oral dose 300 mg/day) was initiated at 24 weeks of gestation and continued to 4 weeks after delivery. The subjects were followed up to 28 weeks postpartum. The effects of TDF on vertical transmission, outcomes of the mothers and infants and virological changes were monitored. TDF dynamically reduced the serum HBV DNA level of the mothers, particularly during the first 4 weeks of treatment. The lower viral loads were maintained in the pregnancies until delivery. Approximately 90% and 33.9% of the TDF-treated mothers had viral loads ≤2000 IU/mL after delivery and at 28 weeks postpartum, respectively. No cervical transmission or adverse effects were observed in the TDF-treated individuals, whereas 13.5% of the infants were infected with HBV in the control group. We conclude that TDF treatment initiated at 24 weeks of gestation in high-viremia, HBsAg/HBeAg-positive mothers efficiently prevents mother-to-child HBV transmission without adverse events in mothers and infants.