bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolite changes in blood predict the onset of tuberculosis
Authors: Weiner January , Maertzdorf Jeroen , Sutherland Jayne S. , Duffy Fergal J. , Thompson Ethan , Suliman Sara , McEwen Gayle , Thiel Bonnie , Parida Shreemanta K. , Zyla Joanna , Hanekom Willem A. , Mohney Robert P. , Boom W. Henry , Mayanja-Kizza Harriet , Howe Rawleigh , Dockrell Hazel M. , Ottenhoff Tom H. M. , Scriba Thomas J. , Zak Daniel E. , Walzl Gerhard , Kaufmann Stefan H. E. ,   The GC6-74 consortium, Abebe Almaz , Abel Brian , Adegbola Richard , Adetifa Ifedayo , Ambrose Lyn , Andersen Peter , Antonio Martin , Aseffa Abraham , van Baarle Debbie , Barker Lew , Bekele Yonas , Bilek Nicole , Black Gillian F. , Bowmaker Mark , Branson Keith , Brennan Michael , Chegou Novel N. , Chilongo Femia , Chung William Kwong , Corrah Tumani , Crampin Ameilia C. , Doherty Mark , Dolganov Gregory , Donkor Simon , Downing Katrina , Fisher Michelle , Franken Kees L. M. C. , French Neil , Geiter Larry , Geluk Annemieke , Golinski Robert , Gorak-Stolinska Patricia , Haks Marielle C. , Hill Philip , Hughes Jane , Hur Yun-Gyoung , Iwnetu Rachel , Jacobson Marc , Joloba Moses , Joosten Simone A. , Kagina Benjamin , Kassa Desta , Kisingo Hussein , Klein Michel R. , Kriel Magdalena , Lalor Maeve , Lee Ji-Sook , Loxton Andre G. , Mahomed Hassan , van Meijgaarden Krista E. , Mesele Tsehayenesh , Miedema Frank , Mihret Adane , Mulenga Humphrey , Muller Stefanie , Mvula Hazzie , Nene Nonhlanhla , Ngwira Bagrey , Nsereko Mary , Okwera Brenda , Ota Martin , Penn-Nicholson Adam , Du Plessis Nelita , Ramachandran S. , Rosenkrands Ida , Sadoff Jerry , Saul Jacky , Schoolnik Gary , Simukonda Felanji , Sizemore Donata , Smith Steven , Ben Smith Anne , van der Spuy Gian , Stanley Kim , Tabb David , Tafesse Mesfin , Tegbaru Belete , Togun Toyin , Tromp Gerhardus , Van Tran , Watkins Kate , Weichold Frank , Weldingh Karin , Yamuah Lawrence , Zalwango Sarah 
Published: November 2018

AbstractNew biomarkers of tuberculosis (TB) risk and disease are critical for the urgently needed control of the ongoing TB pandemic. In a prospective multisite study across Subsaharan Africa, we analyzed metabolic profiles in serum and plasma from HIV-negative, TB-exposed individuals who either progressed to TB 3–24 months post-exposure (progressors) or remained healthy (controls). We generated a trans-African metabolic biosignature for TB, which identifies future progressors both on blinded test samples and in external data sets and shows a performance of 69% sensitivity at 75% specificity in samples within 5 months of diagnosis. These prognostic metabolic signatures are consistent with development of subclinical disease prior to manifestation of active TB. Metabolic changes associated with pre-symptomatic disease are observed as early as 12 months prior to TB diagnosis, thus enabling timely interventions to prevent disease progression and transmission.
Minimizing the electrosorption of water from humid ionic liquids on electrodes
Authors: Bi Sheng , Wang Runxi , Liu Shuai , Yan Jiawei , Mao Bingwei , Kornyshev Alexei A. , Feng Guang 
Published: November 2018

AbstractIn supercapacitors based on ionic liquid electrolytes, small amounts of absorbed water could potentially reduce the electrochemical window of electrolytes and cause performance degradation. The same would take place if ionic liquids are used as solvents for electrocatalysis involving the dissolved molecular species. In this work, we carry out molecular dynamics simulations, with gold and carbon electrodes in typical ionic liquids, hydrophobic and hydrophilic, to study electrosorption of water. We investigate the effects of hydrophobicity/hydrophilicity of ionic liquids and electrodes on interfacial distribution of ions and electrosorbed water. Results reveal that using hydrophilic ionic liquids would help to keep water molecules away from the negatively charged electrodes, even at large electrode polarizations. This conclusion is supported by electrochemical cyclic voltammetry measurements on gold and carbon electrodes in contact with humid ionic liquids. Thereby, our findings suggest potential mechanisms for protection of electrodes from water electrosorption.
The two-fluid dynamics and energetics of the asymmetric magnetic reconnection in laboratory and space plasmas
Authors: Yamada M. , Chen L.-J. , Yoo J. , Wang S. , Fox W. , Jara-Almonte J. , Ji H. , Daughton W. , Le A. , Burch J. , Giles B. , Hesse M. , Moore T. , Torbert R. 
Published: November 2018

AbstractMagnetic reconnection is a fundamental process in magnetized plasma where magnetic energy is converted to plasma energy. Despite huge differences in the physical size of the reconnection layer, remarkably similar characteristics are observed in both laboratory and magnetosphere plasmas. Here we present the comparative study of the dynamics and physical mechanisms governing the energy conversion in the laboratory and space plasma in the context of two-fluid physics, aided by numerical simulations. In strongly asymmetric reconnection layers with negligible guide field, the energy deposition to electrons is found to primarily occur in the electron diffusion region where electrons are demagnetized and diffuse. A large potential well is observed within the reconnection plane and ions are accelerated by the electric field toward the exhaust region. The present comparative study identifies the robust two-fluid mechanism operating in systems over six orders of magnitude in spatial scales and over a wide range of collisionality.
Phase diagram of Bi2Sr2CaCu2O8+δ revisited
Authors: Drozdov I. K. , Pletikosić I. , Kim C.-K. , Fujita K. , Gu G. D. , Davis J. C. Séamus , Johnson P. D. , Božović I. , Valla T. 
Published: November 2018

AbstractIn cuprate superconductors, the doping of carriers into the parent Mott insulator induces superconductivity and various other phases whose characteristic temperatures are typically plotted versus the doping level p. In most materials, p cannot be determined from the chemical composition, but it is derived from the superconducting transition temperature, Tc, using the assumption that the Tc dependence on doping is universal. Here, we present angle-resolved photoemission studies of Bi2Sr2CaCu2O8+δ, cleaved and annealed in vacuum or in ozone to reduce or increase the doping from the initial value corresponding to Tc = 91 K. We show that p can be determined from the underlying Fermi surfaces and that in-situ annealing allows mapping of a wide doping regime, covering the superconducting dome and the non-superconducting phase on the overdoped side. Our results show a surprisingly smooth dependence of the inferred Fermi surface with doping. In the highly overdoped regime, the superconducting gap approaches the value of 2Δ0 = (4 ± 1)kBTc
Single-molecule imaging correlates decreasing nuclear volume with increasing TF-chromatin associations during zebrafish development
Authors: Reisser Matthias , Palmer Anja , Popp Achim P. , Jahn Christopher , Weidinger Gilbert , Gebhardt J. Christof M. 
Published: November 2018

AbstractZygotic genome activation (ZGA), the onset of transcription after initial quiescence, is a major developmental step in many species, which occurs after ten cell divisions in zebrafish embryos. How transcription factor (TF)-chromatin interactions evolve during early development to support ZGA is largely unknown. We establish single molecule tracking in live developing zebrafish embryos using reflected light-sheet microscopy to visualize two fluorescently labeled TF species, mEos2-TBP and mEos2-Sox19b. We further develop a data acquisition and analysis scheme to extract quantitative information on binding kinetics and bound fractions during fast cell cycles. The chromatin-bound fraction of both TFs increases during early development, as expected from a physical model of TF-chromatin interactions including a decreasing nuclear volume and increasing DNA accessibility. For Sox19b, data suggests the increase is mainly due to the shrinking nucleus. Our single molecule approach provides quantitative insight into changes of TF-chromatin associations during the developmental period embracing ZGA.
Empirical modeling of dopability in diamond-like semiconductors
Authors: Miller Samuel A. , Dylla Maxwell , Anand Shashwat , Gordiz Kiarash , Snyder G. Jeffrey , Toberer Eric S. 
Published: November 2018

AbstractCarrier concentration optimization has been an enduring challenge when developing newly discovered semiconductors for applications (e.g., thermoelectrics, transparent conductors, photovoltaics). This barrier has been particularly pernicious in the realm of high-throughput property prediction, where the carrier concentration is often assumed to be a free parameter and the limits are not predicted due to the high computational cost. In this work, we explore the application of machine learning for high-throughput carrier concentration range prediction. Bounding the model within diamond-like semiconductors, the learning set was developed from experimental carrier concentration data on 127 compounds ranging from unary to quaternary. The data were analyzed using various statistical and machine learning methods. Accurate predictions of carrier concentration ranges in diamond-like semiconductors are made within approximately one order of magnitude on average across both p- and n-type dopability. The model fit to empirical data is analyzed to understand what drives trends in carrier concentration and compared with previous computational efforts. Finally, dopability predictions from this model are combined with high-throughput quality factor predictions to identify promising thermoelectric materials.
The hydrogen-induced pitting corrosion mechanism in duplex stainless steel studied by current-sensing atomic force microscopy
Authors: Yakubov Vladislav , Lin Meichao , Volinsky Alex A. , Qiao Lijie , Guo Liqiu 
Published: November 2018

AbstractDuplex stainless steels have excellent corrosion resistance due to their two-phase microstructure and electrically insulating passive film. Nevertheless, hydrogen charging causes deterioration of the corrosion protection mechanisms, resulting in increased pitting susceptibility. In this study, current-sensing atomic force microscopy was used to investigate the electrical properties of the passive film formed on 2507 duplex stainless steel before hydrogen charging. Results were compared with optical images of pitting corrosion initiation after hydrogen charging and FeCl3 exposure. Highest passive film conductivity and current density were seen at grain boundaries, indicating poor passive film development and high pitting probability. High conductivity was also observed on the passive film located at the adjacent austenite phase, alluding to favorable conditions for pitting corrosion propagation. Phases were identified by magnetic force microscopy, while pit initiation with subsequent propagation after hydrogen charging and FeCl3 exposure was observed using optical microscopy. Pitting corrosion initiated at grain boundaries and propagated into the austenite grains. This study identified the pitting initiation and propagation mechanisms in 2507 duplex stainless steel.
Fall webworm genomes yield insights into rapid adaptation of invasive species
Authors: Wu Ningning , Zhang Sufang , Li Xiaowei , Cao Yanghui , Liu Xiaojing , Wang Qinghua , Liu Qun , Liu Huihui , Hu Xiao , Zhou Xuguo J. , James Anthony A. , Zhang Zhen , Huang Yongping , Zhan Shuai 
Published: November 2018

AbstractInvasive species cause considerable ecological and economic damage. Despite decades of broad impacts of invasives on diversity and agriculture, the genetic adaptations and near-term evolution of invading populations are poorly understood. The fall webworm,Hyphantria cunea, a highly successful invasive species that originated in North America, spread throughout the Northern Hemisphere during the past 80 years. Here, we use whole-genome sequencing of invasive populations and transcriptome profiling to probe the underlying genetic bases for the rapid adaptation of this species to new environments and host plants. We find substantial reductions in genomic diversity consistent with founder effects. Genes and pathways associated with carbohydrate metabolism and gustatory receptors are substantially expanded in the webworm genome and show strong signatures of functional polymorphisms in the invasive population. We also find that silk-yielding-associated genes maintained a relatively low level of functional diversity, and identify candidate genes that may regulate the development of silk glands in fall webworms. These data suggest that the fall webworm’s ability to colonize novel hosts, mediated by plasticity in their gustatory capabilities along with an increased ability to utilize novel nutrition sources and substrates, has facilitated the rapid and successful adaptation of the species throughout its range.
Impact of a Narrow Coastal Bay of Bengal Sea Surface Temperature Front on an Indian Summer Monsoon Simulation
Authors: Samanta Dhrubajyoti , Hameed Saji N. , Jin Dachao , Thilakan Vishnu , Ganai Malay , Rao Suryachandra A. , Deshpande Medha 
Published: November 2018

AbstractA dry bias in climatological Central Indian rainfall plagues Indian summer monsoon (ISM) simulations in multiple generations of climate models. Here, using observations and regional climate modeling, we focus on a warm coastal Bay of Bengal sea surface temperature (SST) front and its impact on Central Indian rainfall. The SST front, featuring sharp gradients as large as 0.5 °C/100 km, is colocated with a mixed layer depth (MLD) front, in a region where salinity variations are known to control MLD. Regional climate simulations coupling a regional atmospheric model with an ocean mixed layer model are performed. A simulation with observed MLD climatology reproduces SST, rainfall, and atmospheric circulation associated with ISM reasonably well; it also eliminates the dry bias over Central India significantly. Perturbing MLD structure in the simulations, we isolate the SST front’s impact on the simulated ISM climate state. This experiment offers insights into ISM climatological biases in the coupled NCEP Climate Forecast System version-2. We suggest that the warm SST front is essential to Central Indian rainfall as it helps to sustain deep and intense convection in its vicinity, which may be a source for the vortex cores seeding the monsoon low-pressure systems.
Electrostatic Origins of CO2-Increased Hydrophilicity in Carbonate Reservoirs
Authors: Chen Yongqiang , Sari Ahmad , Xie Quan , Brady Patrick V. , Hossain Md Mofazzal , Saeedi Ali 
Published: November 2018

AbstractInjecting CO2 into oil reservoirs appears to be cost-effective and environmentally friendly due to decreasing the use of chemicals and cutting back on the greenhouse gas emission released. However, there is a pressing need for new algorithms to characterize oil/brine/rock system wettability, thus better predict and manage CO2 geological storage and enhanced oil recovery in oil reservoirs. We coupled surface complexation/CO2 and calcite dissolution model, and accurately predicted measured oil-on-calcite contact angles in NaCl and CaCl2 solutions with and without CO2. Contact angles decreased in carbonated water indicating increased hydrophilicity under carbonation. Lowered salinity increased hydrophilicity as did Ca2+. Hydrophilicity correlates with independently calculated oil-calcite electrostatic bridging. The link between the two may be used to better implement CO2 EOR in fields.
Novel Liposome Eencapsulated Guanosine Di Phosphate based Therapeutic Target against Anemia of Inflammation
Authors: Angmo Stanzin , Rana Shilpa , Yadav Kamalendra , Sandhir Rajat , Singhal Nitin Kumar 
Published: November 2018

AbstractHepcidin, master regulator of iron homeostasis, causes anemia under infectious and inflammatory conditions by reducing intestinal absorption of iron with decreased release of iron from macrophages and liver despite adequate iron stores leading to Anemia of Inflammation (AI). Many therapeutic trials have been carried out but none have been effective due to its adverse effects. In present study, we discover that Guanosine 5’-diphosphate (GDP) encapsulated in lipid vesicle (NH+) was found to inhibit NF-ҝB activation by limiting phosphorylation and degradation of IҝBα, thus, attenuating IL-6 secretion from macrophage cells. Moreover, the suppressed IL-6 levels down regulated JAK2/STAT3 pathway with decrease inflammation-mediated Hamp mRNA transcription (HepG2) and increase iron absorption (Caco2) in HepG2/Caco2 co-culture model. Analogous results were obtained in acute and chronic AI mice model thus, correcting haemoglobin level. These results proved NH + GDP as novel therapeutic agent to overcome limitations and suggests it as potential drug to ameliorate AI.
A Perlin Noise-Based Augmentation Strategy for Deep Learning with Small Data Samples of HRCT Images
Authors: Bae Hyun-Jin , Kim Chang-Wook , Kim Namju , Park BeomHee , Kim Namkug , Seo Joon Beom , Lee Sang Min 
Published: November 2018

AbstractDeep learning is now widely used as an efficient tool for medical image classification and segmentation. However, conventional machine learning techniques are still more accurate than deep learning when only a small dataset is available. In this study, we present a general data augmentation strategy using Perlin noise, applying it to pixel-by-pixel image classification and quantification of various kinds of image patterns of diffuse interstitial lung disease (DILD). Using retrospectively obtained high-resolution computed tomography (HRCT) images from 106 patients, 100 regions-of-interest (ROIs) for each of six classes of image patterns (normal, ground-glass opacity, reticular opacity, honeycombing, emphysema, and consolidation) were selected for deep learning classification by experienced thoracic radiologists. For extra-validation, the deep learning quantification of the six classification patterns was evaluated for 92 HRCT whole lung images for which hand-labeled segmentation masks created by two experienced radiologists were available. FusionNet, a convolutional neural network (CNN), was used for training, test, and extra-validation on classifications of DILD image patterns. The accuracy of FusionNet with data augmentation using Perlin noise (89.5%, 49.8%, and 55.0% for ROI-based classification and whole lung quantifications by two radiologists, respectively) was significantly higher than that with conventional data augmentation (82.1%, 45.7%, and 49.9%, respectively). This data augmentation strategy using Perlin noise could be widely applied to deep learning studies for image classification and segmentation, especially in cases with relatively small datasets.
Mycoplasma hyopneumoniae resides intracellularly within porcine epithelial cells
Authors: Raymond B. B. A. , Turnbull L. , Jenkins C. , Madhkoor R. , Schleicher I. , Uphoff C. C. , Whitchurch C. B. , Rohde M. , Djordjevic S. P. 
Published: November 2018

AbstractEnzootic pneumonia incurs major economic losses to pork production globally. The primary pathogen and causative agent,Mycoplasma hyopneumoniae, colonises ciliated epithelium and disrupts mucociliary function predisposing the upper respiratory tract to secondary pathogens. Alleviation of disease is reliant on antibiotics, vaccination, and sound animal husbandry, but none are effective at eliminatingM. hyopneumoniaefrom large production systems. Sustainable pork production systems strive to lower reliance on antibiotics but lack of a detailed understanding of the pathobiology ofM. hyopneumoniaehas curtailed efforts to develop effective mitigation strategies.M. hyopneumoniaeis considered an extracellular pathogen. Here we show thatM. hyopneumoniaeassociates with integrin β1 on the surface of epithelial cells via interactions with surface-bound fibronectin and initiates signalling events that stimulate pathogen uptake into clathrin-coated vesicles (CCVs) and caveosomes. These early events allowM. hyopneumoniaeto exploit an intracellular lifestyle by commandeering the endosomal pathway. Specifically, we show: (i) using a modified gentamicin protection assay that approximately 8% ofM. hyopneumoniaecells reside intracellularly; (ii) integrin β1 expression specifically co-localises with the deposition of fibronectin precisely whereM. hyopneumoniaecells assemble extracellularly; (iii) anti-integrin β1 antibodies block entry ofM. hyopneumoniaeinto porcine cells; and (iv)M. hyopneumoniaesurvives phagolysosomal fusion, and resides within recycling endosomes that are trafficked to the cell membrane. Our data creates a paradigm shift by challenging the long-held view thatM. hyopneumoniaeis a strict extracellular pathogen and calls forin vivostudies to determine ifM. hyopneumoniaecan traffic to extrapulmonary sites in commercially-reared pigs.
Loss of interneurons and disruption of perineuronal nets in the cerebral cortex following hypoxia-ischaemia in near-term fetal sheep
Authors: Fowke Tania M. , Galinsky Robert , Davidson Joanne O. , Wassink Guido , Karunasinghe Rashika N. , Prasad Jaya D. , Bennet Laura , Gunn Alistair J. , Dean Justin M. 
Published: November 2018

AbstractHypoxia-ischaemia (HI) in term infants is a common cause of brain injury and neurodevelopmental impairment. Development of gamma-aminobutyric acid (GABA)ergic circuitry in the cerebral cortex is a critical event in perinatal brain development. Perineuronal nets (PNNs) are specialised extracellular matrix structures that surround GABAergic interneurons, and are important for their function. Herein, we hypothesised that HI would reduce survival of cortical interneurons and disrupt PNNs in a near-term fetal sheep model of global cerebral ischaemia. Fetal sheep (0.85 gestation) received sham occlusion (n = 5) or 30 min of reversible cerebral ischaemia (HI group; n = 5), and were recovered for 7 days. Expression of interneurons (glutamate decarboxylase [GAD]+; parvalbumin [PV]+) and PNNs (Wisteria floribunda agglutinin, WFA) was assessed in the parasagittal cortex by immunohistochemistry. HI was associated with marked loss of both GAD+ and PV+ cortical interneurons (all layers of the parasagittal cortex and layer 6) and PNNs (layer 6). The expression and integrity of PNNs was also reduced on surviving GAD+ interneurons. There was a trend towards a linear correlation of the proportion of GAD+ neurons that were WFA+ with seizure burden (r2 = 0.76, p = 0.0534). Overall, these data indicate that HI may cause deficits in the cortical GABAergic system involving loss of interneurons and disruption of PNNs, which may contribute to the range of adverse neurological outcomes following perinatal brain injury.
The complete mitochondrial genome of the Caribbean spiny lobster Panulirus argus
Authors: Baeza J. Antonio 
Published: November 2018

AbstractPanulirus argus is a keystone species and target of the most lucrative fishery in the Caribbean region. This study reports, for the first time, the complete mitochondrial genome of Panulirus argus (average coverage depth nucleotide−1 = 70×) assembled from short Illumina 150 bp PE reads. The AT-rich mitochondrial genome of Panulirusargus was 15 739 bp in length and comprised 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. A single 801 bp long intergenic space was assumed to be the D-loop. Most of the PCGs were encoded on the H-strand. The gene order observed in the mitochondrial genome of Panulirus argus corresponds to the presumed Pancrustacean ground pattern. KA/KS ratios calculated for all mitochondrial PCGs showed values < 1, indicating that all these PCGs are evolving under purifying selection. A maximum likelihood phylogenetic analysis (concatenated PCGs [n = 13], 154 arthropods) supported the monophyly of the Achelata and other infraorders within the Decapoda. Mitochondrial PCGs have enough phylogenetic informativeness to explore high-level genealogical relationships in the Pancrustacea. The complete mitochondrial genome of the Caribbean spiny lobster Panulirusargus will contribute to the better understanding of meta-population connectivity in this keystone overexploited species.