bluuebunny/crossref_metadata_2025 huggingface dataset:
A Comparison of Classifiers for Solar Energetic Events
Authors: Barnes Graham , Schanche Nicole , Leka K. D. , Aggarwal Ashna , Reeves Kathy
Published: May 2017

We compare the results of using a Random Forest Classifier with the results of using Nonparametric Discriminant Analysis to classify whether a filament channel (in the case of a filament eruption) or an active region (in the case of a flare) is about to produce an event. A large number of descriptors are considered in each case, but it is found that only a small number are needed in order to get most of the improvement in performance over always predicting the majority class. There is little difference in performance between the two classifiers, and neither results in substantial improvements over simply predicting the majority class.
Multi-wavelength studies of the statistical properties of active galaxies using Big Data
Authors: Mickaelian A. M. , Abrahamyan H. V. , Gyulzadyan M. V. , Mikayelyan G. A. , Paronyan G. M.
Published: May 2017

Statistical studies of active galaxies (both AGN and Starburst) using large multi-wavelength data are presented, including new studies of Markarian galaxies, large sample of IR galaxies, variable radio sources, and large homogeneous sample of X-ray selected AGN. Markarian survey (the First Byurakan Survey) was digitized and the DFBS database was created, as the biggest spectroscopic database by the number of objects involved ( ~ 20 million). This database provides both 2D images and 1D spectra. We have carried out a number of projects aimed at revealing and multi-wavelength studies of active galaxies among optical, X-ray, IR and radio sources. Thousands of X-ray sources were identified from ROSAT, including many AGN (52% among all identified sources). IRAS PSC/FSC sources were studied having accurate positions from WISE and a large extragalactic sample was created for further search for AGNs. The fraction of active galaxies among IR-selected galaxies was estimated as 24%. Variable radio sources at 1.4 GHz were revealed by cross-correlation of NVSS and FIRST catalogues using the method introduced by us for optical variability. Radio-X-ray sources were revealed from NVSS and ROSAT for detection of new active galaxies. Big Data in astronomy is described that provide new possibilities for statistical research of active galaxies and other objects.
Investigation of Spatially Unresolved Magnetic Field Outside Sunspots Using Hinode/SOT Observations
Authors: Botygina Olga , Gordovskyy Mykola , Lozitsky Vsevolod
Published: May 2017

The structure of photospheric magnetic fields outside sunspots is investigated in three active regions using Hinode/Solar Optical Telescope(SOT) observations. We analyze Zeeman effect in FeI 6301.5 and FeI 6302.5 lines and determine the observed magnetic field value Beff for each of them. We find that the line ratio Beff(6301)/Beff(6302) is close to 1.3 in the range Beff < 0.2 kG, and close to 1.0 for 0.8 kG < Beff < 1.2 kG. We find that the observed magnetic field is formed by flux tubes with the magnetic field strengths 1.3 − 2.3 kG even in places with weak observed magnetic field fluxes. We also estimate the diameters of smallest magnetic flux tubes to be 15 − 20 km.
Evolution of the NASA/IPAC Extragalactic Database (NED) into a Data Mining Discovery Engine
Authors: Mazzarella Joseph M. ,   the NED Team
Published: May 2017

We review recent advances and ongoing work in evolving the NASA/IPAC Extragalactic Database (NED) beyond an object reference database into a data mining discovery engine. Updates to the infrastructure and data integration techniques are enabling more than a 10-fold expansion; NED will soon contain over a billion objects with their fundamental attributes fused across the spectrum via cross-identifications among the largest sky surveys (e.g., GALEX, SDSS, 2MASS, AllWISE, EMU), and over 100,000 smaller but scientifically important catalogs and journal articles. The recent discovery of super-luminous spiral galaxies exemplifies the opportunities for data mining and science discovery directly from NED’s rich data synthesis. Enhancements to the user interface, including new APIs, VO protocols, and queries involving derived physical quantities, are opening new pathways for panchromatic studies of large galaxy samples. Examples are shown of graphics characterizing the content of NED, as well as initial steps in exploring the database via interactive statistical visualizations.
What can the programming language Rust do for astrophysics?
Authors: Blanco-Cuaresma Sergi , Bolmont Emeline
Published: May 2017

The astrophysics community uses different tools for computational tasks such as complex systems simulations, radiative transfer calculations or big data. Programming languages like Fortran, C or C++ are commonly present in these tools and, generally, the language choice was made based on the need for performance. However, this comes at a cost: safety. For instance, a common source of error is the access to invalid memory regions, which produces random execution behaviors and affects the scientific interpretation of the results.

In 2015, Mozilla Research released the first stable version of a new programming language named Rust. Many features make this new language attractive for the scientific community, it is open source and it guarantees memory safety while offering zero-cost abstraction.

We explore the advantages and drawbacks of Rust for astrophysics by re-implementing the fundamental parts of Mercury-T, a Fortran code that simulates the dynamical and tidal evolution of multi-planet systems.
From Sky to Earth: Data Science Methodology Transfer
Authors: Mahabal Ashish A. , Crichton Daniel , Djorgovski S. G. , Law Emily , Hughes John S.
Published: May 2017

We describe here the parallels in astronomy and earth science datasets, their analyses, and the opportunities for methodology transfer from astroinformatics to geoinformatics. Using example of hydrology, we emphasize how meta-data and ontologies are crucial in such an undertaking. Using the infrastructure being designed for EarthCube - the Virtual Observatory for the earth sciences - we discuss essential steps for better transfer of tools and techniques in the future e.g. domain adaptation. Finally we point out that it is never a one-way process and there is enough for astroinformatics to learn from geoinformatics as well.
Integrated data access, visualization and analysis for Galactic Plane surveys: the VIALACTEA case
Authors: Molinari Sergio , Butora Robert , Cavuoti Stefano , Molinaro Marco , Riccio Giuseppe , Sciacca Eva , Vitello Fabio , Becciani Ugo , Brescia Massimo , Costa Alessandro , Smareglia Riccardo
Published: May 2017

The VIALACTEA project brings to a common forum the major new-generation surveys of the Milky Way Galactic Plane from 1μm to the radio, both in thermal continuum and in atomic and molecular lines, to attack in a systematic way the characterization of the Milky Way as a star formation engine. Images, catalogues, spectroscopic datacubes and radiative transfer models of the Spectral Energy Distributions (SEDs) of sites of star formation have been incorporated and indexed in the VIALACTEA Knowledge Base (VLKB). The VLKB consists of a combination of a relational database where the VIALACTEA data and metadata are homogenised and stored, and a filesystem-based stored information. This infrastructure allowed, among others, the generation of extensive catalogue for compact sources and extended structures in the Galactic Plane, the implementation of data-mining algorithms for the band-merging of multiwavelength data and expert systems for the automated analysis of molecular line surveys to extract critical kinematical information and derive distances using Galaxy rotation curves and new 3D extinction maps. A new VIALACTEA 3D Visual Analytics interface has been developed that provides integrated access and analysis of continuum and spectroscopic images together with catalogue data directly interfacing with the VLKB.
Learn from every mistake! Hierarchical information combination in astronomy
Authors: Süveges Maria , Fotopoulou Sotiria , Coupon Jean , Paltani Stéphane , Eyer Laurent , Rimoldini Lorenzo
Published: May 2017

Throughout the processing and analysis of survey data, a ubiquitous issue nowadays is that we are spoilt for choice when we need to select a methodology for some of its steps. The alternative methods usually fail and excel in different data regions, and have various advantages and drawbacks, so a combination that unites the strengths of all while suppressing the weaknesses is desirable. We propose to use a two-level hierarchy of learners. Its first level consists of training and applying the possible base methods on the first part of a known set. At the second level, we feed the output probability distributions from all base methods to a second learner trained on the remaining known objects. Using classification of variable stars and photometric redshift estimation as examples, we show that the hierarchical combination is capable of achieving general improvement over averaging-type combination methods, correcting systematics present in all base methods, is easy to train and apply, and thus, it is a promising tool in the astronomical “Big Data” era.
3-D interactive visualisation tools for Hispectral line imaging
Authors: van der Hulst J. M. , Punzo D. , Roerdink J. B. T. M.
Published: May 2017

Upcoming HI surveys will deliver such large datasets that automated processing using the full 3-D information to find and characterize HI objects is unavoidable. Full 3-D visualization is an essential tool for enabling qualitative and quantitative inspection and analysis of the 3-D data, which is often complex in nature. Here we presentSlicerAstro, an open-source extension of3DSlicer, a multi-platform open source software package for visualization and medical image processing, which we developed for the inspection and analysis of HI spectral line data. We describe its initial capabilities, including 3-D filtering, 3-D selection and comparative modelling.
Collaborative visual analytics of radio surveys in the Big Data era
Authors: Vohl Dany , Fluke Christopher J. , Hassan Amr H. , Barnes David G. , Kilborn Virginia A.
Published: May 2017

Radio survey datasets comprise an increasing number of individual observations stored as sets of multidimensional data. In large survey projects, astronomers commonly face limitations regarding: 1) interactive visual analytics of sufficiently large subsets of data; 2) synchronous and asynchronous collaboration; and 3) documentation of the discovery workflow. To support collaborative data inquiry, we present encube, a large-scale comparative visual analytics framework. encube can utilise advanced visualization environments such as the CAVE2 (a hybrid 2D and 3D virtual reality environment powered with a 100 Tflop/s GPU-based supercomputer and 84 million pixels) for collaborative analysis of large subsets of data from radio surveys. It can also run on standard desktops, providing a capable visual analytics experience across the display ecology. encube is composed of four primary units enabling compute-intensive processing, advanced visualisation, dynamic interaction, parallel data query, along with data management. Its modularity will make it simple to incorporate astronomical analysis packages and Virtual Observatory capabilities developed within our community. We discuss how encube builds a bridge between high-end display systems (such as CAVE2) and the classical desktop, preserving all traces of the work completed on either platform – allowing the research process to continue wherever you are.
Ruin problems in Markov-modulated risk models
Authors: Dickson David C.M. , Qazvini Marjan
Published: May 2017

Chen et al. (2014), studied a discrete semi-Markov risk model that covers existing risk models such as the compound binomial model and the compound Markov binomial model. We consider their model and build numerical algorithms that provide approximations to the probability of ultimate ruin and the probability and severity of ruin in a continuous time two-state Markov-modulated risk model. We then study the finite time ruin probability for a discrete m-state model and show how we can approximate the density of the time of ruin in a continuous time Markov-modulated model with more than two states.
Injectable hydrogels for cartilage and bone tissue engineering
Authors: Liu Mei , Zeng Xin , Ma Chao , Yi Huan , Ali Zeeshan , Mou Xianbo , Li Song , Deng Yan , He Nongyue
Published: May 2017

Tissue engineering has become a promising strategy for repairing damaged cartilage and bone tissue. Among the scaffolds for tissue-engineering applications, injectable hydrogels have demonstrated great potential for use as three-dimensional cell culture scaffolds in cartilage and bone tissue engineering, owing to their high water content, similarity to the natural extracellular matrix (ECM), porous framework for cell transplantation and proliferation, minimal invasive properties, and ability to match irregular defects. In this review, we describe the selection of appropriate biomaterials and fabrication methods to prepare novel injectable hydrogels for cartilage and bone tissue engineering. In addition, the biology of cartilage and the bony ECM is also summarized. Finally, future perspectives for injectable hydrogels in cartilage and bone tissue engineering are discussed.
Central and peripheral clocks are coupled by a neuropeptide pathway in Drosophila
Authors: Selcho Mareike , Millán Carola , Palacios-Muñoz Angelina , Ruf Franziska , Ubillo Lilian , Chen Jiangtian , Bergmann Gregor , Ito Chihiro , Silva Valeria , Wegener Christian , Ewer John
Published: May 2017

Animal circadian clocks consist of central and peripheral pacemakers, which are coordinated to produce daily rhythms in physiology and behaviour. Despite its importance for optimal performance and health, the mechanism of clock coordination is poorly understood. Here we dissect the pathway through which the circadian clock of Drosophila imposes daily rhythmicity to the pattern of adult emergence. Rhythmicity depends on the coupling between the brain clock and a peripheral clock in the prothoracic gland (PG), which produces the steroid hormone, ecdysone. Time information from the central clock is transmitted via the neuropeptide, sNPF, to non-clock neurons that produce the neuropeptide, PTTH. These secretory neurons then forward time information to the PG clock. We also show that the central clock exerts a dominant role on the peripheral clock. This use of two coupled clocks could serve as a paradigm to understand how daily steroid hormone rhythms are generated in animals.
Sea-level records from the U.S. mid-Atlantic constrain Laurentide Ice Sheet extent during Marine Isotope Stage 3
Authors: Pico T , Creveling J. R. , Mitrovica J. X.
Published: May 2017

The U.S. mid-Atlantic sea-level record is sensitive to the history of the Laurentide Ice Sheet as the coastline lies along the ice sheet’s peripheral bulge. However, paleo sea-level markers on the present-day shoreline of Virginia and North Carolina dated to Marine Isotope Stage (MIS) 3, from 50 to 35 ka, are surprisingly high for this glacial interval, and remain unexplained by previous models of ice age adjustment or other local (for example, tectonic) effects. Here, we reconcile this sea-level record using a revised model of glacial isostatic adjustment characterized by a peak global mean sea level during MIS 3 of approximately −40 m, and far less ice volume within the eastern sector of the Laurentide Ice Sheet than traditional reconstructions for this interval. We conclude that the Laurentide Ice Sheet experienced a phase of very rapid growth in the 15 kyr leading into the Last Glacial Maximum, thus highlighting the potential of mid-field sea-level records to constrain areal extent of ice cover during glacial intervals with sparse geological observables.
Erratum: Mixing of quantum states: A new route to creating optical activity
Authors: Baimuratov Anvar S. , Tepliakov Nikita V. , Gun’ko Yurii K. , Baranov Alexander V. , Fedorov Anatoly V. , Rukhlenko Ivan D.
Published: May 2017

A correction to this article has been published and is linked from the HTML version of this paper. The error has not been fixed in the paper.
Solitonic conduction of electrotonic signals in neuronal branchlets with polarized microstructure
Authors: Poznanski R. R. , Cacha L. A. , Al-Wesabi Y. M. S. , Ali J. , Bahadoran M. , Yupapin P. P. , Yunus J.
Published: May 2017

A model of solitonic conduction in neuronal branchlets with microstructure is presented. The application of cable theory to neurons with microstructure results in a nonlinear cable equation that is solved using a direct method to obtain analytical approximations of traveling wave solutions. It is shown that a linear superposition of two oppositely directed traveling waves demonstrate solitonic interaction: colliding waves can penetrate through each other, and continue fully intact as the exact pulses that entered the collision. These findings indicate that microstructure when polarized can sustain solitary waves that propagate at a constant velocity without attenuation or distortion in the absence of synaptic transmission. Solitonic conduction in a neuronal branchlet arising from polarizability of its microstructure is a novel signaling mode of electrotonic signals in thin processes (<0.5 μm diameter).
Cathepsin S inhibition combines control of systemic and peripheral pathomechanisms of autoimmune tissue injury
Authors: Tato Maia , Kumar Santhosh V. , Liu Yajuan , Mulay Shrikant R. , Moll Solange , Popper Bastian , Eberhard Jonathan N. , Thomasova Dana , Rufer Arne Christian , Gruner Sabine , Haap Wolfgang , Hartmann Guido , Anders Hans-Joachim
Published: May 2017

Cathepsin(Cat)-S processing of the invariant chain-MHC-II complex inside antigen presenting cells is a central pathomechanism of autoimmune-diseases. Additionally, Cat-S is released by activated-myeloid cells and was recently described to activate protease-activated-receptor-(PAR)-2 in extracellular compartments. We hypothesized that Cat-S blockade targets both mechanisms and elicits synergistic therapeutic effects on autoimmune tissue injury. MRL-(Fas)lpr mice with spontaneous autoimmune tissue injury were treated with different doses of Cat-S inhibitor RO5459072, mycophenolate mofetil or vehicle. Further, female MRL-(Fas)lpr mice were injected with recombinant Cat-S with/without concomitant Cat-S or PAR-2 blockade. Cat-S blockade dose-dependently reversed aberrant systemic autoimmunity, e.g. plasma cytokines, activation of myeloid cells and hypergammaglobulinemia. Especially IgG autoantibody production was suppressed. Of note (MHC-II-independent) IgM were unaffected by Cat-S blockade while they were suppressed by MMF. Cat-S blockade dose-dependently suppressed immune-complex glomerulonephritis together with a profound and early effect on proteinuria, which was not shared by MMF. In fact, intravenous Cat-S injection induced severe glomerular endothelial injury and albuminuria, which was entirely prevented by Cat-S or PAR-2 blockade.In-vitrostudies confirm that Cat-S induces endothelial activation and injury via PAR-2. Therapeutic Cat-S blockade suppresses systemic and peripheral pathomechanisms of autoimmune tissue injury, hence, Cat-S is a promising therapeutic target in lupus nephritis.
Superlattice growth and rearrangement during evaporation-induced nanoparticle self-assembly
Authors: Josten Elisabeth , Wetterskog Erik , Glavic Artur , Boesecke Peter , Feoktystov Artem , Brauweiler-Reuters Elke , Rücker Ulrich , Salazar-Alvarez German , Brückel Thomas , Bergström Lennart
Published: May 2017

Understanding the assembly of nanoparticles into superlattices with well-defined morphology and structure is technologically important but challenging as it requires novel combinations of in-situ methods with suitable spatial and temporal resolution. In this study, we have followed evaporation-induced assembly during drop casting of superparamagnetic, oleate-capped γ-Fe2O3 nanospheres dispersed in toluene in real time with Grazing Incidence Small Angle X-ray Scattering (GISAXS) in combination with droplet height measurements and direct observation of the dispersion. The scattering data was evaluated with a novel method that yielded time-dependent information of the relative ratio of ordered (coherent) and disordered particles (incoherent scattering intensities), superlattice tilt angles, lattice constants, and lattice constant distributions. We find that the onset of superlattice growth in the drying drop is associated with the movement of a drying front across the surface of the droplet. We couple the rapid formation of large, highly ordered superlattices to the capillary-induced fluid flow. Further evaporation of interstitital solvent results in a slow contraction of the superlattice. The distribution of lattice parameters and tilt angles was significantly larger for superlattices prepared by fast evaporation compared to slow evaporation of the solvent.
Human Chitotriosidase: Catalytic Domain or Carbohydrate Binding Module, Who’s Leading HCHT’s Biological Function
Authors: Crasson Oscar , Courtade Gaston , Léonard Raphaël R. , Aachmann Finn Lillelund , Legrand François , Parente Raffaella , Baurain Denis , Galleni Moreno , Sørlie Morten , Vandevenne Marylène
Published: May 2017

Chitin is an important structural component of numerous fungal pathogens and parasitic nematodes. The human macrophage chitotriosidase (HCHT) is a chitinase that hydrolyses glycosidic bonds between the N-acetyl-D-glucosamine units of this biopolymer. HCHT belongs to the Glycoside Hydrolase (GH) superfamily and contains a well-characterized catalytic domain appended to a chitin-binding domain (ChBDCHIT1). Although its precise biological function remains unclear, HCHT has been described to be involved in innate immunity. In this study, the molecular basis for interaction with insoluble chitin as well as with soluble chito-oligosaccharides has been determined. The results suggest a new mechanism as a common binding mode for many Carbohydrate Binding Modules (CBMs). Furthermore, using a phylogenetic approach, we have analysed the modularity of HCHT and investigated the evolutionary paths of its catalytic and chitin binding domains. The phylogenetic analyses indicate that the ChBDCHIT1 domain dictates the biological function of HCHT and not its appended catalytic domain. This observation may also be a general feature of GHs. Altogether, our data have led us to postulate and discuss that HCHT acts as an immune catalyser.
Normalization of adiponectin concentrations by leptin replacement in ob/ob mice is accompanied by reductions in systemic oxidative stress and inflammation
Authors: Frühbeck Gema , Catalán Victoria , Rodríguez Amaia , Ramírez Beatriz , Becerril Sara , Portincasa Piero , Gómez-Ambrosi Javier
Published: May 2017

The circulating concentrations of adiponectin, an antidiabetic adipokine, have been shown to be reduced in obesity, in relation to an increase in inflammation. The aim of the present work was to assess the effect of leptin replacement on adiponectin levels and expression as well as on markers of oxidative stress and inflammation in leptin-deficient ob/ob mice. Twelve-week-old male mice (n = 7–10 per group) were treated with either saline (wild type and ob/ob mice) or leptin (ob/ob mice) for 18 days. A third group of ob/ob mice was treated with saline and pair-fed to the amount of food consumed by the leptin-treated group. Leptin replacement restored values of adiponectin (P < 0.001), reduced circulating 8-isoprostane and serum amyloid A (SAA) levels (P < 0.05 for both), and significantly downregulated the increased gene expression of osteopontin (Spp1, P < 0.05), Saa3 (P < 0.05), Cd68 (P < 0.01), Il6 (P < 0.01) and NADPH oxidase (Nox1 and Nox2, P < 0.01) in the perirenal WAT and Spp1 (P < 0.05) in the liver of ob/ob mice. In cultured adipocytes from ob/ob mice, leptin increased (P < 0.05) the mRNA expression and secretion of adiponectin. We concluded that circulating concentrations of adiponectin are positively regulated by leptin and ameliorate obesity-associated oxidative stress and inflammation in mice.
Population genetics analysis of the Nujiang catfish Creteuchiloglanis macropterus through a genome-wide single nucleotide polymorphisms resource generated by RAD-seq
Authors: Kang Jingliang , Ma Xiuhui , He Shunping
Published: May 2017

Advances in genome scanning using high-throughput sequencing technologies has led to a revolution in studies of non-model organisms. The glyptosternoid fish Creteuchiloglanis macropterus, is widely distributed in the main stem and tributaries of the Nujiang River basin. Here, we analyzed IIB restriction-site-associated DNA (2b-RAD) sequences and mitochondrial DNA sequences, to assess the genomic signature of adaptation by detecting and estimating the degree of genetic differentiation among ten Creteuchiloglanis macropterus populations from the Nujiang River. The analyses revealed significant population differentiation among the up-tributaries, main stem, mid-tributary and low-tributary. Annotation of contigs containing outlier SNPs revealed that the candidate genes showed significant enrichment in several important biological process terms between up-tributaries and low-tributary, and exhibited prominent enrichment in the term macromolecular metabolic process between all tributaries and the main stem. Population dynamics analyses indicated that the Late Pleistocene glaciations strongly influenced the demographic history of C. macropterus. Our results provide strong evidence for the utility of RAD-seq in population genetics studies, and our generated SNP resource should provide a valuable tool for population genomics studies of C. macropterus in the future.
Stiff, light, strong and ductile: nano-structured High Modulus Steel
Authors: Springer H. , Baron C. , Szczepaniak A. , Uhlenwinkel V. , Raabe D.
Published: May 2017

Structural material development for lightweight applications aims at improving the key parameters strength, stiffness and ductility at low density, but these properties are typically mutually exclusive. Here we present how we overcome this trade-off with a new class of nano-structured steel – TiB2 composites synthesised in-situ via bulk metallurgical spray-forming. Owing to the nano-sized dispersion of the TiB2 particles of extreme stiffness and low density – obtained by the in-situ formation with rapid solidification kinetics – the new material has the mechanical performance of advanced high strength steels, and a 25% higher stiffness/density ratio than any of the currently used high strength steels, aluminium, magnesium and titanium alloys. This renders this High Modulus Steel the first density-reduced, high stiffness, high strength and yet ductile material which can be produced on an industrial scale. Also ideally suited for 3D printing technology, this material addresses all key requirements for high performance and cost effective lightweight design.
Analysis of aquaporins in Brassicaceae species reveals high-level of conservation and dynamic role against biotic and abiotic stress in canola
Authors: Sonah Humira , Deshmukh Rupesh K. , Labbé Caroline , Bélanger Richard R.
Published: May 2017

Aquaporins (AQPs) are of vital importance in the cellular transport system of all living organisms. In this study, genome-wide identification, distribution, and characterization of AQPs were determined in Arabidopsis lyrata, Capsella grandiflora, C. rubella, Eutrema salsugineum, Brassica rapa, B. oleracea, and B. napus (canola). Classification and phylogeny of AQPs revealed the loss of XIPs and NIP-IIIs in all species. Characterization of distinctive AQP features showed a high level of conservation in spacing between NPA-domains, and selectivity filters. Interestingly, TIP3s were found to be highly expressed in developing seeds, suggesting their role in seed desiccation. Analysis of available RNA-seq data obtained under biotic and abiotic stresses led to the identification of AQPs involved in stress tolerance mechanisms in canola. In addition, analysis of the effect of ploidy level, and resulting gene dose effect performed with the different combinations of Brassica A and C genomes revealed that more than 70% of AQPs expression were dose-independent, thereby supporting their role in stress alleviation. This first in-depth characterization of Brassicaceae AQPs highlights transport mechanisms and related physiological processes that could be exploited in breeding programs of stress-tolerant cultivars.
NKX6.3 Regulates Reactive Oxygen Species Production by Suppressing NF-kB and DNMT1 Activities in Gastric Epithelial Cells
Authors: Yoon Jung Hwan , Kim Olga , Nam Suk Woo , Lee Jung Young , Park Won Sang
Published: May 2017

NKX6.3 plays an important role in gastric epithelial differentiation and also acts as a gastric tumor suppressor. The specific aim of this study was to determine whether NKX6.3 contributes to gastric mucosal barrier function by regulating reactive oxygen species (ROS) production. NKX6.3 reduced ROS production and regulated expression of anti-oxidant genes, including Hace1. In addition, NKX6.3 reduced DNMT1 expression and activity by down-regulating NF-kB family gene transcription. Silencing of Hace1 recovered ROS production, whereas knock-down of DNMT1 and NF-kB reduced ROS production and induced Hace1 expression by hypomethylating its promoter region. In addition, NKX6.3 inhibited CagA effects on cell growth, ROS production, and NF-kB and DNMT1 activity. In gastric mucosae and cancers, NKX6.3 and Hace1 expression was significantly reduced. The NKX6.3 expression was positively correlated with Hace1 and Nrf2 genes, but negatively correlated with DNMT1. Hypermethylation of Hace1 gene was observed only in gastric mucosae with H. pylori, atrophy and intestinal metaplasia. Thus, these results suggest that NKX6.3 inhibits ROS production by inducing the expression of Hace1 via down-regulating NF-kB and DNMT1 activity in gastric epithelial cells.
Switching of spins and entanglement in surface-supported antiferromagnetic chains
Authors: Sivkov Ilia N. , Bazhanov Dmitry I. , Stepanyuk Valeri S.
Published: May 2017

Previous experimental studies discovered universal growth of chains and nanowires of various chemical elements on a corrugated molecular network of Cu3N on the Cu(110). Herein, performing combined ab initio and quantum Hamiltonian studies we demonstrate that such chains can be used for a fast spin switching and entanglement generation by locally applied magnetic pulses. As an example, we show that in antiferromagnetic Co chains a strong entanglement between ends of chains occurs during spin switching. A novel parity effect in spin dynamics is reported. Even-numbered chains are found to exhibit significantly faster spin switching than odd-numbered counterparts. Moreover, at certain parameters of the system the dimerization effect in the spin dynamics of the chains was found. Our studies give a clear evidence that tailoring spin dynamics and entanglement can be achieved by magnetic fields and by tuning exchange interactions in supported chains.
Complex beam shaping based on an equivalent q-plate system and analysis of its properties using digital holography polarization imaging
Authors: Yang Ching-Han , Fuh Andy Ying-Guey
Published: May 2017

In this study, we generate various complex beams carrying angular momentum (AM) by using a programmable beam shaping system to mimic typical q-plates. When a circularly polarized wave is incident onto the system, the emerging beam reverses its spin handedness and obtains a spatial phase factor. This phase factor can be engineered by designing a computer-generated hologram (CGH) and applying it to a spatial light modulator (SLM) to produce a beam with controllable spatially distributed orbital angular momentum (OAM) density. To determine the properties of the generated fields, we combine digital holography (DH) with the beam shaping system to yield visualizations of the beam intensity, phase, and AM distributions over the transverse plane at different propagation distances. Comparisons of the theoretically and experimentally obtained results show good qualitative agreement. This study advances our understanding and interpretation of AM characteristics produced by a programmable q-plate-like system.
Earlier flowering did not alter pollen limitation in an early flowering shrub under short-term experimental warming
Authors: Pan Cheng-Chen , Feng Qi , Zhao Ha-Lin , Liu Lin-De , Li Yu-Lin , Li Yu-Qiang , Zhang Tong-Hui , Yu Xiao-Ya
Published: May 2017

In animal pollinated plants, phenological shifts caused by climate change may have important ecological consequences. However, no empirical evidence exists at present on the consequences that flowering phenology shifts have on the strength of pollen limitation under experimental warming. Here, we investigated the effects of experimental warming on flowering phenology, flower density, reproductive success, and pollen limitation intensity inCaragana microphyllaand evaluated whether earlier flowering phenology affected plant reproduction and the level of pollen limitation using warmed and unwarmed open top chambers in the Horqin Sandy Land of Inner Mongolia, northern China. The results of this study indicated that artificial warming markedly advanced flower phenology rather than extending the duration of the flowering. Additionally, warming was found to significantly reduce flower density which led to seed production reduction, since there were insignificant effects observed on fruit set and seed number per fruit. Experimental floral manipulations showed that warming did not affect pollen limitation. These results revealed the negative effects of advanced phenology induced by warming on flower density and reproductive output, as well as the neutral effects on reproductive success and pollen limitation intensity of long surviving plants.
Single-cell protein-mRNA correlation analysis enabled by multiplexed dual-analyte co-detection
Authors: Gong Haibiao , Wang Xiaohui , Liu Benjamin , Boutet Stephane , Holcomb Ilona , Dakshinamoorthy Gajalakshmi , Ooi Aik , Sanada Chad , Sun Gang , Ramakrishnan Ramesh
Published: May 2017

We have investigated the correlation between proteins and mRNAs in single cells employing an integrated workflow for dual-analyte co-detection. This is achieved by combining the oligo extension reaction (OER), which converts protein levels to DNA levels, with reverse transcription for mRNA detection. Unsupervised gene expression profiling analysis, including principal component analysis and hierarchical clustering, revealed different aspects of the protein-mRNA relationship. Violin plot analysis showed that some genes exhibited similar distribution patterns for proteins and mRNAs. We also demonstrate that cells can be separated into subpopulations based on their protein-mRNA expression profiles, and that different subpopulations have distinct correlation coefficient values. Our results demonstrated that integrated investigations of mRNA and protein levels in single cells allows comprehensive analysis not attainable at bulk levels.
The Effect of Interleukin 38 on Angiogenesis in a Model of Oxygen-induced Retinopathy
Authors: Zhang Jing , Zhao Ruijuan , Chen Jianping , Jin Jiayi , Yu Ying , Tian Yunzhe , Li Weihua , Wang Wencong , Zhou Hongyan , Bo Su Shao
Published: May 2017

Interleukin 38 (IL-38) is a novel identified cytokine of IL-1 family in which some members are important in inflammation and angiogenesis. However, the role of IL-38 in regulating angiogenesis is unknown. The aim of the present study is to explore the effect of IL-38 on angiogenesis. Oxygen-induced retinopathy (OIR) of C57BL/6 J mice was induced by exposure of hyperoxia (75% oxygen) from postnatal day 7 (P7) to P12 and then returned to room air. The mice were injected with IL-38. At P17, neovascular region (tufts) and avascular area of the retinas were analyzed. The data showed that administration of IL-38 in vivo inhibited retinal angiogenesis significantly. Furthermore, the addition of IL-38 to the cell cultures attenuated the proliferation, scratch wound healing and tube formation of vascular endothelial cells induced by VEGF significantly. Our findings suggest that IL-38 is an antiangiogenic cytokine in pathophysiological settings and may have therapeutic potential for angiogenesis related diseases.
Immune signatures of pathogenesis in the peritoneal compartment during early infection of sheep with Fasciola hepatica
Authors: Ruiz-Campillo Maria Teresa , Molina Hernandez Veronica , Escamilla Alejandro , Stevenson Michael , Perez Jose , Martinez-Moreno Alvaro , Donnelly Sheila , Dalton John P. , Cwiklinski Krystyna
Published: May 2017

Immune signatures of sheep acutely-infected withFasciola hepatica, an important pathogen of livestock and humans were analysed within the peritoneal compartment to investigate early infection. Within the peritoneum,F. hepaticaantibodies coincided with an intense innate and adaptive cellular immune response, with infiltrating leukocytes and a marked eosinophilia (49%). However, while cytokine qPCR analysis revealed IL-10, IL-12, IL-13, IL-23 and TGFβ were elevated, these were not statistically different at 18 days post-infection compared to uninfected animals indicating that the immune response is muted and not yet skewed to a Th2 type response that is associated with chronic disease. Proteomic analysis of the peritoneal fluid identified infection-related proteins, including several structural proteins derived from the liver extracellular matrix, connective tissue and epithelium, and proteins related to the immune system. Periostin and vascular cell adhesion protein 1 (VCAM-1), molecules that mediate leukocyte infiltration and are associated with inflammatory disorders involving marked eosinophilia (e.g. asthma), were particularly elevated in the peritoneum. Immuno-histochemical studies indicated that the source of periostin and VCAM-1 was the inflamed sheep liver tissue. This study has revealed previously unknown aspects of the immunology and pathogenesis associated with acute fascioliasis in the peritoneum and liver.
PCDH18 is frequently inactivated by promoter methylation in colorectal cancer
Authors: Zhou Dan , Tang Weiwei , Su Guoqiang , Cai Mingquan , An Han-Xiang , Zhang Yun
Published: May 2017

Protocadherin18 (PCDH18) was found to be preferentially methylated and inactivated in colorectal cancer (CRC) using bioinformatics tools. However, its biologic role in tumorgenesis remains unclear. Herein, we aimed to elucidate its epigenetic regulation and biological functions in CRC. The methylation status of PCDH18 was significant higher in CRC tissues than in adjacent non-tumor tissues (median, 15.17% vs. median, 0.4438%). Expression level of PCDH18 was significantly lower in primary CRCs than in nonmalignant tissues. Importantly, methylation status of PCDH18 in cell-free DNA of CRC patients was also significantly higher than in healthy subjects. PCDH18 was readily expressed in NCM460 cells, but downregulated in 100% (4/4) of CRC cell lines by promoter methylation, despite its expression could be restored through demethylation treatment. Overexpression of PCDH18 suppressed CRC cell viability, colony formation and migration. Meanwhile, the depletion of PCDH18 by siRNA in NCM460 cells enhanced the colonogenicity and migration ability and promoted β-catenin nuclear accumulation, whereas it inhibited cell cycle arrest. These effects were associated with upregulation of phospho-GSK-3β and cyclin D1, and downregulation of caspase3 and p21. Our results suggested that PCDH18 was a putative tumor suppressor with epigenetic silencing in CRC and a potential biomarker for CRC diagnosis.
Antennal and abdominal transcriptomes reveal chemosensory gene families in the coconut hispine beetle, Brontispa longissima
Authors: Bin Shu-Ying , Qu Meng-Qiu , Li Ke-Ming , Peng Zheng-Qiang , Wu Zhong-Zhen , Lin Jin-Tian
Published: May 2017

Antennal and abdominal transcriptomes of males and females of the coconut hispine beetle Brontispa longissima were sequenced to identify and compare the expression patterns of genes involved in odorant reception and detection. Representative proteins from the chemosensory gene families likely essential for insect olfaction were identified. These include 48 odorant receptors (ORs), 19 ionotropic receptors (IRs), 4 sensory neuron membrane proteins (SNMPs), 34 odorant binding proteins (OBPs) and 16 chemosensory proteins (CSPs). Phylogenetic analysis revealed the evolutionary relationship of these proteins with homologs from Coleopterans or other insects, and led to the identification of putative aggregation pheromone receptors in B. longissima. Comparative expression analysis performed by calculating FPKM values were also validated using quantitative real time-PCR (qPCR). The results revealed that all ORs and antennal IRs, two IR co-receptors (BlonIR8a and BlonIR25a) and one SNMP (BlonSNMP1a) were predominantly expressed in antennae when compared to abdomens, and approximately half of the OBPs (19) and CSPs (7) were enriched in antennae. These findings for the first time reveal the identification of key molecular components in B. longissima olfaction and provide a valuable resource for future functional analyses of olfaction, and identification of potential targets to control this quarantine pest.
Correction: Corrigendum: The contemporary distribution of Trypanosoma cruzi infection in humans, alternative hosts and vectors
Authors: Browne Annie J. , Guerra Carlos A. , Alves Renato Vieira , da Costa Veruska Maia , Wilson Anne L. , Pigott David M. , Hay Simon I. , Lindsay Steve W. , Golding Nick , Moyes Catherine L.
Published: May 2017

Scientific Data 4:170050 doi: 10.1038/sdata.2017.50 (2017); Published 11 April 2017; Updated 30 May 2017 The financial support for this Data Descriptor was not fully acknowledged. The Acknowledgements should have included the following: S.I.H. is funded by a Senior Research Fellowship from the Wellcome Trust [095066].
RiceAtlas, a spatial database of global rice calendars and production
Authors: Laborte Alice G. , Gutierrez Mary Anne , Balanza Jane Girly , Saito Kazuki , Zwart Sander J. , Boschetti Mirco , Murty M.V.R. , Villano Lorena , Aunario Jorrel Khalil , Reinke Russell , Koo Jawoo , Hijmans Robert J. , Nelson Andrew
Published: May 2017

Knowing where, when, and how much rice is planted and harvested is crucial information for understanding the effects of policy, trade, and global and technological change on food security. We developed RiceAtlas, a spatial database on the seasonal distribution of the world’s rice production. It consists of data on rice planting and harvesting dates by growing season and estimates of monthly production for all rice-producing countries. Sources used for planting and harvesting dates include global and regional databases, national publications, online reports, and expert knowledge. Monthly production data were estimated based on annual or seasonal production statistics, and planting and harvesting dates. RiceAtlas has 2,725 spatial units. Compared with available global crop calendars, RiceAtlas is nearly ten times more spatially detailed and has nearly seven times more spatial units, with at least two seasons of calendar data, making RiceAtlas the most comprehensive and detailed spatial database on rice calendar and production.
Evolution of the in vitro degradation of Zn–Mg alloys under simulated physiological conditions
Authors: Alves Marta M. , Prošek Tomáš , Santos Catarina F. , Montemor Maria F.
Published: May 2017

Primary reactions occurring upon Zn-derived materials insertion inside an organism are of utmost importance as chemical species resulting from the degradation of resorbable biomaterials are crucial for the interaction with the surrounding tissues.
A chemically reduced graphene oxide–Au nanocage composite for the electrochemical detection of dopamine and uric acid
Authors: Li Weihao , Ma Lian , Wu Bingxue , Zhang Yue , Li Zhuang
Published: May 2017

Herein, a chemically reduced graphene oxide–Au nanocage (CRGO–AuNCs) composite was synthesized by electrostatic assembly of poly-diallyldimethylammonium chloride (PDDA)-modified CRGO and mercaptosuccinic acid (MSA)-modified Au nanocages.
Guided protein/cell patterning on superhydrophilic polymer brushes functionalized with mussel-inspired polydopamine coatings
Authors: Hou Jianwen , Liu Tao , Chen Runhai , Liu Jingchuan , Chen Jiayue , Zhao Chunyu , Yin Ligang , Li Chunming , Xu Xiaodong , Shi Qiang , Yin Jinghua
Published: May 2017

A simple and versatile method for the fabrication of highly stable and well-defined protein/cell arrays was developed.
Exploration of organic–inorganic hybrid perovskites for surface-enhanced infrared spectroscopy of small molecules
Authors: Chen Jia , Mo Zhi-Hong , Yang Xiao , Zhou Hai-Ling , Gao Qin
Published: May 2017

Organic–inorganic hybrid perovskites allow the infrared absorption of small molecules to be efficiently enhanced.
One-dimensional silicon nanoshuttles simultaneously featuring fluorescent and magnetic properties
Authors: Song Bin , Zhong Yiling , Wang Houyu , Su Yuanyuan , He Yao
Published: May 2017

Fluorescent and magnetic one-dimensional silicon nanoshuttles are prepared in situ through a metal ions-assisted microwave synthetic strategy.
Morphological control of self-assembled multivalent (SAMul) heparin binding in highly competitive media
Authors: Rodrigo Ana C. , Bromfield Stephen M. , Laurini Erik , Posocco Paola , Pricl Sabrina , Smith David K.
Published: May 2017

Shape control – self-assembly of ligands into different morphologies directs their ability to bind heparin.
Observing the dynamic “hot spots” on two-dimensional Au nanoparticles monolayer film
Authors: Zhang Chenjie , You Enming , Jin Qi , Yuan Yaxian , Xu Minmin , Ding Songyuan , Yao Jianlin , Tian Zhongqun
Published: May 2017

Interparticle spacing was controlled by evaporating water on 2D Au nanoparticles arrays.
Reversible formation and cleavage of Pt→Ag dative bonds in a pre-organized cavity of a luminescent heteropolynuclear platinum(ii) complex
Authors: Ueda Misa , Horiuchi Shinnosuke , Sakuda Eri , Nakao Yoshihide , Arikawa Yasuhiro , Umakoshi Keisuke
Published: May 2017

A heteropolynuclear complex can reversibly capture an Ag(i) ion and release it from the pre-organized cavity by the concerted formation and cleavage of Pt→Ag dative bonds and Ag–C(ipso) bonds, respectively.
Kinetics and branching fractions of the hydrogen abstraction reaction from methyl butenoates by H atoms
Authors: Li Xiaoyu , You Xiaoqing , Law Chung K. , Truhlar Donald G.
Published: May 2017

We studied hydrogen abstraction reactions at various sites of unsaturated methyl esters by H atoms, including variational effects, tunneling and multi-structural torsional anharmonicity.
Affinity regulation of the NH3 + H2O system by ionic liquids with molecular interaction analysis
Authors: Huang Weijia , Zheng Danxing , Xia Changxing , Feng Lejun , Dong Li , Jiang Peixue
Published: May 2017

A new strategy of regulating NH3–H2O affinity by adding ILs is proposed and moderate regulation effects are achieved as expected.
A neural network potential energy surface for the NaH2 system and dynamics studies on the H(2S) + NaH(X1Σ+) → Na(2S) + H2(X1Σg+) reaction
Authors: Wang Shufen , Yuan Jiuchuang , Li Huixing , Chen Maodu
Published: May 2017

A new potential energy surface of the NaH2 system is obtained using the neural network method based on high-level energies.
Introducing the triangular BN nanodot or its cooperation with the edge-modification via the electron-donating/withdrawing group to achieve the large first hyperpolarizability in a carbon nanotube system
Authors: Zhang Xueying , Yu Guangtao , Huang Xuri , Chen Wei
Published: May 2017

Doping the triangular BN nanodomain or its cooperation with the edge-modification can significantly improve the NLO properties of CNT systems.