bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-random transmission of parental alleles into crop-wild and crop-weed hybrid lineages separated by a transgene and neutral identifiers in rice
Authors: Wang Zhe , Wang Lei , Wang Zhi , Lu Bao-Rong 
Published: August 2017

AbstractIt is essential to assess environmental impact of transgene flow from genetically engineered crops to their wild or weedy relatives before commercialization. Measuring comparative trials of fitness in the transgene-flow-resulted hybrids plays the key role in the assessment, where the segregated isogenic hybrid lineages/subpopulations with or without a transgene of the same genomic background are involved. Here, we report substantial genomic differentiation between transgene-present and -absent lineages (F2-F3) divided by a glyphosate-resistance transgene from a crop-wild/weed hybrid population in rice. We further confirmed that such differentiation is attributed to increased frequencies of crop-parent alleles in transgenic hybrid lineages at multiple loci across the genome, as estimated by SSR (simple sequence repeat) markers. Such preferential transmission of parental alleles was also found in equally divided crop-wild/weed hybrid lineages with or without a particular neutral SSR identifier. We conclude that selecting either a transgene or neutral marker as an identifier to create hybrid lineages will result in different genomic background of the lineages due to non-random transmission of parental alleles. Non-random allele transmission may misrepresent the outcomes of fitness effects. We therefore propose seeking other means to evaluate fitness effects of transgenes for assessing environmental impact caused by crop-to-wild/weed gene flow.
Riparian plant litter quality increases with latitude
Authors: Boyero Luz , Graça Manuel A. S. , Tonin Alan M. , Pérez Javier , J. Swafford Andrew , Ferreira Verónica , Landeira-Dabarca Andrea , A. Alexandrou Markos , Gessner Mark O. , McKie Brendan G. , Albariño Ricardo J. , Barmuta Leon A. , Callisto Marcos , Chará Julián , Chauvet Eric , Colón-Gaud Checo , Dudgeon David , Encalada Andrea C. , Figueroa Ricardo , Flecker Alexander S. , Fleituch Tadeusz , Frainer André , Gonçalves José F. , Helson Julie E. , Iwata Tomoya , Mathooko Jude , M’Erimba Charles , Pringle Catherine M. , Ramírez Alonso , Swan Christopher M. , Yule Catherine M. , Pearson Richard G. 
Published: August 2017

AbstractPlant litter represents a major basal resource in streams, where its decomposition is partly regulated by litter traits. Litter-trait variation may determine the latitudinal gradient in decomposition in streams, which is mainly microbial in the tropics and detritivore-mediated at high latitudes. However, this hypothesis remains untested, as we lack information on large-scale trait variation for riparian litter. Variation cannot easily be inferred from existing leaf-trait databases, since nutrient resorption can cause traits of litter and green leaves to diverge. Here we present the first global-scale assessment of riparian litter quality by determining latitudinal variation (spanning 107°) in litter traits (nutrient concentrations; physical and chemical defences) of 151 species from 24 regions and their relationships with environmental factors and phylogeny. We hypothesized that litter quality would increase with latitude (despite variation within regions) and traits would be correlated to produce ‘syndromes’ resulting from phylogeny and environmental variation. We found lower litter quality and higher nitrogen:phosphorus ratios in the tropics. Traits were linked but showed no phylogenetic signal, suggesting that syndromes were environmentally determined. Poorer litter quality and greater phosphorus limitation towards the equator may restrict detritivore-mediated decomposition, contributing to the predominance of microbial decomposers in tropical streams.
Serum lysophospholipid levels are altered in dyslipidemic hamsters
Authors: Suárez-García Susana , Caimari Antoni , del Bas Josep Maria , Suárez Manuel , Arola Lluís 
Published: August 2017

AbstractDyslipidemias are common disorders that predispose individuals to severe diseases. It is known that healthy living habits can prevent dyslipidemias if they are diagnosed properly. Therefore, biomarkers that assist in diagnosis are essential. The aim of this study was to identify biomarkers of dyslipidemia progression, which in turn disclose its etiology. These findings will pave the way for examinations of the regulatory mechanisms involved in dyslipidemias. Hamsters were fed either a normal-fat diet (NFD) or a high-fat diet. Some of the NFD-fed animals were further treated with the hyperlipidemic agent Poloxamer 407. Non-targeted metabolomics was used to investigate progressive changes in unknown serum metabolites. The hepatic expression of putative biomarker-related genes was also analyzed. The serum levels of lysophospholipids (Lyso-PLs) and their related enzymes lecithin-cholesterol acyltransferase (LCAT), secreted phospholipase A2(sPLA2) and paraoxonase-1 were altered in dyslipidemic hamsters. Lysophosphatidylcholine levels were increased in diet-induced dyslipidemic groups, whereas lysophosphatidylethanolamine levels increased in response to the chemical treatment. The liver was significantly involved in regulating the levels of these molecules, based on the modified expression of endothelial lipase (Lipg), sPLA2(Pla2g2a) and acyltransferases (LcatandLpcat3). We concluded that Lyso-PL evaluation could aid in the comprehensive diagnosis and management of lipid disorders.
Whole Transcriptome Analysis of Notochord-Derived Cells during Embryonic Formation of the Nucleus Pulposus
Authors: Peck Sun H. , McKee Kendra K. , Tobias John W. , Malhotra Neil R. , Harfe Brian D. , Smith Lachlan J. 
Published: August 2017

AbstractRecapitulation of developmental signals represents a promising strategy for treating intervertebral disc degeneration. During development, embryonic notochord-derived cells (NDCs) are the direct progenitors of cells that populate the adult nucleus pulposus (NP) and are an important source of secreted signaling molecules. The objective of this study was to define global gene expression profiles of NDCs at key stages of embryonic disc formation. NDCs were isolated from Shh-cre;ROSA:YFP mice at embryonic day 12.5 and postnatal day 0, representing opposite ends of the notochord to NP transformation. Differences in global mRNA abundance across this developmental window were established using RNA-Seq. Protein expression of selected molecules was confirmed using immunohistochemistry. Principal component analysis revealed clustering of gene expression at each developmental stage with more than 5000 genes significantly differentially expressed between E12.5 and P0. There was significantly lower mRNA abundance of sonic hedgehog pathway elements at P0 vs E12.5, while abundance of elements of the transforming growth factor-beta and insulin-like growth factors pathways, and extracellular matrix components including collagen 6 and aggrecan, were significantly higher at P0. This study represents the first transcriptome-wide analysis of embryonic NDCs. Results suggest signaling and biosynthesis of NDCs change dramatically as a function of developmental stage.
Manipulating of Different-Polarized Reflected Waves with Graphene-based Plasmonic Metasurfaces in Terahertz Regime
Authors: Deng Li , Wu Yongle , Zhang Chen , Hong Weijun , Peng Biao , Zhu Jianfeng , Li Shufang 
Published: August 2017

AbstractA graphene-based plasmonic metasurface which can independently control different polarized electromagnetic waves with reasonably small losses in terahertz regime is proposed and demonstrated in this paper. This metasurface is composed of graphene based elements. Owing to anisotropic plasmonic resonance of the graphene-based elements, the reflected phases and magnitudes of orthogonally polarized waves can be independently controlled by varying dimensions of the element. Four types of graphene-based plasmonic metasurfaces with different reflected phases distributions are synthesized and simulated, exhibiting diverse functions such as polarized beam splitting, beam deflection, and linear-to-circular polarization conversion. The simulation results demonstrate excellent performances as theoretical expectation. The proposed graphene-based plasmonic metasurface can be applied to realize extremely light-weight, ultra-compact, and high-performances electromagnetic structures for diverse terahertz applications.
Forensic age prediction for saliva samples using methylation-sensitive high resolution melting: exploratory application for cigarette butts
Authors: Hamano Yuya , Manabe Sho , Morimoto Chie , Fujimoto Shuntaro , Tamaki Keiji 
Published: August 2017

AbstractThere is high demand for forensic age prediction in actual crime investigations. In this study, a novel age prediction model for saliva samples using methylation-sensitive high resolution melting (MS-HRM) was developed. The methylation profiles of ELOVL2 and EDARADD showed high correlations with age and were used to predict age with support vector regression. ELOVL2 was first reported as an age predictive marker for saliva samples. The prediction model showed high accuracy with a mean absolute deviation (MAD) from chronological age of 5.96 years among 197 training samples. The model was further validated with an additional 50 test samples (MAD = 6.25). In addition, the age prediction model was applied to saliva extracted from seven cigarette butts, as in an actual crime scene. The MAD (7.65 years) for these samples was slightly higher than that of intact saliva samples. A smoking habit or the ingredients of cigarettes themselves did not significantly affect the prediction model and could be ignored. MS-HRM provides a quick (2 hours) and cost-effective (95% decreased compared to that of DNA chips) method of analysis. Thus, this study may provide a novel strategy for predicting the age of a person of interest in actual crime scene investigations.
Divergent Evolution of Carbonaceous Aerosols during Dispersal of East Asian Haze
Authors: Fang Wenzheng , Andersson August , Zheng Mei , Lee Meehye , Holmstrand Henry , Kim Sang-Woo , Du Ke , Gustafsson Örjan 
Published: August 2017

AbstractWintertime East Asia is plagued by severe haze episodes, characterized by large contributions of carbonaceous aerosols. However, the sources and atmospheric transformations of these major components are poorly constrained, hindering development of efficient mitigation strategies and detailed modelling of effects. Here we present dual carbon isotope (δ13C and Δ14C) signatures for black carbon (BC), organic carbon (OC) and water-soluble organic carbon (WSOC) aerosols collected in urban (Beijing and BC for Shanghai) and regional receptors (e.g., Korea Climate Observatory at Gosan) during January 2014. Fossil sources (>50%) dominate BC at all sites with most stemming from coal combustion, except for Shanghai, where liquid fossil source is largest. During source-to-receptor transport, the δ13C fingerprint becomes enriched for WSOC but depleted for water-insoluble OC (WIOC). This reveals that the atmospheric processing of these two major pools are fundamentally different. The photochemical aging (e.g., photodissociation, photooxidation) during formation and transport can release CO2/CO or short-chain VOCs with lighter carbon, whereas the remaining WSOC becomes increasingly enriched in δ13C. On the other hand, several processes, e.g., secondary formation, rearrangement reaction in the particle phase, and photooxidation can influence WIOC. Taken together, this study highlights high fossil contributions for all carbonaceous aerosol sub-compartments in East Asia, and suggests different transformation pathways for different classes of carbonaceous aerosols.
Mechanism of splenic cell death and host mortality in a Plasmodium yoelii malaria model
Authors: Lacerda-Queiroz Norinne , Riteau Nicolas , Eastman Richard T. , Bock Kevin W. , Orandle Marlene S. , Moore Ian N. , Sher Alan , Long Carole A. , Jankovic Dragana , Su Xin-zhuan 
Published: August 2017

AbstractMalaria is a fatal disease that displays a spectrum of symptoms and severity, which are determined by complex host-parasite interactions. It has been difficult to study the effects of parasite strains on disease severity in human infections, but the mechanisms leading to specific disease phenotypes can be investigated using strains of rodent malaria parasites that cause different disease symptoms in inbred mice. Using a unique mouse malaria model, here we investigated the mechanisms of splenic cell death and their relationship to control of parasitemia and host mortality. C57BL/6 mice infected with Plasmodium yoelii nigeriensis N67C display high levels of pro-inflammatory cytokines and chemokines (IL-6, IFN-γ, TNF-α, CXCL1, and CCL2) and extensive splenic damage with dramatic reduction of splenic cell populations. These disease phenotypes were rescued in RAG2−/−, IFN-γ−/−, or T cell depleted mice, suggesting IFN-γ and T cell mediated disease mechanisms. Additionally, apoptosis was one of the major pathways involved in splenic cell death, which coincides with the peaks of pro-inflammatory cytokines. Our results demonstrate the critical roles of T cells and IFN-γ in mediating splenic cell apoptosis, parasitemia control, and host lethality and thus may provide important insights for preventing/reducing morbidity associated with severe malaria in humans.
Microscale Liquid Transport in Polycrystalline Inverse Opals across Grain Boundaries
Authors: Pham Q. N. , Barako M. T. , Tice J. , Won Y. 
Published: August 2017

AbstractDelivering liquid through the void spaces in porous metals is a daunting challenge for a variety of emerging interface technologies ranging from battery electrodes to evaporation surfaces. Hydraulic transport characteristics of well-ordered porous media are governed by the pore distribution, porosity, and morphology. Much like energy transport in polycrystalline solids, hydraulic transport in semi-ordered porous media is predominantly limited by defects and grain boundaries. Here, we report the wicking performances for porous copper inverse opals having pore diameters from 300 to 1000 nm by measuring the capillary-driven liquid rise. The capillary performance parameter within single crystal domain (K
ij
/R
eff
= 10−3 to 10−2 µm) is an order of magnitude greater than the collective polycrystal (K
eff
/R
eff
= ~10−5 to 10−3 µm) due to the hydraulic resistances (i.e. grain boundaries between individual grains). Inspired by the heterogeneity found in biological systems, we report that the capillary performance parameter of gradient porous copper (K
eff
/R
eff
= ~10−3 µm), comparable to that of single crystals, overcomes hydraulic resistances through providing additional hydraulic routes in three dimensions. The understanding of microscopic liquid transport physics through porous crystals and across grain boundaries will help to pave the way for the spatial design of next-generation heterogeneous porous media.
Black P/graphene hybrid: A fast response humidity sensor with good reversibility and stability
Authors: Phan Duy-Thach , Park Inyong , Park Ah-Ram , Park Cheol-Min , Jeon Ki-Joon 
Published: August 2017

AbstractBlack phosphorus (BP) materials have attracted considerable attention owing to their ultra-sensitive humidity sensing characteristics because of the natural absorption of water (H2O) molecules on the BP surface caused by the specific 2D layer-crystalline structure. On the other hand, the BP-based humidity sensor is less repeatable due to the instability of BP with water molecules and the stability of the sensor is reduced. In this study, this limitation of the BP-based humidity sensor was overcome by preparing a BP/graphene hybrid as a novel humidity sensing nanostructure. The BP/graphene interface improved the stability of the humidity sensor after a few weeks with a linear response within the relative humidity (RH) range of 15–70%. The sensor’s response/recovery speed of the humidity sensor was extremely fast within few seconds. The response (S) of the humidity sensor based on the BP/graphene hybrid is 43.4% at RH = 70%. The estimated response and recovery time of the sensor is only 9 and 30 seconds at RH = 70% at room temperature. The experimental investigation reveals that the BP/graphene hybrid not only improves the reversibility and hysteresis factors but also enhances the stability of the humidity sensor.
Prior Exposure to Zika Virus Significantly Enhances Peak Dengue-2 Viremia in Rhesus Macaques
Authors: George Jeffy , Valiant William G. , Mattapallil Mary J. , Walker Michelle , Huang Yan-Jang S. , Vanlandingham Dana L. , Misamore John , Greenhouse Jack , Weiss Deborah E. , Verthelyi Daniela , Higgs Stephen , Andersen Hanne , Lewis Mark G. , Mattapallil Joseph J. 
Published: August 2017

AbstractStructural and functional homologies between the Zika and Dengue viruses’ envelope proteins raise the possibility that cross-reactive antibodies induced following Zika virus infection might enhance subsequent Dengue infection. Using the rhesus macaque model we show that prior infection with Zika virus leads to a significant enhancement of Dengue-2 viremia that is accompanied by neutropenia, lympocytosis, hyperglycemia, and higher reticulocyte counts, along with the activation of pro-inflammatory monocyte subsets and release of inflammatory mediators. Zika virus infection induced detectable Dengue cross-reactive serum IgG responses that significantly amplified after Dengue-2 virus infection. Serum from Zika virus immune animals collected prior to Dengue-2 infection showed significant capacity for in vitro antibody dependent enhancement of Dengue-1, 2, 3 and 4 serotypes suggesting that pre-existing immunity to Zika virus could potentially enhance infection by heterologous Dengue serotypes. Our results provide first in vivo evidence that prior exposure to Zika virus infection can enhance Dengue infection, which has implications for understanding pathogenesis and the development of vaccines.
Comprehensive transcriptome mining of the direct conversion of mesodermal cells
Authors: Akbari Bijan , Wee Ping , Yaqubi Moein , Mohammadnia Abdulshakour 
Published: August 2017

AbstractThe direct reprogramming of somatic cells is a promising approach for regenerative medicine, especially in the production of mesoderm layer-derived cells. Meta-analysis studies provide precise insight into the undergoing processes and help increase the efficiency of reprogramming. Here, using 27 high-throughput expression data sets, we analyzed the direct reprogramming of mesodermal cells in humans and mice. Fibroblast-derived cells showed a common expression pattern of up- and down-regulated genes that were mainly involved in the suppression of the fibroblast-specific gene expression program, and may be used as markers of the initiation of reprogramming. Furthermore, we found a specific gene expression profile for each fibroblast-derived cell studied, and each gene set appeared to play specific functional roles in its cell type, suggesting their use as markers for their mature state. Furthermore, using data from protein-DNA interactions, we identified the main transcription factors (TFs) involved in the conversion process and ranked them based on their importance in their gene regulatory networks. In summary, our meta-analysis approach provides new insights on the direct conversion of mesodermal somatic cells, introduces a list of genes as markers for initiation and maturation, and identifies TFs for which manipulating their expression may increase the efficiency of direct conversion.
Effect of Fusidic Acid on the Kinetics of Molecular Motions During EF-G-Induced Translocation on the Ribosome
Authors: Belardinelli Riccardo , Rodnina Marina V. 
Published: August 2017

AbstractThe translocation step of protein synthesis entails binding and dissociation of elongation factor G (EF-G), movements of the two tRNA molecules, and motions of the ribosomal subunits. The translocation step is targeted by many antibiotics. Fusidic acid (FA), an antibiotic that blocks EF-G on the ribosome, may also interfere with some of the ribosome rearrangements, but the exact timing of inhibition remains unclear. To follow in real-time the dynamics of the ribosome–tRNA–EF-G complex, we have developed a fluorescence toolbox which allows us to monitor the key molecular motions during translocation. Here we employed six different fluorescence observables to investigate how FA affects translocation kinetics. We found that FA binds to an early translocation intermediate, but its kinetic effect on tRNA movement is small. FA does not affect the synchronous forward (counterclockwise) movements of the head and body domains of the small ribosomal subunit, but exerts a strong effect on the rates of late translocation events, i.e. backward (clockwise) swiveling of the head domain and the transit of deacylated tRNA through the E′ site, in addition to blocking EF-G dissociation. The use of ensemble kinetics and numerical integration unraveled how the antibiotic targets molecular motions within the ribosome-EF-G complex.
Current-direction/amplitude-dependent single channel gating kinetics of mouse pannexin 1 channel: a new concept for gating kinetics
Authors: Nomura Takeshi , Taruno Akiyuki , Shiraishi Makoto , Nakahari Takashi , Inui Toshio , Sokabe Masahiro , Eaton Douglas C. , Marunaka Yoshinori 
Published: August 2017

AbstractThe detailed single-channel gating kinetics of mouse pannexin 1 (mPanx1) remains unknown, although mPanx1 is reported to be a voltage-activated anion-selective channel. We investigated characteristics of single-channel conductances and opening and closing rates of mPanx1 using patch-clamp techniques. The unitary current of mPanx1 shows outward rectification with single-channel conductances of ~20 pS for inward currents and ~80 pS for outward currents. The channel open time for outward currents (Cl− influx) increases linearly as the amplitude of single channel currents increases, while the open time for inward currents (Cl− efflux) is constant irrespective of changes in the current amplitude, as if the direction and amplitude of the unitary current regulates the open time. This is supported by further observations that replacement of extracellular Cl− with gluconate− diminishes the inward tail current (Cl− efflux) at a membrane potential of −100 mV due to the lowered outward current (gluconate− influx) at membrane potential of 100 mV. These results suggest that the direction and rate of charge-carrier movement regulate the open time of mPanx1, and that the previously reported voltage-dependence of Panx1 channel gating is not directly mediated by the membrane potential but rather by the direction and amplitude of currents through the channel.
Electronic structure and topological properties of centrosymmetric MoAs2/WAs2 from first principles
Authors: Chen Jia , Li Yu-Ke , Dai Jianhui , Cao Chao 
Published: August 2017

AbstractWe investigate the electronic structure of group VI-B transition metal di-arsenides (TAs2, T = Mo, W). By comparing the formation energies, the centrosymmetric di-arsenides compounds are energetically more stable, in contrast to the di-phosphorides (MoP2/WP2). Both compounds can be well described by a two-band model with a pair of well-separated electron/hole bands. The electron/hole carrier density is nearly compensated in MoAs2 (|n
e
− n
h
|/n
h
< 1%). The $${{\mathscr{Z}}}_{2}$$

Z

2

classification for all partially occupied bands are topologically strong (1;001), and therefore robust surface states are expected in these materials. Using the adaptive K-mesh method, no energy degenerate state could be found except the spin degeneracy in the whole Brillouin zone, excluding the possibility of intrinsic Dirac or Weyl points near the Fermi level in the system.