bluuebunny/crossref_metadata_2025 huggingface dataset:
Non-destructive detection of cross-sectional strain and defect structure in an individual Ag five-fold twinned nanowire by 3D electron diffraction mapping
Authors: Fu Xin , Yuan Jun
Published: July 2017

Coherent x-ray diffraction investigations on Ag five-fold twinned nanowires (FTNWs) have drawn controversial conclusions concerning whether the intrinsic 7.35° angular gap could be compensated homogeneously through phase transformation or inhomogeneously by forming disclination strain field. In those studies, the x-ray techniques only provided an ensemble average of the structural information from all the Ag nanowires. Here, using three-dimensional (3D) electron diffraction mapping approach, we non-destructively explore the cross-sectional strain and the related strain-relief defect structures of an individual Ag FTNW with diameter about 30 nm. The quantitative analysis of the fine structure of intensity distribution combining with kinematic electron diffraction simulation confirms that for such a Ag FTNW, the intrinsic 7.35° angular deficiency results in an inhomogeneous strain field within each single crystalline segment consistent with the disclination model of stress-relief. Moreover, the five crystalline segments are found to be strained differently. Modeling analysis in combination with system energy calculation further indicates that the elastic strain energy within some crystalline segments, could be partially relieved by the creation of stacking fault layers near the twin boundaries. Our study demonstrates that 3D electron diffraction mapping is a powerful tool for the cross-sectional strain analysis of complex 1D nanostructures.
Determination of the Solid Electrolyte Interphase Structure Grown on a Silicon Electrode Using a Fluoroethylene Carbonate Additive
Authors: Veith Gabriel M. , Doucet Mathieu , Sacci Robert L. , Vacaliuc Bogdan , Baldwin J. Kevin , Browning James F.
Published: July 2017

In this work we explore how an electrolyte additive (fluorinated ethylene carbonate – FEC) mediates the thickness and composition of the solid electrolyte interphase formed over a silicon anode in situ as a function of state-of-charge and cycle. We show the FEC condenses on the surface at open circuit voltage then is reduced to C-O containing polymeric species around 0.9 V (vs. Li/Li+). The resulting film is about 50 Å thick. Upon lithiation the SEI thickens to 70 Å and becomes more organic-like. With delithiation the SEI thins by 13 Å and becomes more inorganic in nature, consistent with the formation of LiF. This thickening/thinning is reversible with cycling and shows the SEI is a dynamic structure. We compare the SEI chemistry and thickness to 280 Å thick SEI layers produced without FEC and provide a mechanism for SEI formation using FEC additives.
Antecedent soil moisture prior to freezing can affect quantity, composition and stability of soil dissolved organic matter during thaw
Authors: Wu Haohao , Xu Xingkai , Cheng Weiguo , Fu Pingqing , Li Fayun
Published: July 2017

There are large amounts of dissolved organic matter (DOM) released into the soil during spring thaw, but its bioavailability and components are still unknown. The quantity, composition and stability of DOM in water extracts of forest soils during thaw were studied after two-month freezing with 9 levels of soil moisture ranging from 10% to 90% water-filled pore space (WFPS), by measuring soil carbon dioxide (CO2) flux, biodegradable dissolved organic carbon (BDOC) and nitrogen (BDON), ultraviolet absorbance and parallel factor analysis of fluorescence excitation-emission matrices. Concentrations of BDOC, BDON, DOC and DON were lowest around 30% WFPS and relatively higher and lower soil moisture both increased DOM and BDOM concentrations in thawing soil. With increasing WFPS, the dominant component of soil DOM changed from humic acid-like substances to fulvic acid-like substances and the biological origin of DOM increased gradually. The protein-like component accounted for 8–20% of soil DOM and was affected by vegetation type and WFPS singly and interactively. The results implied that forest soils with more than 50% WFPS before winter freezing could release large amounts of fulvic acid-like DOM, which would be easily biodegraded and emitted as CO2 or run off with ground water during spring snow thaw.
Structure of Chorismate Mutase-like Domain of DAHPS from Bacillus subtilis Complexed with Novel Inhibitor Reveals Conformational Plasticity of Active Site
Authors: Pratap Shivendra , Dev Aditya , Kumar Vijay , Yadav Ravi , Narwal Manju , Tomar Shailly , Kumar Pravindra
Published: July 2017

3-deoxy-D-arabino-heptulosonate-7-phosphate-synthase (DAHPS) is the first enzyme of the shikimate pathway and is responsible for the synthesis of aromatic amino acids in microorganisms. This pathway is an attractive target for antimicrobial drugs. In Bacillus subtilis, the N-terminal domain of the bifunctional DAHPS enzyme belongs to an AroQ class of chorismate mutase and is functionally homologous to the downstream AroH class chorismate mutase. This is the first structure of chorismate mutase, AroQ (BsCM_2) enzyme from Bacillus subtilis in complex with citrate and chlorogenic acid at 1.9 Å and 1.8 Å resolution, respectively. This work provides the structural basis of ligand binding into the active site of AroQ class of chorismate mutase, while accompanied by the conformational flexibility of active site loop. Molecular dynamics results showed that helix H2′ undergoes uncoiling at the first turn and increases the mobility of loop L1′. The side chains of Arg45, Phe46, Arg52 and Lys76 undergo conformational changes, which may play an important role in DAHPS regulation by the formation of the domain-domain interface. Additionally, binding studies showed that the chlorogenic acid binds to BsCM_2 with a higher affinity than chorismate. These biochemical and structural findings could lead to the development of novel antimicrobial drugs.
Mass Spectrometry Imaging proves differential absorption profiles of well-characterised permeability markers along the crypt-villus axis
Authors: Nilsson Anna , Peric Alexandra , Strimfors Marie , Goodwin Richard J. A. , Hayes Martin A. , Andrén Per E. , Hilgendorf Constanze
Published: July 2017

Knowledge about the region-specific absorption profiles from the gastrointestinal tract of orally administered drugs is a critical factor guiding dosage form selection in drug development. We have used a novel approach to study three well-characterized permeability and absorption marker drugs in the intestine. Propranolol and metoprolol (highly permeable compounds) and atenolol (low-moderate permeability compound) were orally co-administered to rats. The site of drug absorption was revealed by high spatial resolution matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) and complemented by quantitative measurement of drug concentration in tissue homogenates. MALDI-MSI identified endogenous molecular markers that illustrated the villi structures and confirmed the different absorption sites assigned to histological landmarks for the three drugs. Propranolol and metoprolol showed a rapid absorption and shorter transit distance in contrast to atenolol, which was absorbed more slowly from more distal sites. This study provides novel insights into site specific absorption for each of the compounds along the crypt-villus axis, as well as confirming a proximal-distal absorption gradient along the intestine. The combined analytical approach allowed the quantification and spatial resolution of drug distribution in the intestine and provided experimental evidence for the suggested absorption behaviour of low and highly permeable compounds.
NADPH oxidase 4 is required for the generation of macrophage migration inhibitory factor and host defense against Toxoplasma gondii infection
Authors: Kim Ji Hye , Lee Jina , Bae Su-Jin , Kim Yeeun , Park Byung-Joon , Choi Jae-Won , Kwon Jaeyul , Cha Guang-Ho , Yoo Heon Jong , Jo Eun-Kyeong , Bae Yun Soo , Lee Young-Ha , Yuk Jae-Min
Published: July 2017

Nicotinamide adenine dinucleotide phosphate (NADPH) oxidases (Nox) are an important family of catalytic enzymes that generate reactive oxygen species (ROS), which mediate the regulation of diverse cellular functions. Although phagocyte Nox2/gp91phox is closely associated with the activation of host innate immune responses, the roles of Nox family protein duringToxoplasma gondii(T.gondii) infection have not been fully investigated. Here, we found thatT.gondii-mediated ROS production was required for the upregulation of macrophage migration inhibitory factor (MIF) mRNA and protein levels via activation of mitogen-activated protein kinase and nuclear factor-κB signaling in macrophages. Interestingly, MIF knockdown led to a significant increase in the survival of intracellularT.gondiiin bone marrow-derived macrophages (BMDMs). Moreover, Nox4 deficiency, but not Nox2/gp91phox and the cytosolic subunit p47phox, resulted in enhanced survival of the intracellularT.gondiiRH strain and impaired expression ofT.gondii-mediated MIF in BMDMs. Additionally,Nox4-deficient mice showed increased susceptibility to virulent RH strain infection and increased cyst burden in brain tissues and low levels of MIF expression following infection with the avirulent ME49 strain. Collectively, our findings indicate that Nox4-mediated ROS generation plays a central role in MIF production and resistance toT.gondiiinfection.
Transient regulation of three clustered tomato class-I small heat-shock chaperone genes by ethylene is mediated by SlMADS-RIN transcription factor
Authors: Shukla Vijaya , Upadhyay Rakesh K. , Tucker Mark L. , Giovannoni James J. , Rudrabhatla Sairam V. , Mattoo Autar K.
Published: July 2017

Clustered class-I small heat-shock protein (sHSP) chaperone genes, SlHSP17.6, SlHSP20.0 and SlHSP20.1, in tomato are demonstrated to be transcriptionally regulated by ethylene during mature green (MG) fruit transition into ripening. These genes are constitutively expressed at MG fruit stage in two different tomato genotypes as well as in their ripening mutants, including rin, nor and Nr, and an ethylene-deficient transgenic line, ACS2-antisense. Notably, ethylene treatment of the MG fruit led to significant sHSP gene suppression in both wild-types, ACS2-antisense, nor/nor and Nr/Nr, but not the rin/rin mutant. Inability of ethylene to suppress sHSP genes in rin/rin mutant, which harbors MADS-RIN gene mutation, suggests that MADS-RIN transcription factor regulates the expression of these genes. Treatment of the wild type and ACS2-antisense fruit with the ethylene-signaling inhibitor, 1-methylcyclopropane (1-MCP), reversed the sHSP gene suppression. Transcripts of representative ethylene-responsive and ripening-modulated genes confirmed and validated sHSP transcript profile patterns. In silico analysis in conjunction with chromatin immunoprecipitation demonstrated MADS-RIN protein binding to specific CArG motifs present in the promoters of these chaperone genes. The results establish MADS-RIN protein as a transcriptional regulator of these chaperone genes in an ethylene-dependent manner, and that MADS-RIN protein-regulation of sHSPs is integral to tomato fruit ripening.
Virus and dsRNA-triggered transcriptional responses reveal key components of honey bee antiviral defense
Authors: Brutscher Laura M. , Daughenbaugh Katie F. , Flenniken Michelle L.
Published: July 2017

Recent high annual losses of honey bee colonies are associated with many factors, including RNA virus infections. Honey bee antiviral responses include RNA interference and immune pathway activation, but their relative roles in antiviral defense are not well understood. To better characterize the mechanism(s) of honey bee antiviral defense, bees were infected with a model virus in the presence or absence of dsRNA, a virus associated molecular pattern. Regardless of sequence specificity, dsRNA reduced virus abundance. We utilized next generation sequencing to examine transcriptional responses triggered by virus and dsRNA at three time-points post-infection. Hundreds of genes exhibited differential expression in response to co-treatment of dsRNA and virus. Virus-infected bees had greater expression of genes involved in RNAi, Toll, Imd, and JAK-STAT pathways, but the majority of differentially expressed genes are not well characterized. To confirm the virus limiting role of two genes, including the well-characterized gene, dicer, and a probable uncharacterized cyclin dependent kinase in honey bees, we utilized RNAi to reduce their expression in vivo and determined that virus abundance increased, supporting their involvement in antiviral defense. Together, these results further our understanding of honey bee antiviral defense, particularly the role of a non-sequence specific dsRNA-mediated antiviral pathway.
Photosynthetic capacity of senescent leaves for a subtropical broadleaf deciduous tree species Liquidambar formosana Hance
Authors: Luo Zidong , Guan Huade , Zhang Xinping , Liu Na
Published: July 2017

Photosynthetic capacity and leaf life span generally determine how much carbon a plant assimilates during the growing season. Leaves of deciduous tree species start senescence in late season, but whether the senescent leaves still retain capacity of carbon assimilation remains a question. In this study, we investigated leaf phenology and photosynthesis of a subtropical broadleaf deciduous tree species Liquidambar formosana Hance in the central southern continental China. The results show that L. formosana has extended leaf senescence (more than 2 months) with a substantial number of red leaves persisting on the tree. Leaf photosynthetic capacity decreases over season, but the senescent red leaves still maintain relatively high photosynthetic capacity at 42%, 66% and 66% of the mature leaves for net photosynthesis rate, apparent quantum yield, and quantum yield at the light compensation point, respectively. These results indicate that L. formosana may still contribute to carbon sink during leaf senescence.
Studies of global and local entanglements of individual protein chains using the concept of knotoids
Authors: Goundaroulis Dimos , Dorier Julien , Benedetti Fabrizio , Stasiak Andrzej
Published: July 2017

We study here global and local entanglements of open protein chains by implementing the concept of knotoids. Knotoids have been introduced in 2012 by Vladimir Turaev as a generalization of knots in 3-dimensional space. More precisely, knotoids are diagrams representing projections of open curves in 3D space, in contrast to knot diagrams which represent projections of closed curves in 3D space. The intrinsic difference with classical knot theory is that the generalization provided by knotoids admits non-trivial topological entanglement of the open curves provided that their geometry is frozen as it is the case for crystallized proteins. Consequently, our approach doesn’t require the closure of chains into loops which implies that the geometry of analysed chains does not need to be changed by closure in order to characterize their topology. Our study revealed that the knotoid approach detects protein regions that were classified earlier as knotted and also new, topologically interesting regions that we classify as pre-knotted.
Inactivation of DNase1L2 and DNase2 in keratinocytes suppresses DNA degradation during epidermal cornification and results in constitutive parakeratosis
Authors: Fischer Heinz , Buchberger Maria , Napirei Markus , Tschachler Erwin , Eckhart Leopold
Published: July 2017

The stratum corneum of the epidermis constitutes the mammalian skin barrier to the environment. It is formed by cornification of keratinocytes, a process which involves the removal of nuclear DNA. Here, we investigated the mechanism of cornification-associated DNA degradation by generating mouse models deficient of candidate DNA-degrading enzymes and characterizing their epidermal phenotypes. In contrast to Dnase1l2−/− mice and keratinocyte-specific DNase2 knockout mice (Dnase2
Δep
), Dnase1l2−/−Dnase2
Δep
mice aberrantly retained nuclear DNA in the stratum corneum, a phenomenon commonly referred to as parakeratosis. The DNA within DNase1L2/DNase2-deficient corneocytes was partially degraded in a DNase1-independent manner. Isolation of corneocytes, i.e. the cornified cell components of the stratum corneum, and labelling of DNA demonstrated that corneocytes of Dnase1l2−/−Dnase2
Δep
mice contained DNA in a nucleus-shaped compartment that also contained nucleosomal histones but lacked the nuclear intermediate filament protein lamin A/C. Parakeratosis was not associated with altered corneocyte resistance to mechanical stress, changes in transepidermal water loss, or inflammatory infiltrates in Dnase1l2−/−Dnase2
Δep
mice. The results of this study suggest that cornification of epidermal keratinocytes depends on the cooperation of DNase1L2 and DNase2 and indicate that parakeratosis per se does not suffice to cause skin pathologies.
Genome-wide identification of thyroid hormone receptor targets in the remodeling intestine during Xenopus tropicalis metamorphosis
Authors: Fu Liezhen , Das Biswajit , Matsuura Kazuo , Fujimoto Kenta , Heimeier Rachel A. , Shi Yun-Bo
Published: July 2017

Thyroid hormone (T3) affects development and metabolism in vertebrates. We have been studying intestinal remodeling during T3-dependent Xenopus metamorphosis as a model for organ maturation and formation of adult organ-specific stem cells during vertebrate postembryonic development, a period characterized by high levels of plasma T3. T3 is believed to affect development by regulating target gene transcription through T3 receptors (TRs). While many T3 response genes have been identified in different animal species, few have been shown to be direct target genes in vivo, especially during development. Here we generated a set of genomic microarray chips covering about 8000 bp flanking the predicted transcription start sites in Xenopus tropicalis for genome wide identification of TR binding sites. By using the intestine of premetamorphic tadpoles treated with or without T3 and for chromatin immunoprecipitation assays with these chips, we determined the genome-wide binding of TR in the control and T3-treated tadpole intestine. We further validated TR binding in vivo and analyzed the regulation of selected genes. We thus identified 278 candidate direct TR target genes. We further provided evidence that these genes are regulated by T3 and likely involved in the T3-induced formation of adult intestinal stem cells during metamorphosis.
Multicomponent High-throughput Drug Screening via Inkjet Printing to Verify the Effect of Immunosuppressive Drugs on Immune T Lymphocytes
Authors: Choi Moonhyun , Hwang Jangsun , Choi Jonghoon , Hong Jinkee
Published: July 2017

High-throughput drug screening based on a multi-component array can be used to identify a variety of interaction between cells and drugs for suitable purposes. The signaling of immune cells is affected by specific proteins, diverse drug combinations, and certain immunosuppressive drugs. The effect of a drug on an organism is usually complex and involves interactions at multiple levels. Herein, we developed a multilayer fabricating system through the high-throughput assembly of nanofilms with inkjet printing to investigate the effects of immunosuppressive drugs. Immunosuppressive drugs or agents occasionally cause side effects depending on drug combinations or a patient’s condition. By incorporating various drug combinations for understanding interaction between drugs and immune cells, we were able to develop an immunological drug screening kit with immunosuppressive drugs. Moreover, the ability to control the combination of drugs, as well as their potential for high-throughput preparation should be of great benefit to the biomedical and bioanalytical field.
An extended PROSPECT: Advance in the leaf optical properties model separating total chlorophylls into chlorophyll a and b
Authors: Zhang Yao , Huang Jingfeng , Wang Fumin , Blackburn George Alan , Zhang Hankui K. , Wang Xiuzhen , Wei Chuanwen , Zhang Kangyu , Wei Chen
Published: July 2017

The PROSPECT leaf optical model has, to date, well-separated the effects of total chlorophyll and carotenoids on leaf reflectance and transmittance in the 400–800 nm. Considering variations in chlorophyll a:b ratio with leaf age and physiological stress, a further separation of total plant-based chlorophylls into chlorophyll a and chlorophyll b is necessary for advanced monitoring of plant growth. In this study, we present an extended version of PROSPECT model (hereafter referred to as PROSPECT-MP) that can combine the effects of chlorophyll a, chlorophyll b and carotenoids on leaf directional hemispherical reflectance and transmittance (DHR and DHT) in the 400–800 nm. The LOPEX93 dataset was used to evaluate the capabilities of PROSPECT-MP for spectra modelling and pigment retrieval. The results show that PROSPECT-MP can both simultaneously retrieve leaf chlorophyll a and b, and also performs better than PROSPECT-5 in retrieving carotenoids concentrations. As for the simulation of DHR and DHT, the performances of PROSPECT-MP are similar to that of PROSPECT-5. This study demonstrates the potential of PROSPECT-MP for improving capabilities of remote sensing of leaf photosynthetic pigments (chlorophyll a, chlorophyll b and carotenoids) and for providing a framework for future refinements in the modelling of leaf optical properties.
Chelant Enhanced Solution Processing for Wafer Scale Synthesis of Transition Metal Dichalcogenide Thin Films
Authors: Ionescu Robert , Campbell Brennan , Wu Ryan , Aytan Ece , Patalano Andrew , Ruiz Isaac , Howell Stephen W. , McDonald Anthony E. , Beechem Thomas E. , Mkhoyan K. Andre , Ozkan Mihrimah , Ozkan Cengiz S.
Published: July 2017

It is of paramount importance to improve the control over large area growth of high quality molybdenum disulfide (MoS2) and other types of 2D dichalcogenides. Such atomically thin materials have great potential for use in electronics, and are thought to make possible the first real applications of spintronics. Here in, a facile and reproducible method of producing wafer scale atomically thin MoS2 layers has been developed using the incorporation of a chelating agent in a common organic solvent, dimethyl sulfoxide (DMSO). Previously, solution processing of a MoS2 precursor, ammonium tetrathiomolybdate ((NH4)2MoS4), and subsequent thermolysis was used to produce large area MoS2 layers. Our work here shows that the use of ethylenediaminetetraacetic acid (EDTA) in DMSO exerts superior control over wafer coverage and film thickness, and the results demonstrate that the chelating action and dispersing effect of EDTA is critical in growing uniform films. Raman spectroscopy, photoluminescence (PL), x-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FTIR), atomic force microscopy (AFM) and high-resolution scanning transmission electron microscopy (HR-STEM) indicate the formation of homogenous few layer MoS2 films at the wafer scale, resulting from the novel chelant-in-solution method.
Primary fibroblasts from CSPα mutation carriers recapitulate hallmarks of the adult onset neuronal ceroid lipofuscinosis
Authors: Benitez Bruno A. , Sands Mark S.
Published: July 2017

Mutations in the co- chaperone protein, CSPα, cause an autosomal dominant, adult-neuronal ceroid lipofuscinosis (AD-ANCL). The current understanding of CSPα function exclusively at the synapse fails to explain the autophagy-lysosome pathway (ALP) dysfunction in cells from AD-ANCL patients. Here, we demonstrate unexpectedly that primary dermal fibroblasts from pre-symptomatic mutation carriers recapitulate in vitro features found in the brains of AD-ANCL patients including auto-fluorescent storage material (AFSM) accumulation, CSPα aggregates, increased levels of lysosomal proteins and lysosome enzyme activities. AFSM accumulation correlates with CSPα aggregation and both are susceptible to pharmacological modulation of ALP function. In addition, we demonstrate that endogenous CSPα is present in the lysosome-enriched fractions and co-localizes with lysosome markers in soma, neurites and synaptic boutons. Overexpression of CSPα wild-type (WT) decreases lysotracker signal, secreted lysosomal enzymes and SNAP23-mediated lysosome exocytosis. CSPα WT, mutant and aggregated CSPα are degraded mainly by the ALP but this disease-causing mutation exhibits a faster rate of degradation. Co-expression of both WT and mutant CSPα cause a block in the fusion of autophagosomes/lysosomes. Our data suggest that aggregation‐dependent perturbation of ALP function is a relevant pathogenic mechanism for AD-ANCL and supports the use of AFSM or CSPα aggregation as biomarkers for drug screening purposes.
Metabolic pathway and cell adaptation mechanisms revealed through genomic, proteomic and transcription analysis of a Sphingomonas haloaromaticamans strain degrading ortho-phenylphenol
Authors: Perruchon Chiara , Vasileiadis Sotirios , Rousidou Constantina , Papadopoulou Evangelia S. , Tanou Georgia , Samiotaki Martina , Garagounis Constantinos , Molassiotis Athanasios , Papadopoulou Kalliope K. , Karpouzas Dimitrios G.
Published: July 2017

Ortho-phenylphenol (OPP) is a fungicide contained in agro-industrial effluents produced by fruit-packaging plants. Within the frame of developing bio-strategies to detoxify these effluents, an OPP-degrading Sphingomonas haloaromaticamans strain was isolated. Proteins/genes with a putative catabolic role and bacterium adaptation mechanisms during OPP degradation were identified via genomic and proteomic analysis. Transcription analysis of all putative catabolic genes established their role in the metabolism of OPP. The formation of key transformation products was verified by chromatographic analysis. Genomic analysis identified two orthologous operons encoding the ortho-cleavage of benzoic acid (BA) (ben/cat). The second ben/cat operon was located in a 92-kb scaffold along with (i) an operon (opp) comprising genes for the transformation of OPP to BA and 2-hydroxypenta-2,4-dienoate (and genes for its transformation) and (ii) an incomplete biphenyl catabolic operon (bph). Proteomics identified 13 up-regulated catabolic proteins when S. haloaromaticamans was growing on OPP and/or BA. Transcription analysis verified the key role of the catabolic operons located in the 92-kb scaffold, and flanked by transposases, on the transformation of OPP by S. haloaromaticamans. A flavin-dependent monoxygenase (OppA1), one of the most up-regulated proteins in the OPP-growing cells, was isolated via heterologous expression and its catabolic activity was verified in vitro.
Design and validation of a DNA-microarray for phylogenetic analysis of bacterial communities in different oral samples and dental implants
Authors: Parolin Carola , Giordani Barbara , Ñahui Palomino Rogers Alberto , Biagi Elena , Severgnini Marco , Consolandi Clarissa , Caredda Giada , Storelli Stefano , Strohmenger Laura , Vitali Beatrice
Published: July 2017

The quali-quantitative characterization of the oral microbiota is crucial for an exhaustive knowledge of the oral ecology and the modifications of the microbial composition that occur during periodontal pathologies. In this study, we designed and validated a new phylogenetic DNA-microarray (OralArray) to quickly and reliably characterize the most representative bacterial groups that colonize the oral cavity. The OralArray is based on the Ligation Detection Reaction technology associated to Universal Arrays (LDR-UA), and includes 22 probe sets targeted to bacteria belonging to the phyla Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, Fusobacteria, and Spirochaete. The tool is characterized by high specificity, sensitivity and reproducibility. The OralArray was successfully tested and validated on different oral samples (saliva, lingual plaque, supragingival plaque, and healing cap) collected from 10 healthy subjects. For each specimen, a microbial signature was obtained, and our results established the presence of an oral microbial profile specific for each subject. Moreover, the tool was applied to evaluate the efficacy of a disinfectant treatment on the healing caps before their usage. The OralArray is, thus, suitable to study the microbiota associated with various oral sites and to monitor changes arising from therapeutic treatments.
Tonoplast-localized nitrate uptake transporters involved in vacuolar nitrate efflux and reallocation in Arabidopsis
Authors: He Ya-Ni , Peng Jia-Shi , Cai Yao , Liu De-Fen , Guan Yuan , Yi Hong-Ying , Gong Ji-Ming
Published: July 2017

A great proportion of nitrate taken up by plants is stored in vacuoles. Vacuolar nitrate accumulation and release is of great importance to nitrate reallocation and efficient utilization. However, how plants mediate nitrate efflux from vacuoles to cytoplasm is largely unknown. The current study identified NPF5.11, NPF5.12 and NPF5.16 as vacuolar nitrate efflux transporters in Arabidopsis. Histochemical analysis showed that NPF5.11, NPF5.12 and NPF5.16 were expressed preferentially in root pericycle cells and xylem parenchyma cells, and further analysis showed that these proteins were tonoplast-localized. Functional characterization using cRNA-injected Xenopus laevis oocytes showed that NPF5.11, NPF5.12 and NPF5.16 were low-affinity, pH-dependent nitrate uptake transporters. In npf5.11 npf5.12 npf5.16 triple mutant lines, more root-fed 15NO3− was translocated to shoots compared to the wild type control. In the NPF5.12 overexpression lines, proportionally less nitrate was maintained in roots. These data together suggested that NPF5.11, NPF5.12 and NPF5.16 might function to uptake nitrate from vacuoles into cytosol, thus serving as important players to modulate nitrate allocation between roots and shoots.
Continuous and scalable polymer capsule processing for inertial fusion energy target shell fabrication using droplet microfluidics
Authors: Li Jin , Lindley-Start Jack , Porch Adrian , Barrow David
Published: July 2017

High specification, polymer capsules, to produce inertial fusion energy targets, were continuously fabricated using surfactant-free, inertial centralisation, and ultrafast polymerisation, in a scalable flow reactor. Laser-driven, inertial confinement fusion depends upon the interaction of high-energy lasers and hydrogen isotopes, contained within small, spherical and concentric target shells, causing a nuclear fusion reaction at ~150 M°C. Potentially, targets will be consumed at ~1 M per day per reactor, demanding a 5000x unit cost reduction to ~$0.20, and is a critical, key challenge. Experimentally, double emulsions were used as templates for capsule-shells, and were formed at 20 Hz, on a fluidic chip. Droplets were centralised in a dynamic flow, and their shapes both evaluated, and mathematically modeled, before subsequent shell solidification. The shells were photo-cured individually, on-the-fly, with precisely-actuated, millisecond-length (70 ms), uniform-intensity UV pulses, delivered through eight, radially orchestrated light-pipes. The near 100% yield rate of uniform shells had a minimum 99.0% concentricity and sphericity, and the solidification processing period was significantly reduced, over conventional batch methods. The data suggest the new possibility of a continuous, on-the-fly, IFE target fabrication process, employing sequential processing operations within a continuous enclosed duct system, which may include cryogenic fuel-filling, and shell curing, to produce ready-to-use IFE targets.
Conflict between conservation and development: cash forest encroachment in Asian elephant distributions
Authors: Liu Peng , Wen Hui , Harich Franziska K. , He Changhuan , Wang Lanxin , Guo Xianming , Zhao Jianwei , Luo Aidong , Yang Hongpei , Sun Xiao , Yu Yang , Zheng Shaobo , Guo Jing , Li Li , Zhang Li
Published: July 2017

Over the last 4 decades, China has undergone major economic development, resulting in considerable impacts on its wildlife populations and habitats. It is essential to quantify the conflict between development and conservation to assist with policy-making because forestry policies and market trends affected indirectly the distribution of Asian elephants. Here, we mapped the historical distribution of elephants versus human land use. Elephant distributions appear to occur in unbroken natural forests only. However, over the 40-year period, the distribution ranges have become smaller and fragmented, with natural forest area also declining by 16%. The monoculture of cash trees is encroaching on natural forests. Over the past 10 years, rubber plantations have become concentrated in the south, with extensive natural forests and scattered rubber farms being converted to tea plantations, due to changes in governmental policies and product prices. Through mapping the spatial changes in the distribution of rubber and tea plantations, our study is expected to help local managers to incorporate the needs of endangered elephants through creating space when planning plantations, especially in Xishuangbanna and the south part of Pu’er. In conclusion, restoring elephant habitat and establishing ecological corridors are critical for the survival of elephants in this region.
The burdens of lung cancer involved multiple primary cancers and its occurring patterns–SEER Analysis between 1973 and 2006
Authors: Mao Rui , Chen Tao , Zhou Fangyu , Jiang Weili , Yang Xiaorong , Ai Zisheng , Li Mu , Qin Linlin , Wang Long , Fei Ke , Chen Chang
Published: July 2017

The prognosis of malignancies has improved in recent years, subsequent primary cancers (SPCs) have become more frequent. This study investigates the patterns of lung cancer involved multiple primary cancers. We enrolled 206,619 primary lung cancer patients and 2,071,922 patients with other primary malignancies from Surveillance, Epidemiology and End Results (SEER) database. Observed annual risk (OAR) and absolute numbers were used to describe the risk of SPC and observed cases of SPC per 10,000 person-years at risk. Overall, OAR of SPCs following lung cancer was 176.28. At follow-up, 41.26% of SPCs occurred within 12–59 months while the highest OAR appeared after 120 months. The overall OAR of subsequent lung cancer after other malignancies was 27.90. Overall, the highest OAR and the highest absolute numbers of subsequent lung cancers were noticed 60–119 months and over 120 months post-diagnosis, respectively. Ten related cancers were listed. Our findings encourage surveillance for 10 common SPCs in lung cancer survivors during follow-up as well as screening for lung cancer after 10 common malignancies.
CXCL10 is produced in hepatitis A virus-infected cells in an IRF3-dependent but IFN-independent manner
Authors: Sung Pil Soo , Hong Seon-Hui , Lee Jeewon , Park Su-Hyung , Yoon Seung Kew , Chung Woo Jin , Shin Eui-Cheol
Published: July 2017

Acute hepatitis A caused by hepatitis A virus (HAV) infection is accompanied by severe liver injury in adult patients, and the liver injury is associated with the production of chemokines. Herein, we investigated the mechanism of how HAV infection induces the production of CXCR3 and CCR5 chemokines, such as CXCL10, CCL4 and CCL5. The production of CXCL10, CCL4 and CCL5 was markedly increased by HAV (HM-175/18f) infection in the culture of primary human hepatocytes and HepG2 cells. In particular, CXCL10 was produced in HAV-infected cells, not in neighboring uninfected cells. Moreover, these chemokines were significantly increased in the sera of acute hepatitis A patients. The production of IFN-λs was also robustly induced by HAV infection, and the blocking of secreted IFN-λs partially abrogated the production of CCL4 and CCL5 in HAV-infected cells. However, CXCL10 production was not decreased by the blocking of IFN-λs. Instead, CXCL10 production was reduced by silencing the expression of RIG-I-like receptor (RLR) signal molecules, such as mitochondrial antiviral signaling protein and interferon regulatory factor 3, in HAV-infected cells. In conclusion, HAV infection strongly induces the production of helper 1 T cell-associated chemokines, particularly CXCL10 via RLR signaling, even without secreted IFNs.
Dietary acrylamide exposure was associated with mild cognition decline among non-smoking Chinese elderly men
Authors: Liu Zhao-min , Tse Lap Ah , Chen Bailing , Wu Suyang , Chan Dicken , Kowk Timothy , Woo Jean , Xiang Yu-Tao , Wong Samuel Yeung-shan
Published: July 2017

The aim of the study is to explore the longitudinal association of dietary acrylamide exposure with cognitive performance in Chinese elderly. The analysis was conducted among 2534 non-smoking elderly men and women based on a prospective study, Mr. and Ms. OS Hong Kong. Dietary acrylamide intake was assessed by food frequency questionnaires with data on local food contamination, derived from the first Hong Kong Total Diet Study. Global cognitive function was assessed by Cantonese version of Mini-Mental State Exam (MMSE) at the baseline and the 4th year of follow-up. Multivariable-adjusted linear and logistic regression models were used to assess the associations of dietary acrylamide with MMSE score changes or risk of poor cognition. The results indicated that among men with MMSE ≥ 18, each one SD increase of acrylamide decreased MMSE score by 7.698% (95%CI: −14.943%, −0.452%; p = 0.037). Logistic regression revealed an increased risk of poor cognition (MMSE ≤ 26) in men with HR of 3.356 (1.064~10.591, p = 0.039). The association became non-significance after further adjustment for telomere length. No significant association was observed in women. Dietary acrylamide exposure was associated with a mild cognitive decline or increased risk of poor cognition over a 4-year period in non-smoking Chinese elderly men.
Non-invasive 3D and 360° optical imaging of micro-particles
Authors: El Arnaout Toufic , Cullen P. J.
Published: July 2017

Scanning electron microscopy and X-ray microtomography are useful methods for high resolution shape imaging. Visible microscopy is also common, however, developing a low-cost and customizable system for surface and shape investigation of optically active particles is challenging. In this work, we demonstrate an assembly offering good light sensitivity, flexibility of illumination and contrasts from varying angles. The design was applied, together with recent programs for focus-stacking, to analyze crystals of taurine, L-glutamic acid, acetylsalicylic acid, and copper sulfate, along with digital 3D-360° modelling of phosphorescent [Ru(bpy)3]Cl2 and strontium aluminate particles. We further tested the approach for real time monitoring of size, shape and texture analysis of fat filled milk particles and acid whey powders. The findings show proof of concept for detailed feature imaging of particles directly from the process environment.
Comparisons of three different methods for defining sarcopenia: An aspect of cardiometabolic risk
Authors: Kim Tae Nyun , Park Man Sik , Lee Eun Joo , Chung Hye Soo , Yoo Hye Jin , Kang Hyun Joo , Song Wook , Baik Sei Hyun , Choi Kyung Mook
Published: July 2017

Appraisal of muscle mass is important when considering the serious consequences of sarcopenia in an aging society. However, the associations between sarcopenia and its clinical outcomes might vary according to the method applied in its diagnosis. We compared the relationships between cardiometabolic risk parameters and sarcopenia defined according to three different diagnostic methods using dual-energy X-ray absorptiometry (DXA) and computed tomography (CT). Appendicular skeletal muscle mass (ASM) adjusted by height squared and BMI (ASM/height2 and ASM/BMI) measured using DXA and thigh muscle cross-sectional area (tmCSA) adjusted by weight (tmCSA/weight) measured using CT were used as indices of muscle mass. Sarcopenia was defined as two standard deviations below either the mean ASM/height2, ASM/BMI, or tmCSA/weight of a young reference group. ASM/BMI and tmCSA/weight showed a negative relationship with several components of metabolic syndrome and HOMA-IR, whereas ASM/height2 was positively associated with theses cardiometabolic risk factors. Logistic regression analyses demonstrated that ASM/BMI-defined sarcopenia was significantly associated with increased HOMA-IR (P = 0.01) and prevalence of visceral obesity (P = 0.03) and metabolic syndrome (P = 0.025), while ASM/height2- and tmCSA/weight-defined sarcopenia were not. ASM/BMI-defined sarcopenia exhibits a closer relationship with cardiometabolic risk factors than does ASM/height2- or tmCSA/weight-defined sarcopenia.
The association of serum adiponectin with abdominal aortic calcification in Japanese male hemodialysis patients: a cross-sectional observational study
Authors: Sakura Takeshi , Okuno Senji , Nishio Eriko , Norimine Kyoko , Ishimura Eiji , Yamakawa Tomoyuki , Shoji Shigeichi , Inaba Masaaki
Published: July 2017

The negative relation of serum adiponectin to atherosclerosis becomes a positive association in patients with chronic kidney disease (CKD). We conducted a small-scale cross-sectional observational study, in 101 Japanese male hemodialysis patients, to examine the relationship of serum adiponectin and leptin to abdominal aortic calcification (AAC). The presence of AAC was evaluated from simple X-ray radiographs of the left lateral abdomen. Serum adiponectin was significantly higher in AAC-positive patients [18.8 (13.0–28.1) μg/mL] than in AAC-negative patients [15.4 (8.9–22.8) μg/mL] (p = 0.03), whereas serum leptin did not differ significantly between the two groups. Multiple logistic regression analysis showed that log adiponectin, but not log leptin, was independently and significantly associated in a positive manner with AAC (odds ratio: 16.31, 95% confidence interval: 1.70–156.41, p = 0.02), after adjustment for age, body weight, percentage body fat, hemodialysis duration, prevalence of diabetes mellitus, and other risk factors. In conclusion, we found a positive and independent association of serum adiponectin with AAC in male hemodialysis patients, indicating that the reversed association between serum adiponectin and atherosclerosis in patients with CKD dose not result from increased serum adiponectin due to the impaired urinary secretion.
Recent increased identification and transmission of HIV-1 unique recombinant forms in Sweden
Authors: Neogi Ujjwal , Siddik Abu Bakar , Kalaghatgi Prabhav , Gisslén Magnus , Bratt Göran , Marrone Gaetano , Sönnerborg Anders
Published: July 2017

A temporal increase in non-B subtypes has earlier been described in Sweden by us and we hypothesized that this increased viral heterogeneity may become a hotspot for the development of more complex and unique recombinant forms (URFs) if the epidemics converge. In the present study, we performed subtyping using four automated tools and phylogenetic analysis by RAxML of pol gene sequences (n = 5246) and HIV-1 near full-length genome (HIV-NFLG) sequences (n = 104). A CD4+ T-cell decline trajectory algorithm was used to estimate time of HIV infection. Transmission clusters were identified using the family-joining method. The analysis of HIV-NFLG and pol gene described 10.6% (11/104) and 2.6% (137/5246) of the strains as URFs, respectively. An increasing trend of URFs was observed in recent years by both approaches (p = 0·0082; p < 0·0001). Transmission cluster analysis using the pol gene of all URFs identified 14 clusters with two to eight sequences. Larger transmission clusters of URFs (BF1 and 01B) were observed among MSM who mostly were sero-diagnosed in recent time. Understanding the increased appearance and transmission of URFs in recent years could have importance for public health interventions and the use of HIV-NFLG would provide better statistical support for such assessments.
DYRK1B mutations associated with metabolic syndrome impair the chaperone-dependent maturation of the kinase domain
Authors: Abu Jhaisha Samira , Widowati Esti W. , Kii Isao , Sonamoto Rie , Knapp Stefan , Papadopoulos Chrisovalantis , Becker Walter
Published: July 2017

Two missense mutations of the DYRK1B gene have recently been found to co-segregate with a rare autosomal-dominant form of metabolic syndrome. This gene encodes a member of the DYRK family of protein kinases, which depend on tyrosine autophosphorylation to acquire the catalytically active conformation. The mutations (H90P and R102C) affect a structural element named DYRK homology (DH) box and did not directly interfere with the conformation of the catalytic domain in a structural model of DYRK1B. Cellular assays showed that the mutations did not alter the specific activity of mature kinase molecules. However, a significant part of the mutant DYRK1B protein accumulated in detergent-insoluble cytoplasmic aggregates and was underphosphorylated on tyrosine. The mutant DYRK1B variants were more vulnerable to the HSP90 inhibitor ganetespib and showed enhanced binding to the co-chaperone CDC37 as compared to wild type DYRK1B. These results support the hypothesis that the mutations in the DH box interfere with the maturation of DYRK1B by tyrosine autophosphorylation and compromise the conformational stability of the catalytic domain, which renders the kinase susceptible to misfolding.
Tumor-Derived Exosomes Induce the Formation of Neutrophil Extracellular Traps: Implications For The Establishment of Cancer-Associated Thrombosis
Authors: Leal Ana C. , Mizurini Daniella M. , Gomes Tainá , Rochael Natalia C. , Saraiva Elvira M. , Dias Marcos S. , Werneck Claudio C. , Sielski Micheli S. , Vicente Cristina P. , Monteiro Robson Q.
Published: July 2017

Cancer patients are at an increased risk of developing thromboembolic complications. Several mechanisms have been proposed to explain cancer-associated thrombosis including the release of tumor-derived extracellular vesicles and the activation of host vascular cells. It was proposed that neutrophil extracellular traps (NETs) contribute to the prothrombotic phenotype in cancer. In this study, we evaluated the possible cooperation between tumor-derived exosomes and NETs in cancer-associated thrombosis. Female BALB/c mice were orthotopically injected with 4T1 breast cancer cells. The tumor-bearing animals exhibited increased levels of plasma DNA and myeloperoxidase in addition to significantly increased numbers of circulating neutrophils. Mice were subjected to either Rose Bengal/laser-induced venous thrombosis or ferric chloride-induced arterial thrombosis models. The tumor-bearing mice exhibited accelerated thrombus formation in both models compared to tumor-free animals. Treatment with recombinant human DNase 1 reversed the prothrombotic phenotype of tumor-bearing mice in both models. Remarkably, 4T1-derived exosomes induced NET formation in neutrophils from mice treated with granulocyte colony-stimulating factor (G-CSF). In addition, tumor-derived exosomes interacted with NETs under static conditions. Accordingly, the intravenous administration of 4T1-derived exosomes into G-CSF-treated mice significantly accelerated venous thrombosis in vivo. Taken together, our observations suggest that tumor-derived exosomes and neutrophils may act cooperatively in the establishment of cancer-associated thrombosis.