bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractRecent 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

AbstractPhotosynthetic 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

AbstractWe 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

AbstractThe 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

AbstractThyroid 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

AbstractHigh-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

AbstractThe 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

AbstractIt 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

AbstractMutations 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

AbstractOrtho-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

AbstractThe 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

AbstractA 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

AbstractHigh 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

AbstractOver 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

AbstractThe 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.