bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanowire arrays restore vision in blind mice
Authors: Tang Jing , Qin Nan , Chong Yan , Diao Yupu , Yiliguma  , Wang Zhexuan , Xue Tian , Jiang Min , Zhang Jiayi , Zheng Gengfeng 
Published: February 2018

AbstractThe restoration of light response with complex spatiotemporal features in retinal degenerative diseases towards retinal prosthesis has proven to be a considerable challenge over the past decades. Herein, inspired by the structure and function of photoreceptors in retinas, we develop artificial photoreceptors based on gold nanoparticle-decorated titania nanowire arrays, for restoration of visual responses in the blind mice with degenerated photoreceptors. Green, blue and near UV light responses in the retinal ganglion cells (RGCs) are restored with a spatial resolution better than 100 µm. ON responses in RGCs are blocked by glutamatergic antagonists, suggesting functional preservation of the remaining retinal circuits. Moreover, neurons in the primary visual cortex respond to light after subretinal implant of nanowire arrays. Improvement in pupillary light reflex suggests the behavioral recovery of light sensitivity. Our study will shed light on the development of a new generation of optoelectronic toolkits for subretinal prosthetic devices.
Probing of sub-picometer vertical differential resolutions using cavity plasmons
Authors: Chen Wen , Zhang Shunping , Deng Qian , Xu Hongxing 
Published: February 2018

AbstractPlasmon rulers can be used for resolving ultrasmall environmental, dimensional, and material changes owing to their high sensitivity associated with a light-scattering spectral shift in response to changes in the separation between plasmonic nanostructures. Here, we show, in several experimental setups, how cavity plasmons in a metal nanowire-on-mirror setup can be used to probe vertical dimensional changes with sub-picometer differential resolutions using two carefully chosen material systems. Specifically, we monitor the dielectric layer thickness changes in response to growth using atomic-layer deposition and to thermal expansion, demonstrating a sensitivity of 14-nm spectral shift per Ångström thickness change and 0.58 pm of vertical differential resolution, respectively. The findings confirm theoretical predictions and highlight the potential use of cavity plasmons in some ultrasensitive sensing applications.
Somatic mutagenesis in satellite cells associates with human skeletal muscle aging
Authors: Franco Irene , Johansson Anna , Olsson Karl , Vrtačnik Peter , Lundin Pär , Helgadottir Hafdis T. , Larsson Malin , Revêchon Gwladys , Bosia Carla , Pagnani Andrea , Provero Paolo , Gustafsson Thomas , Fischer Helene , Eriksson Maria 
Published: February 2018

AbstractHuman aging is associated with a decline in skeletal muscle (SkM) function and a reduction in the number and activity of satellite cells (SCs), the resident stem cells. To study the connection between SC aging and muscle impairment, we analyze the whole genome of single SC clones of the leg muscle vastus lateralis from healthy individuals of different ages (21–78 years). We find an accumulation rate of 13 somatic mutations per genome per year, consistent with proliferation of SCs in the healthy adult muscle. SkM-expressed genes are protected from mutations, but aging results in an increase in mutations in exons and promoters, targeting genes involved in SC activity and muscle function. In agreement with SC mutations affecting the whole tissue, we detect a missense mutation in a SC propagating to the muscle. Our results suggest somatic mutagenesis in SCs as a driving force in the age-related decline of SkM function.
Precipitation of binary quasicrystals along dislocations
Authors: Yang Zhiqing , Zhang Lifeng , Chisholm Matthew F. , Zhou Xinzhe , Ye Hengqiang , Pennycook Stephen J. 
Published: February 2018

AbstractDislocations in crystals naturally break the symmetry of the bulk, introducing local atomic configurations with symmetries such as fivefold rings. But dislocations do not usually nucleate aperiodic structure along their length. Here we demonstrate the formation of extended binary quasicrystalline precipitates with Penrose-like random-tiling structures, beginning with chemical ordering within the pentagonal structure at cores of prismatic dislocations in Mg–Zn alloys. Atomic resolution observations indicate that icosahedral chains centered along [0001] pillars of Zn interstitial atoms are formed templated by the fivefold rings at dislocation cores. They subsequently form columns of rhombic and elongated hexagonal tiles parallel to the dislocation lines. Quasicrystalline precipitates are formed by random tiling of these rhombic and hexagonal tiles. Such precipitation may impact dislocation glide and alloy strength.
Quantitative Imaging of Regional Aerosol Deposition, Lung Ventilation and Morphology by Synchrotron Radiation CT
Authors: Porra L. , Dégrugilliers L. , Broche L. , Albu G. , Strengell S. , Suhonen H. , Fodor G. H. , Peták F. , Suortti P. , Habre W. , Sovijärvi A. R. A. , Bayat S. 
Published: February 2018

AbstractTo understand the determinants of inhaled aerosol particle distribution and targeting in the lung, knowledge of regional deposition, lung morphology and regional ventilation, is crucial. No single imaging modality allows the acquisition of all such data together. Here we assessed the feasibility of dual-energy synchrotron radiation imaging to this end in anesthetized rabbits; both in normal lung (n = 6) and following methacholine (MCH)-induced bronchoconstriction (n = 6), a model of asthma. We used K-edge subtraction CT (KES) imaging to quantitatively map the regional deposition of iodine-containing aerosol particles. Morphological and regional ventilation images were obtained, followed by quantitative regional iodine deposition maps, after 5 and 10 minutes of aerosol administration. Iodine deposition was markedly inhomogeneous both in normal lung and after induced bronchoconstrition. Deposition was significantly reduced in the MCH group at both time points, with a strong dependency on inspiratory flow in both conditions (R2 = 0.71; p < 0.0001). We demonstrate for the first time, the feasibility of KES CT for quantitative imaging of lung deposition of aerosol particles, regional ventilation and morphology. Since these are among the main factors determining lung aerosol deposition, we expect this imaging approach to bring new contributions to the understanding of lung aerosol delivery, targeting, and ultimately biological efficacy.
Single amino acid in V2 encoded by TYLCV is responsible for its self-interaction, aggregates and pathogenicity
Authors: Zhao Wenhao , Ji Yinghua , Wu Shuhua , Ma Xiaofang , Li Shuo , Sun Feng , Cheng Zhaobang , Zhou Yijun , Fan Yongjian 
Published: February 2018

AbstractThe V2 protein encoded by Begomovirus is essential for virus infection and is involved in multiple functions, such as virus movement and suppression of the host defence response. In this study, we reported that V2 encoded by the Tomato yellow leaf curl virus (TYLCV), which is one of the most devastating tomato-infecting begomoviruses, could interact with itself and a S71A mutation of V2 (V2S71A) abolished its self-interaction. Fluorescence results showed that V2 localized primarily in the cytoplasm and around the nucleus. Site-directed mutagenesis V2S71A had the similar subcellular localization, but V2S71A formed fewer large aggregates in the cytoplasm compared to wild-type V2, whereas the level of aggregates came to a similar after treatment with MG132, which indicates that the S71A mutation might affect 26S proteasome-mediated degradation of V2 aggregates. Meanwhile, heterologous expression of V2S71A from a Potato virus X vector induced mild symptoms compared to wild-type V2, delay of virus infection associated with mild symptoms was observed in plants inoculated with TYLCV-S71A, which indicates that the amino acid on position 71 is also involved in the pathogenicity of V2. To the best of our knowledge, this report is the first to state that the S71A mutation of V2 encoded by TYLCV affects the self-interaction, aggregate formation and pathogenicity of V2.
The cytoprotective role of DJ-1 and p45 NFE2 against human primary alveolar type II cell injury and emphysema
Authors: Tan Li Hui , Bahmed Karim , Lin Chih-Ru , Marchetti Nathaniel , Bolla Sudhir , Criner Gerard J. , Kelsen Steven , Madesh Muniswamy , Kosmider Beata 
Published: February 2018

AbstractEmphysema is characterized by irreversibly enlarged airspaces and destruction of alveolar walls. One of the factors contributing to this disease pathogenesis is an elevation in extracellular matrix (ECM) degradation in the lung. Alveolar type II (ATII) cells produce and secrete pulmonary surfactants and proliferate to restore the epithelium after damage. We isolated ATII cells from control non-smokers, smokers and patients with emphysema to determine the role of NFE2 (nuclear factor, erythroid-derived 2). NFE2 is a heterodimer composed of two subunits, a 45 kDa (p45 NFE2) and 18 kDa (p18 NFE2) polypeptides. Low expression of p45 NFE2 in patients with emphysema correlated with a high ECM degradation. Moreover, we found that NFE2 knockdown increased cell death induced by cigarette smoke extract. We also studied the cross talk between p45 NFE2 and DJ-1. DJ-1 protein is a redox-sensitive chaperone that protects cells from oxidative stress. We detected that cigarette smoke significantly increased p45 NFE2 levels in DJ-1 KO mice compared to wild-type mice. Our results indicate that p45 NFE2 expression is induced by exposure to cigarette smoke, has a cytoprotective activity against cell injury, and its downregulation in human primary ATII cells may contribute to emphysema pathogenesis.
A mouse model of miR-96, miR-182 and miR-183 misexpression implicates miRNAs in cochlear cell fate and homeostasis
Authors: Weston Michael D. , Tarang Shikha , Pierce Marsha L. , Pyakurel Umesh , Rocha-Sanchez Sonia M. , McGee JoAnn , Walsh Edward J. , Soukup Garrett A. 
Published: February 2018

AbstractGermline mutations in Mir96, one of three co-expressed polycistronic miRNA genes (Mir96, Mir182, Mir183), cause hereditary hearing loss in humans and mice. Transgenic FVB/NCrl- Tg(GFAP-Mir183,Mir96,Mir182)MDW1 mice (Tg1MDW), which overexpress this neurosensory-specific miRNA cluster in the inner ear, were developed as a model system to identify, in the aggregate, target genes and biologic processes regulated by the miR-183 cluster. Histological assessments demonstrate Tg1MDW/1MDW homozygotes have a modest increase in cochlear inner hair cells (IHCs). Affymetrix mRNA microarray data analysis revealed that downregulated genes in P5 Tg1MDW/1MDW cochlea are statistically enriched for evolutionarily conserved predicted miR-96, miR-182 or miR-183 target sites. ABR and DPOAE tests from 18 days to 3 months of age revealed that Tg1MDW/1MDW homozygotes develop progressive neurosensory hearing loss that correlates with histologic assessments showing massive losses of both IHCs and outer hair cells (OHCs). This mammalian miRNA misexpression model demonstrates a potency and specificity of cochlear homeostasis for one of the dozens of endogenously co-expressed, evolutionally conserved, small non-protein coding miRNA families. It should be a valuable tool to predict and elucidate miRNA-regulated genes and integrated functional gene expression networks that significantly influence neurosensory cell differentiation, maturation and homeostasis.
Amyloid-β with isomerized Asp7 cytotoxicity is coupled to protein phosphorylation
Authors: Zatsepina O. G. , Kechko O. I. , Mitkevich V. A. , Kozin S. A. , Yurinskaya M. M. , Vinokurov M. G. , Serebryakova M. V. , Rezvykh A. P. , Evgen’ev M. B. , Makarov A. A. 
Published: February 2018

AbstractNeuronal dysfunction and loss associated with the accumulation of amyloid-β (Aβ) in the form of extracellular amyloid plaques and hyperphosphorylated tau in the form of intraneuronal neurofibrillary tangles represent key features of Alzheimer’s disease (AD). Amyloid plaques found in the brains of AD patients are predominantly composed of Aβ42 and its multiple chemically or structurally modified isoforms. Recently, we demonstrated that Aβ42 with isomerised Asp7 (isoAβ42) which is one of the most abundant Aβ isoform in plaques, exhibited high neurotoxicity in human neuronal cells. Here, we show that, in SH-SY5Y neuroblastoma cells, the administration of synthetic isoAβ42 rather than intact Aβ42 resulted in a significantly higher level of protein phosphorylation, especially the phosphorylation of tau, tubulins, and matrin 3. IsoAβ42 induced a drastic reduction of tau protein levels. Our data demonstrate, for the first time, that isoAβ42, being to date the only known synthetic Aβ species to cause AD-like amyloidogenesis in an animal AD model, induced cell death by disabling structural proteins in a manner characteristic of that observed in the neurons of AD patients. The data emphasize an important role of isoAβ42 in AD progression and provide possible neurotoxicity paths for this particular isoform.
Solution processable and optically switchable 1D photonic structures
Authors: Paternò Giuseppe M. , Iseppon Chiara , D’Altri Alessia , Fasanotti Carlo , Merati Giulia , Randi Mattia , Desii Andrea , Pogna Eva A. A. , Viola Daniele , Cerullo Giulio , Scotognella Francesco , Kriegel Ilka 
Published: February 2018

AbstractWe report the first demonstration of a solution processable, optically switchable 1D photonic crystal which incorporates phototunable doped metal oxide nanocrystals. The resulting device structure shows a dual optical response with the photonic bandgap covering the visible spectral range and the plasmon resonance of the doped metal oxide the near infrared. By means of a facile photodoping process, we tuned the plasmonic response and switched effectively the optical properties of the photonic crystal, translating the effect from the near infrared to the visible. The ultrafast bandgap pumping induces a signal change in the region of the photonic stopband, with recovery times of several picoseconds, providing a step toward the ultrafast optical switching. Optical modeling uncovers the importance of a complete modeling of the variations of the dielectric function of the photodoped material, including the high frequency region of the Drude response which is responsible for the strong switching in the visible after photodoping. Our device configuration offers unprecedented tunability due to flexibility in device design, covering a wavelength range from the visible to the near infrared. Our findings indicate a new protocol to modify the optical response of photonic devices by optical triggers only.
An integrated microfluidic device for the sorting of yeast cells using image processing
Authors: Yu Bo Yang , Elbuken Caglar , Shen Chong , Huissoon Jan Paul , Ren Carolyn L. 
Published: February 2018

AbstractThe process of detection and separation of yeast cells based on their morphological characteristics is critical to the understanding of cell division cycles, which is of vital importance to the understanding of some diseases such as cancer. The traditional process of manual detection is usually tedious and inconsistent. This paper presents a microfluidic device integrated with microvalves for fluid control for the sorting of yeast cells using image processing algorithms and confirmation based on their fluorescent tag. The proposed device is completely automated, low cost and easy to implement in an academic research setting. Design details of the integrated microfluidic system are highlighted in this paper, along with experimental validation. Real time cell sorting was demonstrated with a cell detection rate of 12 cells per minute.
Controlling and modelling the wetting properties of III-V semiconductor surfaces using re-entrant nanostructures
Authors: Ng Wing H. , Lu Yao , Liu Huiyun , Carmalt Claire J. , Parkin Ivan P. , Kenyon Anthony J. 
Published: February 2018

AbstractInorganic semiconductors such as III-V materials are very important in our everyday life as they are used for manufacturing optoelectronic and microelectronic components with important applications span from energy harvesting to telecommunications. In some applications, these components are required to operate in harsh environments. In these cases, having waterproofing capability is essential. Here we demonstrate design and control of the wettability of indium phosphide based multilayer material (InP/InGaAs/InP) using re-entrant structures fabricated by a fast electron beam lithography technique. This patterning technique enabled us to fabricate highly uniform nanostructure arrays with at least one order of magnitude shorter patterning times compared to conventional electron beam lithography methods. We reduced the surface contact fraction significantly such that the water droplets may be completely removed from our nanostructured surface. We predicted the wettability of our patterned surface by modelling the adhesion energies between the water droplet and both the patterned surface and the dispensing needle. This is very useful for the development of coating-free waterproof optoelectronic and microelectronic components where the coating may hinder the performance of such devices and cause problems with semiconductor fabrication compatibility.
Non-empirical identification of trigger sites in heterogeneous processes using persistent homology
Authors: Kimura Masao , Obayashi Ippei , Takeichi Yasuo , Murao Reiko , Hiraoka Yasuaki 
Published: February 2018

AbstractMacroscopic phenomena, such as fracture, corrosion, and degradation of materials, are associated with various reactions which progress heterogeneously. Thus, material properties are generally determined not by their averaged characteristics but by specific features in heterogeneity (or ‘trigger sites’) of phases, chemical states, etc., where the key reactions that dictate macroscopic properties initiate and propagate. Therefore, the identification of trigger sites is crucial for controlling macroscopic properties. However, this is a challenging task. Previous studies have attempted to identify trigger sites based on the knowledge of materials science derived from experimental data (‘empirical approach’). However, this approach becomes impractical when little is known about the reaction or when large multi-dimensional datasets, such as those with multiscale heterogeneities in time and/or space, are considered. Here, we introduce a new persistent homology approach for identifying trigger sites and apply it to the heterogeneous reduction of iron ore sinters. Four types of trigger sites, ‘hourglass’-shaped calcium ferrites and ‘island’- shaped iron oxides, were determined to initiate crack formation using only mapping data depicting the heterogeneities of phases and cracks without prior mechanistic information. The identification of these trigger sites can provide a design rule for reducing mechanical degradation during reduction.
Phospholipase D functional ablation has a protective effect in an Alzheimer’s disease Caenorhabditis elegans model
Authors: Bravo Francisca Vaz , Da Silva Jorge , Chan Robin Barry , Di Paolo Gilbert , Teixeira-Castro Andreia , Oliveira Tiago Gil 
Published: February 2018

AbstractPhospholipase D (PLD) is a key player in the modulation of multiple aspects of cell physiology and has been proposed as a therapeutic target for Alzheimer’s disease (AD). Here, we characterize a PLD mutant, pld-1, using the Caenorhabditis elegans animal model. We show that pld-1 animals present decreased phosphatidic acid levels, that PLD is the only source of total PLD activity and that pld-1 animals are more sensitive to the acute effects of ethanol. We further show that PLD is not essential for survival or for the normal performance in a battery of behavioral tests. Interestingly, pld-1 animals present both increased size and lipid stores levels. While ablation of PLD has no important effect in worm behavior, its ablation in an AD-like model that overexpresses amyloid-beta (Aβ), markedly improves various phenotypes such as motor tasks, prevents susceptibility to a proconvulsivant drug, has a protective effect upon serotonin treatment and reverts the biometric changes in the Aβ animals, leading to the normalization of the worm body size. Overall, this work proposes the C. elegans model as a relevant tool to study the functions of PLD and further supports the notion that PLD has a significant role in neurodegeneration.
Alleviation of drought stress in pulse crops with ACC deaminase producing rhizobacteria isolated from acidic soil of Northeast India
Authors: Saikia Juthika , Sarma Rupak K. , Dhandia Rajashree , Yadav Archana , Bharali Rupjyoti , Gupta Vijai K. , Saikia Ratul 
Published: February 2018

AbstractThe agricultural crops are often affected by the scarcity of fresh water. Seasonal drought is a major constraint on Northeast Indian agriculture. Almost 80% of the agricultural land in this region is acidic and facing severe drought during the winter period. Apart from classical breeding and transgenic approaches, the application of plant-growth-promoting bacteria (PGPB) is an alternative strategy for improving plant fitness under stressful conditions. The 1-aminocyclopropane-1-carboxylate (ACC) deaminase-producing PGPB offer drought stress tolerance by regulating plant ethylene levels. The aim of the present study was to evaluate the consortium effect of three ACC-deaminase producing rhizobacteria – Ochrobactrum pseudogrignonenseRJ12, Pseudomonas sp.RJ15 and Bacillus subtilisRJ46 on drought stress alleviation in Vigna mungo L. and Pisum sativum L. Consortium treatment significantly increase seed germination percentage, root length, shoot length, and dry weight of treated plants. An elevated production of reactive oxygen species scavenging enzymes and cellular osmolytes; higher leaf chlorophyll content; increase in relative water content and root recovery intension were observed after consortium treatment in comparison with the uninoculated plants under drought conditions. The consortium treatment decreased the ACC accumulation and down-regulated ACC-oxidase gene expression. This consortium could be an effective bio-formulator for crop health improvement in drought-affected acidic agricultural fields.
Understanding the high l-valine production in Corynebacterium glutamicum VWB-1 using transcriptomics and proteomics
Authors: Zhang Hailing , Li Yanyan , Wang Chenhui , Wang Xiaoyuan 
Published: February 2018

AbstractToward the elucidation of the advanced mechanism of l-valine production by Corynebacterium glutamicum, a highly developed industrial strain VWB-1 was analyzed, employing the combination of transcriptomics and proteomics methods. The transcriptional level of 1155 genes and expression abundance of 96 proteins were changed significantly by the transcriptome and proteome comparison of VWB-1 and ATCC 13869. It was indicated that the key genes involved in the biosynthesis of l-valine, ilvBN, ilvC, ilvD, ilvE were up-regulated in VWB-1, which together made prominent contributions in improving the carbon flow towards l-valine. The l-leucine and l-isoleucine synthesis ability were weakened according to the down-regulation of leuB and ilvA. The up-regulation of the branched chain amino acid transporter genes brnFE promoted the l-valine secretion capability of VWB-1. The NADPH and ATP generation ability of VWB-1 were strengthened through the up-regulation of the genes involved in phosphate pentose pathway and TCA pathway. Pyruvate accumulation was achieved through the weakening of the l-lactate, acetate and l-alanine pathways. The up-regulation of the genes coding for elongation factors and ribosomal proteins were beneficial for l-valine synthesis in C. glutamicum. All information acquired were useful for the genome breeding of better industrial l-valine producing strains.