bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combined genetic approaches yield a 48% diagnostic rate in a large cohort of French hearing-impaired patients
Authors: Baux D. , Vaché C. , Blanchet C. , Willems M. , Baudoin C. , Moclyn M. , Faugère V. , Touraine R. , Isidor B. , Dupin-Deguine D. , Nizon M. , Vincent M. , Mercier S. , Calais C. , García-García G. , Azher Z. , Lambert L. , Perdomo-Trujillo Y. , Giuliano F. , Claustres M. , Koenig M. , Mondain M. , Roux A. F. 
Published: November 2017

AbstractHearing loss is the most common sensory disorder and because of its high genetic heterogeneity, implementation of Massively Parallel Sequencing (MPS) in diagnostic laboratories is greatly improving the possibilities of offering optimal care to patients. We present the results of a two-year period of molecular diagnosis that included 207 French families referred for non-syndromic hearing loss. Our multi-step strategy involved (i) DFNB1 locus analysis, (ii) MPS of 74 genes, and (iii) additional approaches including Copy Number Variations, in silico analyses, minigene studies coupled when appropriate with complete gene sequencing, and a specific assay for STRC. This comprehensive screening yielded an overall diagnostic rate of 48%, equally distributed between DFNB1 (24%) and the other genes (24%). Pathogenic genotypes were identified in 19 different genes, with a high prevalence of GJB2, STRC, MYO15A, OTOF, TMC1, MYO7A and USH2A. Involvement of an Usher gene was reported in 16% of the genotyped cohort. Four de novo variants were identified. This study highlights the need to develop several molecular approaches for efficient molecular diagnosis of hearing loss, as this is crucial for genetic counselling, audiological rehabilitation and the detection of syndromic forms.
A simple high throughput assay to evaluate water consumption in the fruit fly
Authors: Lau Man-Tat , Lin Yong Qi , Kisling Stefan , Cotterell James , Wilson Yana A. , Wang Qiao-Ping , Khuong Thang M. , Bakhshi Noman , Cole Tiffany A. , Oyston Lisa J. , Cole Adam R. , Neely G. Gregory 
Published: November 2017

AbstractWater intake is essential for survival and thus under strong regulation. Here, we describe a simple high throughput system to monitor water intake over time in Drosophila. The design of the assay involves dehydrating fly food and then adding water back separately so flies either eat or drink. Water consumption is then evaluated by weighing the water vessel and comparing this back to an evaporation control. Our system is high throughput, does not require animals to be artificially dehydrated, and is simple both in design and implementation. Initial characterisation of homeostatic water consumption shows high reproducibility between biological replicates in a variety of experimental conditions. Water consumption was dependent on ambient temperature and humidity and was equal between sexes when corrected for mass. By combining this system with the Drosophila genetics tools, we could confirm a role for ppk28 and DopR1 in promoting water consumption, and through functional investigation of RNAseq data from dehydrated animals, we found DopR1 expression in the mushroom body was sufficient to drive consumption and enhance water taste sensitivity. Together, we provide a simple high throughput water consumption assay that can be used to dissect the cellular and molecular machinery regulating water homeostasis in Drosophila.
High throughput deep sequencing reveals the important roles of microRNAs during sweetpotato storage at chilling temperature
Authors: Xie Zeyi , Wang Aiming , Li Hongmin , Yu Jingjing , Jiang Jiaojiao , Tang Zhonghou , Ma Daifu , Zhang Baohong , Han Yonghua , Li Zongyun 
Published: November 2017

AbstractSweetpotato (Impomoea batatas L.) is a globally important economic food crop with a potential of becoming a bioenergy and pharmaceutical crop. Thus, studying the molecular mechanism of tuberous root development and storage is very important. However, not too much progress has been made in this field. In this study, we employed the next generation high-throughput deep sequencing technology to sequence all small RNAs and degradome of sweetpotato for systematically investigating sweetpotato response to chilling stress during storage. A total of 190 known microRNAs (miRNAs) and 191 novel miRNAs were identified, and 428 transcripts were targeted by 184 identified miRNAs. More importantly, we identified 26 miRNAs differentially expressed between chilling stress and control conditions. The expression of these miRNAs and their targets was also confirmed by qRT-PCR. Integrated analysis of small RNAs and degradome sequencing reveals that miRNA-mediated SA signaling, ABA-dependent, and ROS response pathways are involved in sweetpotato root response to chilling stress during storage.
Modeling of the jasmonate signaling pathway in Arabidopsis thaliana with respect to pathophysiology of Alternaria blight in Brassica
Authors: Pathak Rajesh Kumar , Baunthiyal Mamta , Pandey Neetesh , Pandey Dinesh , Kumar Anil 
Published: November 2017

AbstractThe productivity of Oilseed Brassica, one of the economically important crops of India, is seriously affected by the disease, Alternaria blight. The disease is mainly caused by two major necrotrophic fungi, Alternaria brassicae and Alternaria brassicicola which are responsible for significant yield losses. Till date, no resistant source is available against Alternaria blight, hence plant breeding methods can not be used to develop disease resistant varieties. Jasmonate mediated signalling pathway, which is known to play crucial role during defense response against necrotrophs, could be strengthened in Brassica plants to combat the disease. Since scanty information is available in Brassica-Alternaria pathosystems at molecular level therefore, in the present study efforts have been made to model jasmonic acid pathway in Arabidopsis thaliana to simulate the dynamic behaviour of molecular species in the model. Besides, the developed model was also analyzed topologically for investigation of the hubs node. COI1 is identified as one of the promising candidate genes in response to Alternaria and other linked components of plant defense mechanisms against the pathogens. The findings from present study are therefore informative for understanding the molecular basis of pathophysiology and rational management of Alternaria blight for securing food and nutritional security.
Low temperature and low salinity drive putatively adaptive growth differences in populations of threespine stickleback
Authors: Gibbons Taylor C. , Rudman Seth M. , Schulte Patricia M. 
Published: November 2017

AbstractColonisation can expose organisms to novel combinations of abiotic and biotic factors and drive adaptive divergence. Yet, studies investigating the interactive effects of multiple abiotic factors on the evolution of physiological traits remain rare. Here we examine the effects of low salinity, low temperature, and their interaction on the growth of three North American populations of threespine stickleback (Gasterosteus aculeatus). In north-temperate freshwater habitats, stickleback populations experience a combination of low salinity and low winter temperatures that are not experienced by the ancestral marine and anadromous populations. Here we show that both salinity and temperature, and their interaction, have stronger negative effects on marine and anadromous populations than a freshwater population. Freshwater stickleback showed only a ~20% reduction in specific growth rate when exposed to 4 °C, while marine and anadromous stickleback showed sharp declines (82% and 74% respectively) under these conditions. The modest decreases in growth in freshwater stickleback in fresh water in the cold strongly suggest that this population has the capacity for physiological compensation to offset the negative thermodynamic effects of low temperature on growth. These results are suggestive of adaptive evolution in response to the interactive effects of low salinity and low temperature during freshwater colonisation.
Selective uptake and sensing of nitrate in poly(3,4-ethylenedioxythiophene)
Authors: Rudd Sam , Dalton Michael , Buss Peter , Treijs Amanda , Portmann Michael , Ktoris Nick , Evans Drew 
Published: November 2017

AbstractNitrogen (N) as a nutrient, in the form of nitrate (NO3−), is essential for plant growth. Chemical fertilizers are used to increase crop yields, but overuse can lead to forms of environmental pollution necessitating methods to detect and monitor the level of NO3−in-situ in agricultural soils. Herein we report for the first time the NO3− selectivity of the inherently conducting polymer poly (3,4-ethylenedioxythiophene) (PEDOT). This selectivity occurs when PEDOT thin films are exposed to an aqueous environment containing not only NO3−, but a mixture of other ions present in concentrations (ppm) typical of real agricultural soil. The PEDOT sensitivity to absorb NO3− from solution is determined to be <1 ppm.
Uncovering different states of topological defects in schlieren textures of a nematic liquid crystal
Authors: Ohzono Takuya , Katoh Kaoru , Wang Chenguang , Fukazawa Aiko , Yamaguchi Shigehiro , Fukuda Jun-ichi 
Published: November 2017

AbstractTopological defects are ubiquitously found in physical systems and therefore have been an important research subject of not only condensed matter physics but also cosmology. However, their fine structures remain elusive because of the microscopic scales involved. In the case of a liquid crystal, optical microscopy, although routinely used for the identification of liquid crystal phases and associated defects, does not have resolution high enough to distinguish fine structures of topological defects. Here we show that polarised and fluorescence microscopy, with the aid of numerical calculations on the orientational order and resulting image distortions, can uncover the structural states of topological defects with strengthm =  ±1 in a thin cell of a nematic liquid crystal. Particularly, defects withm = +1 exhibit four different states arising from chiral symmetry breaking and up-down symmetry breaking. Our results demonstrate that optical microscopy is still a powerful tool to identify fine states of liquid crystalline defects.
Influenza virus Matrix Protein M1 preserves its conformation with pH, changing multimerization state at the priming stage due to electrostatics
Authors: Shtykova Eleonora V. , Dadinova Liubov A. , Fedorova Natalia V. , Golanikov Andrey E. , Bogacheva Elena N. , Ksenofontov Alexander L. , Baratova Liudmila A. , Shilova Liudmila A. , Tashkin Vsevolod Yu. , Galimzyanov Timur R. , Jeffries Cy M. , Svergun Dmitri I. , Batishchev Oleg V. 
Published: November 2017

AbstractInfluenza A virus matrix protein M1 plays an essential role in the virus lifecycle, but its functional and structural properties are not entirely defined. Here we employed small-angle X-ray scattering, atomic force microscopy and zeta-potential measurements to characterize the overall structure and association behavior of the full-length M1 at different pH conditions. We demonstrate that the protein consists of a globular N-terminal domain and a flexible C-terminal extension. The globular N-terminal domain of M1 monomers appears preserved in the range of pH from 4.0 to 6.8, while the C-terminal domain remains flexible and the tendency to form multimers changes dramatically. We found that the protein multimerization process is reversible, whereby the binding between M1 molecules starts to break around pH 6. A predicted electrostatic model of M1 self-assembly at different pH revealed a good agreement with zeta-potential measurements, allowing one to assess the role of M1 domains in M1-M1 and M1-lipid interactions. Together with the protein sequence analysis, these results provide insights into the mechanism of M1 scaffold formation and the major role of the flexible and disordered C-terminal domain in this process.
Image Fiber-Based Miniature Suspended Solid Sensor with High Accuracy and a Large Dynamic Range
Authors: Qi Pengfei , Lin Lie , Huang Rui , Zhao Sicong , Tian Haolin , Li Shuai , Zhang Qinghe , Liu Weiwei 
Published: November 2017

AbstractAn image fiber-based miniature suspended solid sensor has been demonstrated. The diameter of the sensor is only a few millimeters. A superhydrophobic material is coated on the end of the image fiber to avoid the adsorption of suspended solids and bubbles. Multiple parameters, including mass concentration, morphology and particle sizes of suspended solids, can be visually measured in real time. Dynamic ranges of 0 ~100 kg/m3, full range accuracies of ±2‰ and a response time of 0.05 s were experimentally realized for the mass concentration measurements. Determinations of particle sizes of the suspended solids are also presented by means of digital image processing. This new technique will significantly advance ultralow-intrusion measurements in studies on the dynamics of suspended solids.
Addition of a histone deacetylase inhibitor increases recombinant protein expression in Medicago truncatula cell cultures
Authors: Santos Rita B. , Pires Ana Sofia , Abranches Rita 
Published: November 2017

AbstractPlant cell cultures are an attractive platform for the production of recombinant proteins. A major drawback, hindering the establishment of plant cell suspensions as an industrial platform, is the low product yield obtained thus far. Histone acetylation is associated with increased transcription levels, therefore it is expected that the use of histone deacetylase inhibitors would result in an increase in mRNA and protein levels. Here, this hypothesis was tested by adding a histone deacetylase inhibitor, suberanilohydroxamic acid (SAHA), to a cell line of the model legume Medicago truncatula expressing a recombinant human protein. Histone deacetylase inhibition by SAHA and histone acetylation levels were studied, and the effect of SAHA on gene expression and recombinant protein levels was assessed by digital PCR. SAHA addition effectively inhibited histone deacetylase activity resulting in increased histone acetylation. Higher levels of transgene expression and accumulation of the associated protein were observed. This is the first report describing histone deacetylase inhibitors as inducers of recombinant protein expression in plant cell suspensions as well as the use of digital PCR in these biological systems. This study paves the way for employing epigenetic strategies to improve the final yields of recombinant proteins produced by plant cell cultures.
The serine proteinase hepsin is an activator of pro-matrix metalloproteinases: molecular mechanisms and implications for extracellular matrix turnover
Authors: Wilkinson David J. , Desilets Antoine , Lin Hua , Charlton Sarah , del Carmen Arques Maria , Falconer Adrian , Bullock Craig , Hsu Yu-Chen , Birchall Kristian , Hawkins Alastair , Thompson Paul , Ferrell William R. , Lockhart John , Plevin Robin , Zhang Yadan , Blain Emma , Lin Shu-Wha , Leduc Richard , Milner Jennifer M. , Rowan Andrew D. 
Published: November 2017

AbstractIncreasing evidence implicates serine proteinases in the proteolytic cascades leading to the pathological destruction of extracellular matrices such as cartilage in osteoarthritis (OA). We have previously demonstrated that the type II transmembrane serine proteinase (TTSP) matriptase acts as a novel initiator of cartilage destruction via the induction and activation of matrix metalloproteinases (MMPs). Hepsin is another TTSP expressed in OA cartilage such that we hypothesized this proteinase may also contribute to matrix turnover. Herein, we demonstrate that addition of hepsin to OA cartilage in explant culture induced significant collagen and aggrecan release and activated proMMP-1 and proMMP-3. Furthermore, hepsin directly cleaved the aggrecan core protein at a novel cleavage site within the interglobular domain. Hepsin expression correlated with synovitis as well as tumour necrosis factor α expression, and was induced in cartilage by a pro-inflammatory stimulus. However, a major difference compared to matriptase was that hepsin demonstrated markedly reduced capacity to activate proteinase-activated receptor-2. Overall, our data suggest that hepsin, like matriptase, induces potent destruction of the extracellular matrix whilst displaying distinct efficiencies for the cleavage of specific substrates.
Early-Mid Pleistocene genetic differentiation and range expansions as exemplified by invasive Eurasian Bunias orientalis (Brassicaceae) indicates the Caucasus as key region
Authors: Koch Marcus A. , Michling Florian , Walther Andrea , Huang Xiao-Chen , Tewes Lisa , Müller Caroline 
Published: November 2017

AbstractTurkish Warty cabbage,Bunias orientalisL. (Brassicaceae) is a perennial herb known for its 250 years of invasion history into Europe and worldwide temperate regions. Putative centers of origin were debated to be located in Turkey, the Caucasus or Eastern Europe. Based on the genetic variation from the nuclear and plastid genomes, we identified two major gene pools in the Caucasian-Irano-Turanian region and close to the Northern Caucasus, respectively. These gene pools are old and started to diverge and expand approximately 930 kya in the Caucasus. Pleistocene glaciation and deglaciation cycles favoured later expansion of a European gene pool 230 kya, which was effectively separated from the Caucasian-Irano-Turanian gene pool. Although the European gene pool is genetically less diverse, it has largely served as source for colonization of Western and Northern Europe in modern times with rare observations of genetic contributions from the Caucasian-Irano-Turanian gene pool such as in North-East America. This study largely utilized herbarium material to take advantage of a biodiversity treasure trove providing biological material and also giving access to detailed collection information.
Development of a plasmid free CRISPR-Cas9 system for the genetic modification of Mucor circinelloides
Authors: Nagy Gábor , Szebenyi Csilla , Csernetics Árpád , Vaz Amanda Grace , Tóth Eszter Judit , Vágvölgyi Csaba , Papp Tamás 
Published: November 2017

AbstractMucor circinelloides and other members of Mucorales are filamentous fungi, widely used as model organisms in basic and applied studies. Although genetic manipulation methods have been described for some Mucoral fungi, construction of stable integrative transformants by homologous recombination has remained a great challenge in these organisms. In the present study, a plasmid free CRISPR-Cas9 system was firstly developed for the genetic modification of a Mucoral fungus. The described method offers a rapid but robust tool to obtain mitotically stable mutants of M. circinelloides via targeted integration of the desired DNA. It does not require plasmid construction and its expression in the recipient organism. Instead, it involves the direct introduction of the guide RNA and the Cas9 enzyme and, in case of homology directed repair (HDR), the template DNA into the recipient strain. Efficiency of the method for non-homologous end joining (NHEJ) and HDR was tested by disrupting two different genes, i.e. carB encoding phytoene dehydrogenase and hmgR2 encoding 3-hydroxy-3-methylglutaryl-CoA reductase, of M. circinelloides. Both NHEJ and HDR resulted in stable gene disruption mutants. While NHEJ caused extensive deletions upstream from the protospacer adjacent motif, HDR assured the integration of the deletion cassette at the targeted site.
New energy with ZnS: novel applications for a standard transparent compound
Authors: D’Amico Pino , Calzolari Arrigo , Ruini Alice , Catellani Alessandra 
Published: November 2017

AbstractWe revise the electronic and optical properties of ZnS on the basis of first principles simulations, in view of novel routes for optoelectronic and photonic devices, such as transparent conductors and plasmonic applications. In particular, we consider doping effects, as induced by Al and Cu. It is shown that doping ZnS with Al imparts a n-character and allows for a plasmonic activity in the mid-IR that can be exploited for IR metamaterials, while Cu doping induces a spin dependent p-type character to the ZnS host, opening the way to the engineering of transparent p-n junctions, p-type transparent conductive materials and spintronic applications. The possibility of promoting the wurtzite lattice, presenting a different symmetry with respect to the most stable and common zincblende structure, is explored. Homo- and heterojunctions to twin ZnO are discussed as a possible route to transparent metamaterial devices for communications and energy.
Input voltage sharing control scheme for input series and output series DC/DC converters using paralleled MOSFETs
Authors: Qu Lu , Zhang Donglai 
Published: November 2017

This study proposes an input‐voltage‐sharing control scheme for use in input‐series‐output‐series (ISOS) systems. An ISOS system consists of a set of closed‐loop DC/DC converters. Each converter has a metal–oxide–semiconductor field‐effect transistor (MOSFET) connected in parallel on the input side that is controlled by an input‐voltage‐sharing loop. The MOSFET works in the linear region to adjust the input power equilibrium. The proposed control scheme makes the closed‐loop converters function as power devices that can be combined quickly and flexibly according to the specific voltage conversion requirements, which greatly shortens the time required to develop an ISOS system. The design principle of the input‐voltage‐sharing loop and the time and frequency domain simulation results are also provided in this study. A 600 W prototype composed of two DC/DC converters was built and employed to verify the steady state and dynamic characteristics of the proposed control scheme.
Recent Advances in the Catalytic Asymmetric Construction of Phosphorus-Substituted Quaternary Carbon Stereocenters
Authors: Chen Long 
Published: November 2017

Phosphorus-substituted quaternary carbon stereocenters exist widely in drugs and biologically active compounds. Catalytic asymmetric synthesis of such quaternary carbon stereogenic centers is of significant importance, with four synthetic strategies being established. This review summarizes the recent progress in this field, including the advantages and limitations of each strategy, briefly discusses the reaction mechanisms and challenges, and outlines synthetic opportunities still open.1	Introduction2	Asymmetric Hydrophosphonylation3	Asymmetric Electrophilic Phosphination4	Asymmetric Functionalization of P-Substituted Methine Compounds5	Asymmetric Addition to α-Keto- or α-Ketiminophosphonates6	Conclusion
Recent Progress in Catalytic Enantioselective Desymmetrization of Prochiral Organosilanes for the Synthesis of Silicon-Stereogenic Compounds
Authors: Shintani Ryo 
Published: November 2017

It is highly important to develop efficient synthetic methods for various enantioenriched chiral compounds due to their high significance in our life. In this regard, asymmetric catalysis is one of the most attractive ways of synthesizing such compounds from achiral precursors. Although various methods have been developed for the enantio­selective preparation of carbon-stereogenic compounds, the corresponding methods for silicon-stereogenic compounds are much less established. In particular, little progress has been made on catalytic enantioselective synthesis using prochiral organosilanes until recently. This account focuses on the recent progress in the catalytic enantio­selective preparation of silicon-stereogenic organosilanes through ­desymmetrization of prochiral organosilanes.1	Introduction2	Desymmetrization of Diorganodihydrosilanes3	Desymmetrization of Tetraorganosilanes3.1	Desymmetrization through Cleavage of Silicon–Carbon Bonds3.2	Desymmetrization without Cleavage of Silicon–Carbon Bonds4	Conclusion