bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of the tendency for the electronic conductivity to change during alcoholic fermentation
Authors: Li Chongwei , Wang Yue , Sha Shuang , Yin He , Zhang Huilin , Wang Yongsheng , Zhao Bo , Song Fuqiang 
Published: April 2019

AbstractThe observation that the electronic conductivity begins to decease and then increases during alcoholic fermentation was first discovered in our work. To explain the tendency experiments were conducted to investigate the effect of the reducing sugar concentration, ethanol concentration, cell density, pH and ionic concentration. The results showed that the ionic concentration, reducing sugar concentration, cell concentration, pH and especially the ethanol concentration caused a change of the electronic conductivity. From 0 h to 60 h, the ethanol concentration had a significant negative correlation with the conductivity, which decreased with increasing ethanol concentration during fermentation. From 60 h to 68 h, when the ethanol concentration remained unchanged, the total ionic concentration had a significant positive correlation with the electronic conductivity, which increased with increasing ionic concentration (pH value decreases, cell autolysis). Thus, when the electronic conductivity reached its lowest point, the alcoholic content was the greatest. We concluded that it is feasible to directly reflect the change of the ethanol concentration using the change of the electronic conductivity by constructing a mathematical model. The results of this model could be applied for the completely on-line monitoring of the alcoholic fermentation process and for determining the end point of fermentation.
Calibrating the tree of vipers under the fossilized birth-death model
Authors: Šmíd Jiří , Tolley Krystal A. 
Published: April 2019

AbstractScaling evolutionary trees to time is essential for understanding the origins of clades. Recently developed methods allow including the entire fossil record known for the group of interest and eliminated the need for specifying prior distributions for node ages. Here we apply the fossilized birth-death (FBD) approach to reconstruct the diversification timeline of the viperines (subfamily Viperinae). Viperinae are an Old World snake subfamily comprising 102 species from 13 genera. The fossil record of vipers is fairly rich and well assignable to clades due to the unique vertebral and fang morphology. We use an unprecedented sampling of 83 modern species and 13 genetic markers in combination with 197 fossils representing 28 extinct taxa to reconstruct a time-calibrated phylogeny of the Viperinae. Our results suggest a late Eocene-early Oligocene origin with several diversification events following soon after the group’s establishment. The age estimates inferred with the FBD model correspond to those from previous studies that were based on node dating but FBD provides notably narrower credible intervals around the node ages. Viperines comprise two African and an Eurasian clade, but the ancestral origin of the subfamily is ambiguous. The most parsimonious scenarios require two transoceanic dispersals over the Tethys Sea during the Oligocene.
Life-long reduction in myomiR expression does not adversely affect skeletal muscle morphology
Authors: Vechetti Ivan J. , Wen Yuan , Chaillou Thomas , Murach Kevin A. , Alimov Alexander P. , Figueiredo Vandre C. , Dal-Pai-Silva Maeli , McCarthy John J. 
Published: April 2019

AbstractWe generated an inducible, skeletal muscle-specific Dicer knockout mouse to deplete microRNAs in adult skeletal muscle. Following tamoxifen treatment, Dicer mRNA expression was significantly decreased by 87%. Wild-type (WT) and Dicer knockout (KO) mice were subjected to either synergist ablation or hind limb suspension for two weeks. There was no difference in muscle weight with hypertrophy or atrophy between WT and KO groups; however, even with the significant loss of Dicer expression, myomiR (miR-1, -133a and -206) expression was only reduced by 38% on average. We next aged WT and KO mice for ~22 months following Dicer inactivation to determine if myomiR expression would be further reduced over a prolonged timeframe and assess the effects of myomiR depletion on skeletal muscle phenotype. Skeletal muscle Dicer mRNA expression remained significantly decreased by 80% in old KO mice and sequencing of cloned Dicer mRNA revealed the complete absence of the floxed exons in KO skeletal muscle. Despite a further reduction of myomiR expression to ~50% of WT, no change was observed in muscle morphology between WT and KO groups. These results indicate the life-long reduction in myomiR levels did not adversely affect skeletal muscle phenotype and suggest the possibility that microRNA expression is uniquely regulated in skeletal muscle.
MoNa – A Cost-Efficient, Portable System for the Nanoinjection of Living Cells
Authors: Simonis Matthias , Sandmeyer Alice , Greiner Johannes , Kaltschmidt Barbara , Huser Thomas , Hennig Simon 
Published: April 2019

AbstractInjection techniques to deliver macromolecules to cells such as microinjection have been around for decades with applications ranging from probing whole organisms to the injection of fluorescent molecules into single cells. A similar technique that has raised recent interest is nanoinjection. The pipettes used here are much smaller and allow for the precise deposition of molecules into single cells via electrokinetics with minimal influence on the cells’ health. Unfortunately, the equipment utilized for nanoinjection originates from scanning ion conductance microscopy (SICM) and is therefore expensive and not portable, but usually fixed to a specific microscope setup. The level of precision that these systems achieve is much higher than what is needed for the more robust nanoinjection process. We present Mobile Nanoinjection (MoNa), a portable, cost-efficient and easy to build system for the injection of single cells. Sacrificing unnecessary sub-nanometer accuracy and low ion current noise levels, we were able to inject single living cells with high accuracy. We determined the noise of the MoNa system and investigated the injection conditions for 16 prominent fluorescent labels and fluorophores. Further, we performed proof of concepts by injection of ATTO655-Phalloidin and MitoTracker Deep Red to living human osteosarcoma (U2OS) cells and of living adult human inferior turbinate stem cells (ITSC’s) following neuronal differentiation with the MoNa system. We achieved significant cost reductions of the nanoinjection technology and gained full portability and compatibility to most optical microscopes.
Functional detection of botulinum neurotoxin serotypes A to F by monoclonal neoepitope-specific antibodies and suspension array technology
Authors: von Berg Laura , Stern Daniel , Pauly Diana , Mahrhold Stefan , Weisemann Jasmin , Jentsch Lisa , Hansbauer Eva-Maria , Müller Christian , Avondet Marc A. , Rummel Andreas , Dorner Martin B. , Dorner Brigitte G. 
Published: April 2019

AbstractBotulinum neurotoxins (BoNTs) are the most potent toxins known and cause the life threatening disease botulism. Sensitive and broad detection is extremely challenging due to the toxins’ high potency and molecular heterogeneity with several serotypes and more than 40 subtypes. The toxicity of BoNT is mediated by enzymatic cleavage of different synaptic proteins involved in neurotransmitter release at serotype-specific cleavage sites. Hence, active BoNTs can be monitored and distinguished in vitro by detecting their substrate cleavage products. In this work, we developed a comprehensive panel of monoclonal neoepitope antibodies (Neo-mAbs) highly specific for the newly generated N- and/or C-termini of the substrate cleavage products of BoNT serotypes A to F. The Neo-mAbs were implemented in a set of three enzymatic assays for the simultaneous detection of two BoNT serotypes each by monitoring substrate cleavage on colour-coded magnetic Luminex-beads. For the first time, all relevant serotypes could be detected in parallel by a routine in vitro activity assay in spiked serum and food samples yielding excellent detection limits in the range of the mouse bioassay or better (0.3–80 pg/mL). Therefore, this work represents a major step towards the replacement of the mouse bioassay for botulism diagnostics.
Low genetic diversity and shallow population structure in the endangered vulture, Gyps coprotheres
Authors: Kleinhans Courtneë , Willows-Munro Sandi 
Published: April 2019

AbstractGlobally, vulture species are experiencing major population declines. The southern African Cape vulture (Gyps coprotheres) has undergone severe population collapse which has led to a listing of Endangered by the IUCN. Here, a comprehensive genetic survey ofG. coprotheresis conducted using microsatellite markers. Analyses revealed an overall reduction in heterozygosity compared to other vulture species that occur in South Africa (Gypaetus barbatus,Necrosyrtes monachus, andGyps africanus). Bayesian clustering analysis and principal coordinate analysis identified shallow, subtle population structuring across South Africa. This provides some support for regional natal philopatry in this species. Despite recent reductions in population size, a genetic bottleneck was not detected by the genetic data. TheG. coprotheres, however, did show a significant deficiency of overall heterozygosity. This, coupled with the elevated levels of inbreeding and reduced effective population size, suggests thatG. coprotheresis genetically depauperate. Given that genetic variation is considered a prerequisite for adaptation and population health, the low genetic diversity withinG. coprotherespopulations is of concern and has implications for the future management and conservation of this species.
Extracellular small non-coding RNA contaminants in fetal bovine serum and serum-free media
Authors: Mannerström Bettina , Paananen Riku O. , Abu-Shahba Ahmed G. , Moilanen Jukka , Seppänen-Kaijansinkko Riitta , Kaur Sippy 
Published: April 2019

AbstractIn the research field of extracellular vesicles (EVs), the use of fetal bovine serum (FBS) depleted of EVs for in vitro studies is advocated to eliminate the confounding effects of media derived EVs. EV-depleted FBS may either be prepared by ultracentrifugation or purchased commercially. Nevertheless, these preparations do not guarantee an RNA-free FBS for in vitro use. In this study we address the RNA contamination issue, of small non-coding (nc)RNA in vesicular or non-vesicular fractions of FBS, ultracentrifugation EV-depleted FBS, commercial EV-depleted FBS, and in our recently developed filtration based EV-depleted FBS. Commercially available serum- and xeno-free defined media were also screened for small ncRNA contamination. Our small ncRNA sequencing data showed that all EV-depleted media and commercially available defined media contained small ncRNA contaminants. Out of the different FBS preparations studied, our ultrafiltration-based method for EV depletion performed the best in depleting miRNAs. Certain miRNAs such miR-122 and miR-203a proved difficult to remove completely and were found in all media. Compared to miRNAs, other small ncRNA (snRNA, Y RNA, snoRNA, and piRNA) were difficult to eliminate from all the studied media. Additionally, our tested defined media contained miRNAs and other small ncRNAs, albeit at a much lower level than in serum preparations. Our study showed that no media is free of small ncRNA contaminants. Therefore, in order to screen for baseline RNA contamination in culturing media, RNA sequencing data should be carefully controlled by adding a media sample as a control. This should be a mandatory step before performing cell culture experiments in order to eliminate the confounding effects of media.
Implications of the strain irreversibility cliff on the fabrication of particle-accelerator magnets made of restacked-rod-process Nb3Sn wires
Authors: Cheggour Najib , Stauffer Theodore C. , Starch William , Goodrich Loren F. , Splett Jolene D. 
Published: April 2019

AbstractThe strain irreversibility cliff (SIC), marking the abrupt change of the intrinsic irreversible strain limit εirr,0 as a function of heat-treatment (HT) temperature θ in Nb3Sn superconducting wires made by the restacked-rod process (RRP®), is confirmed in various wire designs. It adds to the complexity of reconciling conflicting requirements on conductors for fabricating magnets. Those intended for the high-luminosity upgrade of the Large Hardon Collider (LHC) at the European Organization for Nuclear Research (CERN) facility require maintaining the residual resistivity ratio RRR of conductors above 150 to ensure stability of magnets against quenching. This benchmark may compromise the conductors’ mechanical integrity if their εirr,0 is within or at the bottom of SIC. In this coupled investigation of strain and RRR properties to fully assess the implications of SIC, we introduce an electro-mechanical stability criterion that takes into account both aspects. For standard-Sn billets, this requires a strikingly narrow HT temperature window that is impractical. On the other hand, reduced-Sn billets offer a significantly wider choice of θ, not only for ensuring that εirr,0 is located at the SIC plateau while RRR ≥ 150, but also for containing the strain-induced irreversible degradation of the conductor’s critical-current beyond εirr,0. This study suggests that HT of LHC magnets, made of reduced-Sn wires having a Nb/Sn ratio of 3.6 and 108/127 restacking architecture, be operated at θ in the range of 680 to 695 °C (when the dwell time is 48 hours).
Augmenting Bragg Reflection with Polymer-sustained Conical Helix
Authors: Joshi Vinay , Paterson Daniel A. , Storey John M. D. , Imrie Corrie T. , Chien Liang-Chy 
Published: April 2019

AbstractThere has been a recent surge of interest in smart materials and devices with stimuli-responsive properties for optical modulations. Cholesteric liquid crystals (CLCs) are a unique class of light-manipulating materials, and strongly interact with light and other electromagnetic (EM) waves. Because of their intricate helical structure, new properties of CLC have emerged revealing unique optical behavior that has resulted in rewriting Braggs’ law for how light interacts with soft materials. The aim of this work is to push the limits of spectral tuning with a new method of augmenting light-cholesteric interactions using a polymer-sustained conical helix (PSCH) structure. We experimentally explore the reversibility of reflective wavelength modulation and validate the mechanism enhanced by a polymer-sustained helicoidal structure via theoretical analyses. The conical helix structure of a CLC, formed by low-field-induced oblique orientation of cholesteric helices, is comprised of a chiral dopant, a conventional nematic, and bimesogenic and trimesogenic nematics. Polymerizing a small amount of a reactive mesogen in the CLC with an applied electric field produces a templated helical polymer network that enables three switched optical states, including light-scattering and transparent states as well as color reflection in response to an applied increasing or decreasing electric field. An electro-activated PSCH optical film covers a wide color space, which is appropriate for tunable color device applications. We envisage that this PSCH material will lead to new avenues for controlling EM waves in imaging and thermal control, smart windows and electronic papers.
A prospective randomized, double-blind, placebo-controlled, dose-response relationship study to investigate efficacy of fructo-oligosaccharides (FOS) on human gut microflora
Authors: Tandon Disha , Haque Mohammed Monzoorul , Gote Manoj , Jain Manish , Bhaduri Anirban , Dubey Ashok Kumar , Mande Sharmila S. 
Published: April 2019

AbstractFructo-oligosaccharides (FOS), a prebiotic supplement, is known for its Bifidogenic capabilities. However, aspects such as effect of variable quantities of FOS intake on gut microbiota, and temporal dynamics of gut microbiota (transitioning through basal, dosage, and follow-up phases) has not been studied in detail. This study investigated these aspects through a randomized, double-blind, placebo-controlled, dose-response relationship study. The study involved 80 participants being administered FOS at three dose levels (2.5, 5, and 10 g/day) or placebo (Maltodextrin 10 g/day) during dosage phase. Microbial DNA extracted from fecal samples collected at 9 intervening time-points was sequenced and analysed. Results indicate that FOS consumption increased the relative abundance of OTUs belonging to Bifidobacterium and Lactobacillus. Interestingly, higher FOS dosage appears to promote, in contrast to Maltodextrin, the selective proliferation of OTUs belonging to Lactobacillus. While consumption of prebiotics increased bacterial diversity, withdrawal led to its reduction. Apart from probiotic bacteria, a significant change was also observed in certain butyrate-producing microbes like Faecalibacterium, Ruminococcus and Oscillospira. The positive impact of FOS on butyrate-producing bacteria and FOS-mediated increased bacterial diversity reinforces the role of prebiotics in conferring beneficial functions to the host.
An innovation for microstructural modification and mechanical improvement of TiAl alloy via electric current application
Authors: Chen Zhanxing , Ding Hongsheng , Chen Ruirun , Guo Jingjie , Fu Hengzhi 
Published: April 2019

AbstractIn this article, microstructural evolution during the solidification of Ti-48Al-2Cr-2Nb with current density, as well as the formation mechanisms, are discussed, along with the impacts on microhardness and hot compression properties. The applied electric current promotes the solidification from the α primary phase to a largely β solidification in Ti-48Al-2Cr-2Nb. With an increase in supercooling, the solidification process have a tendency to change from an α-led primary phase to (α + β)-led primary phase. The primary dendrites, grain size, and lamellar spacing show a tendency to decrease first before increasing with increasing current density. Microhardness and high-temperature yield strength increase with a decrease in primary dendrite spacing, grain size, and lamellar spacing. Correlations between primary dendrite spacing, lamellar spacing, microhardness, yield strength, and current density are described by a fitting formula. An increase of α2 phase, due to the application of electric current, results in improved microhardness. The yield strength of Ti-48Al-2Cr-2Nb alloy increases linearly with microhardness. Yield stress increases with a decrease in microstructure parameters, in accordance with the Hall–Petch equation. The predominant modification mechanism with electric current application for TiAl solidification is the variation of supercooling and temperature gradients ahead of the mush zone due to Joule heating.
Azoreductase activity of dye-decolorizing bacteria isolated from the human gut microbiota
Authors: Zahran Sara A. , Ali-Tammam Marwa , Hashem Abdelgawad M. , Aziz Ramy K. , Ali Amal E. 
Published: April 2019

AbstractThe gut microbiota enriches the human gene pool and contributes to xenobiotic metabolism. Microbial azoreductases modulate the reduction of azo-bonds, activating produgs and azo polymer-coated dosage forms, or degrading food additives. Here, we aimed to screen the healthy human gut microbiota for food colorant-reducing activity and to characterize factors modulating it. Four representative isolates from screened fecal samples were identified as E. coli (AZO-Ec), E. faecalis (AZO-Ef), E. avium (AZO-Ev) and B. cereus (AZO-Bc). Both AZO-Ef and AZO-Ev decolorized amaranth aerobically and microaerophilically while AZO-Ec and AZO-Bc had higher aerobic reduction rates. The isolates varied in their activities against different dyes, and the azo-reduction activity mostly followed zero-order reaction kinetics, with a few exceptions. Additionally, the isolates had different pH dependence, e.g., AZO-Ec was not affected by pH variation while AZO-Bc exhibited variable degradation kinetics at different pH levels. Cell-free extracts showed NADH-dependent enzymatic activities 14–19 times higher than extracellular fractions. FMN did not affect the reducing activity of AZO-Ef cell-free extract, whereas AZO-Ec, AZO-Ev and AZO-Bc had significantly higher reduction rates in its presence (P values = 0.02, 0.0001 and 0.02, respectively). Using Degenerate primers allowed the amplification of azoreductase genes, whose sequences were 98–99% similar to genes encoding FMN-dependent-NADH azoreductases.
Identification of Allosteric Inhibitors against Active Caspase-6
Authors: Tubeleviciute-Aydin Agne , Beautrait Alexandre , Lynham Jeffrey , Sharma Gyanesh , Gorelik Alexei , Deny Ludovic J. , Soya Naoto , Lukacs Gergely L. , Nagar Bhushan , Marinier Anne , LeBlanc Andrea C. 
Published: April 2019

AbstractCaspase-6 is a cysteine protease that plays essential roles in programmed cell death, axonal degeneration, and development. The excess neuronal activity of Caspase-6 is associated with Alzheimer disease neuropathology and age-dependent cognitive impairment. Caspase-6 inhibition is a promising strategy to stop early stage neurodegenerative events, yet finding potent and selective Caspase-6 inhibitors has been a challenging task due to the overlapping structural and functional similarities between caspase family members. Here, we investigated how four rare non-synonymous missense single-nucleotide polymorphisms (SNPs), resulting in amino acid substitutions outside human Caspase-6 active site, affect enzyme structure and catalytic efficiency. Three investigated SNPs were found to align with a putative allosteric pocket with low sequence conservation among human caspases. Virtual screening of 57,700 compounds against the putative Caspase-6 allosteric pocket, followed byin vitrotesting of the best virtual hits in recombinant human Caspase-6 activity assays identified novel allosteric Caspase-6 inhibitors with IC50andKivalues ranging from ~2 to 13 µM. This report may pave the way towards the development and optimisation of novel small molecule allosteric Caspase-6 inhibitors and illustrates that functional characterisation of rare natural variants holds promise for the identification of allosteric sites on other therapeutic targets in drug discovery.
Concurrent climate extremes in the key wheat producing regions of the world
Authors: Toreti Andrea , Cronie Ottmar , Zampieri Matteo 
Published: April 2019

AbstractClimate extremes have profound impacts on key socio-economic sectors such as agriculture. In a changing climate context, characterised by an intensification of these extremes and where the population is expected to grow, exposure and vulnerability must be accurately assessed. However, most risk assessments analyse extremes independently, thus potentially being overconfident in the resilience of the socio-economic sectors. Here, we propose a novel approach to defining and characterising concurrent climate extremes (i.e. extremes occurring within a specific temporal lag), which is able to identify spatio-temporal dependences without making any strict assumptions. The method is applied to large-scale heat stress and drought events in the key wheat producing regions of the world, as these extremes can cause serious yield losses and thus trigger market shocks. Wheat regions likely to have concurrent extremes (heat stress and drought events) are identified, as well as regions independent of each other or inhibiting each other in terms of these extreme events. This tool may be integrated in all risk assessments but could also be used to explore global climate teleconnections.