bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular dynamics simulation on the allosteric analysis of the c‐di‐GMP class I riboswitch induced by ligand binding
Authors: Li Chaoqun , Zhao Xiaojia , Xie Pengtao , Hu Junping , Bi Huimin 
Published: July 2018

AbstractRiboswitches are RNA molecules that regulate gene expression using conformation change, affected by binding of small molecule ligands. Although a number of ligand‐bound aptamer complex structures have been solved, it is important to know ligand‐free conformations of the aptamers in order to understand the mechanism of specific binding by ligands. In this paper, we use dynamics simulations on a series of models to characterize the ligand‐free and ligand‐bound aptamer domain of the c‐di‐GMP class I (GEMM‐I) riboswitch. The results revealed that the ligand‐free aptamer has a stable state with a folded P2 and P3 helix, an unfolded P1 helix and open binding pocket. The first Mg ions binding to the aptamer is structurally favorable for the successive c‐di‐GMP binding. The P1 helix forms when c‐di‐GMP is successive bound. Three key junctions J1/2, J2/3 and J1/3 in the GEMM‐I riboswitch contributing to the formation of P1 helix have been found. The binding of the c‐di‐GMP ligand to the GEMM‐I riboswitch induces the riboswitch's regulation through the direct allosteric communication network in GEMM‐I riboswitch from the c‐di‐GMP binding sites in the J1/2 and J1/3 junctions to the P1 helix, the indirect ones from those in the J2/3 and P2 communicating to P1 helix via the J1/2 and J1/3 media.
In vivo sliding distance on the metal‐on‐polyethylene total hip arthroplasty articulation using patient‐specific gait analysis
Authors: Peng Yun , Arauz Paul , An Shuai , Kwon Young‐Min 
Published: July 2018

ABSTRACTMetal‐on‐polyethylene (MoP) is the most commonly used bearing surface in primary total hip arthroplasty (THA). Polyethylene wear debris remains a major concern. Studies investigating the wear performance based on patient‐specific in vivo kinematics and component orientation remains largely lacking. The primary goal of this study was to identify patterns of the distribution of sliding distance and cross‐shear ratio among THA patients. A validated approach combining dual fluoroscopic imaging system and computed‐tomography was utilized to quantify in vivo gait kinematics and component orientations in 48 total hips. The distribution of accumulated sliding distance and cross‐shear ratio over the polyethylene bearing surface was calculated and analyzed using principal component analysis (PCA). Strong patient‐specific variation in sliding distance and cross‐shear ratio was observed. PCA detected two principal components (PCs) of the sliding distance that together contribute to 94.8% of the total variation. PCA detected four PCs that together contribute to 86% of the total variation of the cross‐shear ratio. Regression analysis identified a positive association between cross‐shear magnitude and axial and frontal range of motion (RoM). Increased cup inclination, stem anteversion, and reduced cup anteversion may lead to superiorly distributed high cross‐shear region, potentially accelerating wear. Our study investigated, in vivo sliding distance and cross‐shear pattern using a comprehensive patient‐specific dataset and detected several wear indicators under in vivo conditions. These findings provided useful reference values that may help to assess wear in MoP THA patients. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:3151–3160, 2018.
Polystyrene Foam with High Cell Density and Small Cell Size by Compression‐Injection Molding and Core Back Foaming Technique: Evolution of Cells in Cavity
Authors: Bai Tiantian , Dong Binbin , Xiao Mengjun , Liu Hu , Wang Ning , Wang Yaming , Wang Chao , Liu Chuntai , Cao Wei , Zhang Jiaoxia , Ma Yong , Guo Zhanhu 
Published: July 2018

AbstractMany efforts have been made to obtain uniform cell structures from foam injection molding techniques. However, cell nucleation mechanism and complex dynamics during the cell formation have rarely been well understood. Here, high‐pressure foam injection molding (HPFIM) is achieved by combining the injection–compression molding with core back foaming (ICMCBF) technique. The influences of compression pressure and time on the cell structure of polystyrene foam during the foaming process are studied. Compared with low pressure for conventional foam injection molding, high compression pressure (200 bar) and fast pressure drop rate of ICMCBF endow the foam with the highest cell density (1.59 × 107 cells cm−3), and the smallest cell size (15 µm). The tensile strength and impact strength are enhanced by about 60% (from 22.3 to 35.6 MPa) and 80% (from 3.6 to 6.8 MPa), respectively. This study gives a critical understanding of the cell nucleation and growth mechanism of the foam injection molding and supplies a new strategy for the fabrication of foam with uniform cell structure.
Barley Products of Different Fiber Composition Selectively Change Microbiota Composition in Rats
Authors: Teixeira Cristina , Prykhodko Olena , Alminger Marie , Fåk Hållenius Frida , Nyman Margareta 
Published: July 2018

ScopeSeveral dietary fiber properties are suggested to be important for the profiling of the microbiota composition, but those characteristics are rather unclear. Whether different physico‐chemical properties of barley dietary fiber influence the gut microbiota composition is investigated.Methods and resultsSeven diets containing equal amounts of dietary fiber from barley malts, brewer's spent grain (BSG), and barley extracts, resulting in varying amounts of β‐glucan, soluble arabinoxylan, and insoluble arabinoxylan in the diets were given to conventional rats. Malts increased microbiota alpha diversity more than BSG and the extracts. The intake of soluble arabinoxylan was related to Akkermansia and propionic acid formation in the cecum of rats, whereas β‐glucan and/or insoluble arabinoxylan were attributed to some potentially butyrate‐producing bacteria (e.g., Lactobacillus, Blautia, and Allobaculum).ConclusionThis study demonstrates that there is a potential to stimulate butyrate‐ and propionate‐producing bacteria in the cecum of rats with malt products of specific fiber properties. Moreover, BSG, a by product from beer production, added to malt can possibly be used to further modulate the microbiota composition, toward a higher butyric acid formation. A complex mixture of fiber as in the malts is of greater importance for microbiota diversity than purer fiber extracts.
The Impact of Nutritional Interventions in Pregnant Women on DNA Methylation Patterns of the Offspring: A Systematic Review
Authors: Andraos Stephanie , de Seymour Jamie Violet , O'Sullivan Justin Martin , Kussmann Martin 
Published: July 2018

AbstractEpidemiological studies have consistently demonstrated that environmental exposures in early life are associated with later‐life health status and disease susceptibility. Epigenetic modifications, such as DNA methylation, have been suggested as potential mechanisms linking the intrauterine environment with offspring health status. The present systematic review compiles peer‐reviewed randomized controlled trials assessing the impact of maternal nutritional interventions on DNA methylation patterns of the offspring. The results of the included trials are consistent with micronutrient supplementation not significantly affecting offspring tissue DNA methylation patterns, yet subgrouping by sex, BMI, and smoking status increased the significance of nutritional supplementation on DNA methylation. Maternal BMI and smoking status as well as offspring sex were factors influencing offspring DNA methylation responsiveness to nutritional interventions during pregnancy. Future research should aim at assessing the impact of nutritional interventions on DNA methylation patterns of neonates comparing single versus multi‐micronutrient supplementation, within populations having high versus low baseline nutritional statuses.
Scaling limits to large area perovskite solar cell efficiency
Authors: Wilkinson Ben , Chang Nathan L. , Green Martin A. , Ho‐Baillie Anita W.Y. 
Published: July 2018

AbstractPerovskite solar cells have demonstrated efficiencies over 20%, but this has not been reproduced at large areas. We explore the theoretical limit to single large area perovskite solar cell efficiency, with different front conductive layers: first, the standard n‐i‐p structure with a transparent conductive electrode (TCE) at the substrate, and then structures that include a front metal grid. We model and optimize the impact of the thickness of the TCE and the dimensions of the grid elements to balance series resistance, parasitic absorption in the TCE layer, and shading losses to maximize efficiency. The results of the optimization suggest that the efficiency of the standard design can be significantly improved simply by selecting the optimum TCE thicknesses for the cell size. However, the poor scaling of the standard design prevents the fabrication of efficient large area cells. Adding a metal grid allows the efficiency of large area cells (156 mm × 156 mm) to approach that of small cells and exceed 20%. The maximum efficiency is limited by the minimum width of the metal grid elements and the sheet resistance of the metal grid material. In this context, the performances of fluorine‐doped tin oxide and indium tin oxide as TCE materials were compared, with indium tin oxide found to be superior. We also explore the limits of performance when connecting multiple cells in series to form a large area minimodule and determine the conditions when a front grid is beneficial. Design rules are presented that allow researchers to calculate the optimum cell parameters for high efficiency.
Machine learning PV system performance analyser
Authors: Rodrigues Sandy , Ramos Helena Geirinhas , Morgado‐Dias Fernando 
Published: July 2018

AbstractMachine learning techniques (MLTs) can create accurate predictions of solar outputs that are used in photovoltaic system performance analysis. The issue with MLT application is the requirement for large amounts of historical data for training the prediction models that is not always available. Since the photovoltaic system behaviour is non‐linear due to the unpredictable nature of the weather conditions throughout the year, MLT training requires annual historical data to create the prediction model. The photovoltaic system production meters only store up to 3 months of historical power values. This information served as motivation to research different types of MLTs, in search of one that would accurately predict the daily solar energy values of a photovoltaic system based on the available 3‐month historical data. The aim of this work is to implement a photovoltaic system performance analyser that estimates daily solar alternating current energy outputs for any rooftop photovoltaic system, based on daily solar irradiation values, without being influenced by the seasons of the year nor the photovoltaic system installation location. Therefore, 5 MLTs were studied and compared, which include the regression tree, artificial neural network, multigene genetic programming, Gaussian process, and the support vector machine for regression. Results show that the regression tree MLT provides acceptable results to be used in all locations and all seasons of the year, while the support vector machine for regression is best for spring and summer training dataset months, and the Gaussian process is best for the autumn and winter training dataset months.
The Sperm Proteome of the Echiuran Urechis unicinctus (Annelida, Echiura)
Authors: Qin Zhenkui , Zhang Yanjie , Mu Huawei , Zhang Zhifeng , Qiu Jian‐Wen 
Published: July 2018

AbstractSperm proteins presumably play critical roles in reproduction, but in many non‐model animals their identities are unknown. A total of 147 sperm proteins from the echiuran worm Urechis unicinctus, the first sperm proteome in the phylum Annelida, are reported. The echiuran sperm proteome can be classified into diverse functional groups: energy metabolism (31%), protein synthesis and degradation (18%), spermatogenesis and sperm motility (12%), signal pathway (11%), ion channel and transport proteins (6%), cytoskeleton (4%), immunity and stress responses (3%), and fertilization (1%). These results will facilitate studies of mechanisms of fertilization in echiurans, as well as comparative studies of reproduction and evolution across lophotrochozoans. Data are available via ProteomeXchange with identifier PXD009176.
Simultaneous Quantification of the Acetylome and Succinylome by ‘One‐Pot’ Affinity Enrichment
Authors: Basisty Nathan , Meyer Jesse G , Wei Lei , Gibson Bradford W , Schilling Birgit 
Published: July 2018

AbstractProtein posttranslational modifications (PTMs) are of increasing interest in biomedical research, yet studies rarely examine more than one PTM. One barrier to multi‐PTM studies is the time cost for both sample preparation and data acquisition, which scale linearly with the number of modifications. The most prohibitive requirement is often the need for large amounts of sample, which must be increased proportionally with the number of PTM enrichment steps. Here, a streamlined, quantitative label‐free proteomic workflow—“one‐pot” PTM enrichment—that enables comprehensive identification and quantification of peptides containing acetylated and succinylated lysine residues from a single sample containing as little as 1 mg mitochondria protein is described. Coupled with a label‐free, data‐independent acquisition (DIA), 2235 acetylated and 2173 succinylated peptides with the one‐pot method are identified and quantified and peak areas are shown to be highly correlated between the one‐pot and traditional single‐PTM enrichments. The ‘one‐pot’ method makes possible detection of multiple PTMs occurring on the same peptide, and it is shown that it can be used to make unique biological insights into PTM crosstalk. Compared to single‐PTM enrichments, the one‐pot workflow has equivalent reproducibility and enables direct assessment of PTM crosstalk from biological samples in less time from less tissue.
Quantitative Proteomic Analysis of Cell Responses to Electroporation, a Classical Gene Delivery Approach
Authors: Zhao Minzhi , Zhao Deyao , Ma Yan , Hu Zhiyuan , Wei Zewen 
Published: July 2018

AbstractElectroporation, as an established nonviral technology for breaching cell membrane, has been accepted for the delivery of nucleic acids. Despite satisfactory delivery efficiencies have been achieved on multiple cell kinds by simply exhausting all possible electrical parameters, electroporation is still inefficient, or even invalid, for various kinds of cells. This is largely due to the lack of comprehensive understanding of cell responses to electrical stimulation at biological aspect. Moreover, a systematically investigation of protein variation of electroporated cells is also required for biosafety evaluation before clinically applying electroporation. By employing quantitative proteomic analysis, the biological mechanism of electroporation is explored from the molecular level. The results reveal that electrical stimulations widely influence many biological processes including nucleic acid stabilization, protein synthesis, cytoskeleton dynamic, inflammation, and cell apoptosis. It is found that several antivirus‐related processes appeared in the enrichment results. Moreover, SAMD9, a broad spectrum antiviral and antitumor factor, is dramatically downregulated on easy‐to‐transfect cells while electroporation can not alter SAMD9 expression on hard‐to‐transfect cells, hinting that electroporation, a pure physical treatment, can induce antivirus‐like defensive responses and the altering of SAMD9 can be used to predict the effectiveness of electroporation on transfecting specific kinds of cells.
Fabrication of Ultra‐Fine TATB/HMX Cocrystal Using a Compound Solvent
Authors: Hou Conghua , Zhang Yuanping , Chen Yunge , Jia Xinlei , Zhang Shimin , Tan Yingxin 
Published: July 2018

AbstractA novel energetic cocrystal predicted to exhibit greater power and lower sensitivity, consisting of 1,3,5‐triamino‐2,4,6‐trinitrobenzene (TATB) and cyclotetramethylenetetranitramine (HMX) is presented. The TATB/HMX cocrystals were prepared using a compound solvent of [Emim]Ac and DMSO at 80 °C by recrystallization. Structural characterizations and thermal properties of the raw materials and cocrystals were systematically investigated by scanning electron microscopy (SEM), X‐ray diffraction, fourier‐transform infrared spectroscopy, fourier transform raman spectroscopy and differential scanning calorimetry. The SEM results indicated that microparticles are hexagonal in shape and ∼2 μm in size. The formation of cocrystals originates from the N−H⋅⋅⋅O hydrogen bonding between ‐NO2 (HMX) and ‐NH2 (TATB). Naturally, compared to raw HMX, the impact sensitivity of the cocrystals is reduced. The EXPLO5 program showed TATB/HMX with desirable detonation performance.
Genomic screening of new putative antiviral lectins from Amazonian cyanobacteria based on a bioinformatics approach
Authors: Siqueira Andrei Santos , Lima Alex Ranieri Jerônimo , Aguiar Delia Cristina Figueira , Santos Alberdan Silva , Vianez Júnior João Lídio da Silva Gonçalves , Gonçalves Evonnildo Costa 
Published: July 2018

AbstractLectins are proteins of nonimmune origin, which are capable of recognizing and binding to glycoconjugate moieties. Some of them can block the interaction of viral glycoproteins to the host cell receptors acting as antiviral agents. Although cyanobacterial lectins have presented broad biotechnological potential, little research has been directed to Amazonian Cyanobacterial diversity. In order to identify new antiviral lectins, we performed genomic analysis in seven cyanobacterial strains from Coleção Amazônica de Cianobactérias e Microalgas (CACIAM). We found 75 unique CDS presenting one or more lectin domains. Since almost all were annotated as hypothetical proteins, we used homology modeling and molecular dynamics simulations to evaluate the structural and functional properties of three CDS that were more similar to known antiviral lectins. Nostoc sp. CACIAM 19 as well as Tolypothrix sp. CACIAM 22 strains presented cyanovirin‐N homologues whose function was confirmed by binding free energy calculations. Asn, Glu, Thr, Lys, Leu, and Gly, which were described as binding residues for cyanovirin, were also observed on those structures. As for other known cyanovirins, those residues in both our models also made favorable interactions with dimannose. Finally, Alkalinema sp. CACIAM 70d presented one CDS, which was identified as a seven‐bladed beta‐propeller structure with binding sites predicted for sialic acid and N‐acetylglucosamine. Despite its singular structure, our analysis suggested this molecule as a new putative antiviral lectin. Overall, the identification and the characterization of new lectins and their homologues are a promising area in antiviral research, and Amazonian cyanobacteria present biotechnological potential to be explored in this regard.
DrugMetab: An Integrated Machine Learning and Lexicon Mapping Named Entity Recognition Method for Drug Metabolite
Authors: Wu Heng‐Yi , Lu Deshun , Hyder Mustafa , Zhang Shijun , Quinney Sara K. , Desta Zeruesenay , Li Lang 
Published: July 2018

Drug metabolites (DMs) are critical in pharmacology research areas, such as drug metabolism pathways and drug‐drug interactions. However, there is no terminology dictionary containing comprehensive drug metabolite names, and there is no named entity recognition (NER) algorithm focusing on drug metabolite identification. In this article, we developed a novel NER system, DrugMetab, to identify DMs from the PubMed abstracts. DrugMetab utilizes the features characterized from the Part‐of‐Speech, drug index, and pre/suffix, and determines DMs within context. To evaluate the performance, a gold‐standard corpus was manually constructed. In this task, DrugMetab with sequential minimal optimization (SMO) classifier achieves 0.89 precision, 0.77 recall, and 0.83 F‐measure in the internal testing set; and 0.86 precision, 0.85 recall, and 0.86 F‐measure in the external validation set. We further compared the performance between DrugMetab and whatizitChemical, which was designed for identifying small molecules or chemical entities. DrugMetab outperformed whatizitChemical, which had a lower recall rate of 0.65.
Scour depths at sites selected for spawning by brown trout (Salmo trutta) along a longitudinal gradient of a North American mountain river
Authors: Meredith C. S. , Budy P. , Schmidt J. C. 
Published: July 2018

AbstractIn the Intermountain West, USA, fry of fall‐spawning brown trout (Salmo trutta) are susceptible to scour‐related mortality because they are still in the gravel during spring snowmelt run‐off events. The goal of our research was to understand patterns of gravel scour on the Logan River, Utah, in relation to brown trout spawning and whether mobility of spawning gravels could explain the absence of brown trout from higher elevations. We collected data to characterize local entrainment potential at spawning gravels longitudinally on the Logan River during 2009 and 2010 spring flood events. We used scour chains to measure scour depth at spawning locations, and we also examined the position of redds in channel cross sections in relation to the centre line. The flood magnitude in both years approximated the 2‐year flood magnitude, but the flood in 2009 was much longer in duration. Scour at 27% of scour chain locations exceeded the estimated median upper limit of developing fry in 2009, whereas scour at 0% of locations exceeded this depth in 2010. Brown trout spawned in locations with similar entrainment potential at both mid and high elevations, which contributed to a lack of trend in scour depth with elevation. In addition, the majority of areas chosen for spawning were channel margins. The relationship between local entrainment potential at spawning gravels and scour depth was similar for the mid‐elevation canyon zone with medium brown trout density and the high‐elevation noncanyon zone with low brown trout density. In a low‐elevation backwater zone containing high densities of brown trout, scour was high despite low levels of entrainment potential. Overall, findings suggest that spawning gravel scour is not limiting brown trout abundance at high elevations in this system given shallow scour depths overall and a general lack of increase in scour depth with increasing elevation/distance upstream.
Flexible, Flame‐Resistant, and Dendrite‐Impermeable Gel‐Polymer Electrolyte for Li–O2/Air Batteries Workable Under Hurdle Conditions
Authors: Zou Xiaohong , Lu Qian , Zhong Yijun , Liao Kaiming , Zhou Wei , Shao Zongping 
Published: July 2018

AbstractGel‐polymer electrolytes are considered as a promising candidate for replacing the liquid electrolytes to address the safety concerns in Li–O2/air batteries. In this work, by taking advantage of the hydrogen bond between thermoplastic polyurethane and aerogel SiO2 in gel polymer, a highly crosslinked quasi‐solid electrolyte (FST‐GPE) with multifeatures of high ionic conductivity, high mechanical flexibility, favorable flame resistance, and excellent Li dendrite impermeability is developed. The resulting gel‐polymer Li–O2/air batteries possess high reaction kinetics and stabilities due to the unique electrode–electrolyte interface and fast O2 diffusion in cathode, which can achieve up to 250 discharge–charge cycles (over 1000 h) in oxygen gas. Under ambient air atmosphere, excellent performances are observed for coin‐type cells over 20 days and for prototype cells working under extreme bending conditions. Moreover, the FST‐GPE electrolyte also exhibits durability to protect against fire, dendritic Li, and H2O attack, demonstrating great potential for the design of practical Li–O2/air batteries.