bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of HGF‐binding aptamers with the combination of G4 promoter‐derived aptamer selection and in silico maturation
Authors: Yokoyama Tomomi , Tsukakoshi Kaori , Yoshida Wataru , Saito Taiki , Teramoto Kentaro , Savory Nasa , Abe Koichi , Ikebukuro Kazunori 
Published: June 2017

ABSTRACTWe describe the selection of aptamers based on bioinformatics‐based approaches without Systematic Evolution of Ligands by EXponential enrichment (SELEX). SELEX is a potent method; however, it is time intensive and the PCR‐amplification step, which is essential step for SELEX, leads to the loss of good aptamers. We have developed an aptamer‐screening method, G4 promoter‐derived aptamer selection (G4PAS), and an aptamer‐improving method, in silico maturation (ISM). They are based on in silico sequence selection and computer assisted directed evolution, respectively. In this study, we succeeded in identifying new aptamers against hepatocyte growth factor (HGF) by G4PAS as well as improving the specificity of the HGF aptamers by ISM. Using ISM improved the specificity of the aptamer for HGF by up to 45‐fold in comparison with the original aptamer. These methods enable easy and efficient identification of good aptamers, and the combination of G4PAS with ISM can thus serve as a potent approach for aptamer identification. Biotechnol. Bioeng. 2017;114: 2196–2203. © 2017 Wiley Periodicals, Inc.
Fermentation strategy for second generation ethanol production from sugarcane bagasse hydrolyzate by Spathaspora passalidarum and Scheffersomyces stipitis
Authors: Nakanishi Simone C. , Soares Lauren B. , Biazi Luiz Eduardo , Nascimento Viviane M. , Costa Aline C. , Rocha George Jackson M. , Ienczak Jaciane L. 
Published: June 2017

ABSTRACTAlcoholic fermentation of released sugars in pretreatment and enzymatic hydrolysis of biomass is a central feature for second generation ethanol (E2G) production. Saccharomyces cerevisiae used industrially in the production of first generation ethanol (E1G) convert sucrose, fructose, and glucose into ethanol. However, these yeasts have no ability to ferment pentose (xylose). Therefore, the present work has focused on E2G production by Scheffersomyces stipitis and Spathaspora passalidarum. The fermentation strategy with high pitch, cell recycle, fed‐batch mode, and temperature decrease for each batch were performed in a hydrolyzate obtained from a pretreatment at 130°C with NaOH solution (1.5% w/v) added with 0.15% (w/w) of anthraquinone (AQ) and followed by enzymatic hydrolysis. The process strategy has increased volumetric productivity from 0.35 to 0.38 g · L−1 · h−1 (first to third batch) for S. stipitis and from 0.38 to 0.81 g · L−1 · h−1 for S. passalidarum (first to fourth batch). Mass balance for the process proposed in this work showed the production of 177.33 kg ethanol/ton of sugar cane bagasse for S. passalidarum compared to 124.13 kg ethanol/ton of sugar cane bagasse for S. stipitis fermentation. The strategy proposed in this work can be considered as a promising strategy in the production of second generation ethanol. Biotechnol. Bioeng. 2017;114: 2211–2221. © 2017 Wiley Periodicals, Inc.
Vitamin D enhances omega‐3 polyunsaturated fatty acids‐induced apoptosis in breast cancer cells
Authors: Yang Jing , Zhu Shenglong , Lin Guangxiao , Song Ci , He Zhao 
Published: June 2017

AbstractBreast cancer is a leading type of cancer in women and generally classified into three subtypes of ER+/PR+, HER2+ and triple negative. Both omega‐3 polyunsaturated fatty acids and vitamin D3 play positive role in the reduction of breast cancer incidence. However, whether combination of omega‐3 polyunsaturated fatty acids and vitamin D3 has stronger protective effect on breast carcinogenesis still remains unknown. In this study, we show that the combination of ω‐3 free fatty acids (ω‐3 FFAs) and 1α, 25‐dihydroxy‐vitamin D3 (VD3) dramatically enhances cell apoptosis among three subtypes of breast cancer cell lines. Bcl‐2 and total PARP protein levels are decreased in combined treatment MCF‐7 and SK‐BR‐3 cells. Caspase signals play a vital role in cell apoptosis induced by combination. Moreover, Raf‐MAPK signaling pathway is involved in the apoptosis induction by combination of ω‐3 FFAs+VD3. These results demonstrate that the induction of cell apoptosis by combined treatment is dependent on different signaling pathways in three subtypes of breast cancer cell lines.
Coinage Metal Superatomic Cores: Insights into Their Intrinsic Stability and Optical Properties from Relativistic DFT Calculations
Authors: Gam Franck , Paez‐Hernandez Dayan , Arratia‐Perez Ramiro , Liu C. W. , Kahlal Samia , Saillard Jean‐Yves , Muñoz‐Castro Alvaro 
Published: June 2017

AbstractCoinage‐metal atomically precise nanoclusters are made of a well‐defined metallic core embedded in a ligand‐protecting outer shell. Whereas gold derivatives are particularly well documented, examples of silver nanoclusters are somewhat limited and copper species remain particularly scare. Our DFT relativistic calculations on superatomic metallic cores indicate that copper species are almost as stable as gold clusters and more stable than their silver counterparts. Thus, for silver superatomic cores, the role of the stabilizing ligands is more crucial in the stabilization of the overall structure, in comparison to copper and gold. Hence, the chemistry of the earlier counterparts of gold, especially copper, should grow quickly with at least characterizations of species related to that found in the heavier elements in the triad, which requires tackling synthetic challenges. Time‐dependent (TD)‐DFT calculations show that with an increase of the cluster core nuclearity, the absorption bands are redshifted, allowing us to differentiate between the clusters types. Moreover, the optical properties of the silver cores are fairly different from that of their Cu and Au relatives.
Iron‐Catalyzed Radical Decarboxylative Oxyalkylation of Terminal Alkynes with Alkyl Peroxides
Authors: Zhu Xiaotao , Ye Changqing , Li Yajun , Bao Hongli 
Published: June 2017

AbstractAn iron‐catalyzed oxyalkylation of alkynes with alkyl peroxides as the alkylating reagents has been investigated. Alkyl peroxides are readily available from aliphatic acids and serve simultaneously as the alkylating reagents and internal oxidants. Primary, secondary, and tertiary alkyl groups of aliphatic acids were readily incorporated into C−C triple bonds and diverse α‐alkylated ketones were synthesized. Mechanism studies revealed that this reaction involves highly reactive alkyl free radicals. A unique equilibrium between lauric acid and water catalyzed by the iron(III) catalyst was observed.
Base‐Mediated Generation of Ketenimines from Ynamides: Direct Access to Azetidinimines by an Imino‐Staudinger Synthesis
Authors: Romero Eugénie , Minard Corinne , Benchekroun Mohamed , Ventre Sandrine , Retailleau Pascal , Dodd Robert H. , Cariou Kevin 
Published: June 2017

AbstractYnamides were used as precursors for the in situ generation of highly reactive ketenimines that could be trapped with imines in a [2+2] cycloaddition. This imino‐Staudinger synthesis led to a variety of imino‐analogs of β‐lactams, namely azetidinimines (20 examples), that could be further functionalized through a broad range of transformations.
Effect of process parameters on droplet spreading behaviour over porous surface
Authors: Basit Abdul , KuShaari KuZilati , Siwayanan Parthiban , Azeem Babar 
Published: June 2017

AbstractDroplet spreading behaviour over a porous surface is a complex phenomenon, and is a basic component of many industrial processes, for example the spray coating process. The coating process has wide applications and this includes coating of urea fertilizer to produce slow release urea. The quality of coating film in such applications is affected by many factors, one of them being droplet spreading on the substrate. Droplet spreading behaviour is affected by process parameters such as viscosity, density, surface tension, impact velocity, porosity, etc. Droplet spreading on a porous surface involves penetration into the porous surface and spreading on the surface. Previously, the effect of individual process parameters has been studied. The current work aims at finding the interactive effect of process parameters on droplet spreading behaviour by using response surface methodology. The combined effect of liquid viscosity, impact velocity, and surface porosity has been studied on contact angle, spreading factor, and residual drop volume. The results show that minimum contact angle can be achieved with maximum impact velocity, minimum porosity, and minimal liquid viscosity. Similar behaviour was observed with droplet residual volume. Maximum spreading factor was attained at minimum viscosity and porosity while impact velocity was at maximum level.
Acyclic Nucleoside Phosphonates Containing 9‐Deazahypoxanthine and a Five‐Membered Heterocycle as Selective Inhibitors of Plasmodial 6‐Oxopurine Phosphoribosyltransferases
Authors: Kaiser Martin Maxmilian , Baszczyňski Ondřej , Hocková Dana , Poštová‐Slavětínská Lenka , Dračínský Martin , Keough Dianne T. , Guddat Luke W. , Janeba Zlatko 
Published: June 2017

AbstractAcyclic nucleoside phosphonates (ANPs) are an important class of therapeutic drugs that act as antiviral agents by inhibiting viral DNA polymerases and reverse transcriptases. ANPs containing a 6‐oxopurine unit instead of a 6‐aminopurine or pyrimidine base are inhibitors of the purine salvage enzyme, hypoxanthine‐guanine‐[xanthine] phosphoribosyltransferase (HG[X]PRT). Such compounds, and their prodrugs, are able to arrest the growth of Plasmodium falciparum (Pf) in cell culture. A new series of ANPs were synthesized and tested as inhibitors of human HGPRT, PfHGXPRT, and Plasmodium vivax (Pv) HGPRT. The novelty of these compounds is that they contain a five‐membered heterocycle (imidazoline, imidazole, or triazole) inserted between the acyclic linker(s) and the nucleobase, namely, 9‐deazahypoxanthine. Five of the compounds were found to be micromolar inhibitors of PfHGXPRT and PvHGPRT, but no inhibition of human HGPRT was observed under the same assay conditions. This demonstrates selectivity of these types of compounds for the two parasitic enzymes compared to the human counterpart and confirms the importance of the chemical nature of the acyclic moiety in conferring affinity/selectivity for these three enzymes.
Labeling DNA Replication Foci to Visualize Chromosome Territories In Vivo
Authors: Maya‐Mendoza Apolinar , Jackson Dean A. 
Published: June 2017

AbstractWhile a detailed understanding of chromatin dynamics is needed to explain how higher‐order chromatin organization influences nuclear function, the molecular principles that regulate chromatin mobility in mammalian nuclei remain largely unknown. Here we describe experimental tools to follow chromatin dynamics by labeling DNA during S phase. Using these methods, we have found that foci labeled during early and mid/late S phase have significantly different dynamic behavior. Spatially constrained heterochromatic foci restrict long‐range transformations of the chromosome territory (CT) structure while providing a structural framework on which highly mobile euchromatic foci undergo positional oscillations that drive local changes in the chromosome shape. Despite often dramatic mobility, we have demonstrated a preservation of structural integrity which ensures that DNA from neighboring CTs is not able to mix freely within the same nuclear space. Finally, other potential applications of the presented protocols are discussed. © 2017 by John Wiley & Sons, Inc.
Super‐Resolution Microscopy and Single‐Protein Tracking in Live Bacteria Using a Genetically Encoded, Photostable Fluoromodule
Authors: Saurabh Saumya , Perez Adam M. , Comerci Colin J. , Shapiro Lucy , Moerner W. E. 
Published: June 2017

AbstractVisualization of dynamic protein structures in live cells is crucial for understanding the mechanisms governing biological processes. Fluorescence microscopy is a sensitive tool for this purpose. In order to image proteins in live bacteria using fluorescence microscopy, one typically genetically fuses the protein of interest to a photostable fluorescent tag. Several labeling schemes are available to accomplish this. Particularly, hybrid tags that combine a fluorescent or fluorogenic dye with a genetically encoded protein (such as enzymatic labels) have been used successfully in multiple cell types. However, their use in bacteria has been limited due to challenges imposed by a complex bacterial cell wall. Here, we describe the use of a genetically encoded photostable fluoromodule that can be targeted to cytosolic and membrane proteins in the Gram negative bacterium Caulobacter crescentus. Additionally, we summarize methods to use this fluoromodule for single protein imaging and super‐resolution microscopy using stimulated emission depletion. © 2017 by John Wiley & Sons, Inc.
Femtosecond Charge‐Injection Dynamics at Hybrid Perovskite Interfaces
Authors: Grancini Giulia , Viola Daniele , Lee Yonghui , Saliba Michael , Paek Sanghyun , Cho Kyung Taek , Orlandi Simonetta , Cavazzini Marco , Fungo Fernando , Hossain Mohammad I. , Belaidi Abdelhak , Tabet Nouar , Pozzi Gianluca , Cerullo Giulio , Nazeeruddin Mohammad Khaja 
Published: June 2017

AbstractWith a power conversion efficiency (PCE) exceeding 22 %, perovskite solar cells (PSCs) have thrilled photovoltaic research. However, the interface behavior is still not understood and is a hot topic of research: different processes occur over a hierarchy of timescales, from femtoseconds to seconds, which makes perovskite interface physics intriguing. Herein, through femtosecond transient absorption spectroscopy with spectral coverage extending into the crucial IR region, the ultrafast interface‐specific processes at standard and newly molecularly engineered perovskite interfaces in state‐of‐the‐art PSCs are interrogated. Ultrafast interfacial charge injection occurs with a time constant of 100 fs, resulting in hot transfer from energetic charges and setting the timescale for the first step involved in the complex charge‐transfer process. This is also true for 20 % efficient devices measured under real operation, for which the femtosecond injection is followed by a slower picosecond component. These findings provide compelling evidence for the femtosecond interfacial charge‐injection step and demonstrate a robust method for the straightforward identification of interfacial non‐equilibrium processes on the ultrafast timescale.
Microbiota Analysis Using an Illumina MiSeq Platform to Sequence 16S rRNA Genes
Authors: Rapin Alexis , Pattaroni Céline , Marsland Benjamin J. , Harris Nicola L. 
Published: June 2017

AbstractThe microbiota have been shown to play an important role in diverse biological processes including immunity, metabolism, and digestion. Assessing the exact composition of the microbiota has proven challenging due to the often unknown growth specificities of its members, and culture‐based approaches typically fail to capture the complete diversity of microorganisms present. Next Generation Sequencing (NGS) methods provide an efficient means to gather information about cultured and uncultured members of the microbiota. This article provides a method to characterize bacterial communities in terms of species composition using high‐throughput sequencing. Briefly, by extracting the entire DNA content of a microbiota sample and performing a targeted high‐throughput sequencing of the 16S rRNA gene, a phylogenetic marker for prokaryotes, prediction of the composition of the entire bacterial community is made possible. © 2017 by John Wiley & Sons, Inc.
Synthesis of Oligodeoxynucleotides Containing a C8‐2′‐Deoxyguanosine Adduct Formed by the Carcinogen 3‐Nitrobenzanthrone
Authors: Chatterjee Arindom , Malik Chanchal K. , Basu Ashis K. 
Published: June 2017

AbstractThis unit describes the detailed procedure in five parts for the synthesis of the C8‐2′‐deoxyguanosine‐3‐aminobenzanthrone adduct located in a desired site in an oligonucleotide. The synthesis of the protected 2′‐deoxyguanosine, O
6‐benzyl‐N
2‐DMTr‐3′‐5′‐bisTBDMS‐C8‐Br‐2′‐deoxyguanosine, is described in the first part. The synthesis of the reduced carcinogen 3‐aminobenzanthrone is detailed in part two. The third part outlines the key step of the adduct formation between the reduced carcinogen and the protected nucleoside by a palladium‐catalyzed cross coupling reaction. The final two parts describe phosphoramidite synthesis from the nucleoside‐carcinogen adduct followed by its site‐specific incorporation into DNA by solid‐phase oligonucleotide synthesis. The adducted oligonucleotides are purified by reversed‐phase HPLC and characterized by mass spectrometry. © 2017 by John Wiley & Sons, Inc.
Plant iTRAQ‐Based Proteomics
Authors: Handakumbura Pubudu P. , Hixson Kim K. , Purvine Samuel O. , Jansson Christer , Paša‐Tolić Ljiljana 
Published: June 2017

AbstractWe present a simple one‐pot extraction protocol, which rapidly isolates hydrophilic metabolites, lipids, and proteins from the same pulverized plant sample. Also detailed is a global plant proteomics sample preparation method utilizing iTRAQ multiplexing reagents that enables deep proteome coverage due to the use of HPLC fractionation of the peptides prior to mass spectrometric analysis. We have successfully used this protocol on several different plant tissues (e.g., roots, stems, leaves) from different plants (e.g., sorghum, poplar, Arabidopsis, soybean), and have been able to successfully detect and quantify thousands of proteins. Multiplexing strategies such as iTRAQ and the bioinformatics strategy outlined here, ultimately provide insight into which proteins are significantly changed in abundance between two or more groups (e.g., control, perturbation). Our bioinformatics strategy yields z‐score values, which normalize the expression data into a format that can easily be cross‐compared with other expression data (i.e., metabolomics, transcriptomics) obtained from different analytical methods and instrumentation. © 2017 by John Wiley & Sons, Inc.
Preparation of Large‐Grained α‐High Strength Gypsum with FGD Gypsum
Authors: Shao Duoduo , Zhao Bin , Zhang Hongqi , Wang Zhiguang , Shi Cuijie , Cao Jilin 
Published: June 2017

Using FGD gypsum as the raw material, short columnar‐shaped α‐calcium sulfate hemihydrate can be prepared with succinic acid in hydrothermal autoclave method with a low salt content. The influence of washing times, slurry concentration, salt content, reaction temperature, pH and the amount of succinic acid were investigated. The research shows that: short columnar α‐calcium sulfate hemihydrate with the length of 50 μm and length‐diameter ratio of 1, dry compressive strength of which is similar to 40 grade was obtained at the slurry concentration of 14%, salt content of 3%, succinic acid of 0.07% after three times washing under 115°C without the change of pH value. After 5 times circulation of mother liquid, the morphology of the product had no significant difference with the initial product and recycling rate of sodium chloride was not less than 90%.
Quantitative NMR Approach to Optimize the Formation of Chemical Building Blocks from Abundant Carbohydrates
Authors: Elliot Samuel G. , Tolborg Søren , Sádaba Irantzu , Taarning Esben , Meier Sebastian 
Published: June 2017

AbstractThe future role of biomass‐derived chemicals relies on the formation of diverse functional monomers in high yields from carbohydrates. Recently, it has become clear that a series of α‐hydroxy acids, esters, and lactones can be formed from carbohydrates in alcohol and water solvents using tin‐containing catalysts such as Sn‐Beta. These compounds are potential building blocks for polyesters bearing additional olefin and alcohol functionalities. An NMR approach was used to identify, quantify, and optimize the formation of these building blocks in the Sn‐Beta‐catalyzed transformation of abundant carbohydrates. Record yields of the target molecules can be achieved by obstructing competing reactions through solvent selection.
Direct Electro‐oxidation of Dimethyl Ether on Pt−Cu Nanochains
Authors: Gavriel Bar , Sharabi Ronit , Elbaz Lior 
Published: June 2017

AbstractA new platinum–copper alloy electrocatalyst for the direct electro‐oxidation of dimethyl ether (DME) has been synthesized in an easy and low‐cost approach and studied by using an array of techniques, including X‐ray diffraction, scanning electron microscopy, high‐resolution transmission electron microscopy, and elemental analysis. Structural characterization revealed that the synthesized PtCu nanoparticles (3 nm on average) formed homogeneous nanochains without aggregation of metallic platinum or copper. The catalyst's activity towards electro‐oxidation of DME was tested using cyclic voltammetry (CV) and in membrane‐electrode assembly (MEA) in a full cell and was found to be promising. The direct DME fuel cell (DDMEFC) studied in this work has relatively high energy density, of 13.5 mW cm−1 and thus shows great potential as fuel for low power fuel cells. The newly synthesized PtCu catalyst exhibited almost double the performance of commercial PtRu in electrocatalytic DME oxidation.
New cooperative strategy for cognitive radios with wireless powered primary users
Authors: Azmat Freeha , Zhou Yulin , Chen Yunfei 
Published: June 2017

SummaryConventional strategy for cognitive radios does not assume any energy harvesting capability at the primary users. However, this is not the case when primary users are wirelessly powered, especially in wireless sensor works that are widely used in the Internet of Things. In this paper, we propose a new cooperative strategy where the secondary user transmits data if the primary users are detected to be idle or harvest energy, in contrast to conventional strategy where the secondary user only transmits data if the primary users are detected idle. The performances of this new strategy are analysed. Numerical results show that primary user can achieve energy gain from the transmission of secondary user and that secondary user can also achieve throughput gain by transmitting data when primary user performs energy harvesting. On the other hand, secondary user harvests less energy on average using the new strategy as it has to transmit data when primary user harvests energy.
Food insecurity and eating disorder pathology
Authors: Becker Carolyn Black , Middlemass Keesha , Taylor Brigitte , Johnson Clara , Gomez Francesca 
Published: June 2017

AbstractObjectiveThe primary aim of this study was to investigate eating disorder (ED) pathology in those living with food insecurity. A secondary aim was to investigate whether any‐reason dietary restraint, weight self‐stigma, and worry increased as level of food insecurity increased.MethodParticipants (N = 503) seeking food from food pantries completed questionnaires assessing level of food insecurity, demographics, ED pathology, dietary restraint, weight self‐stigma, and worry.ResultsConsistent with hypotheses, participants with the highest level of food insecurity (i.e., adults who reported having hungry children in their household) also endorsed significantly higher levels of binge eating, overall ED pathology, any‐reason dietary restraint, weight self‐stigma, and worry compared to participants with lower levels of food insecurity. Contrary to hypotheses, compensatory behaviors also increased as level of food insecurity worsened. Overall, 17% of those in the child hunger food insecurity group reported clinically significant ED pathology.DiscussionThis is the first study to assess the full spectrum of ED pathology in a low‐income, marginalized population with food insecurity. Given that food insecurity is a global concern, results from this study suggest that greater attention to the association between ED pathology and food insecurity is warranted by researchers around the world.