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https://www.readbyqxmd.com/read/28934693/enzyme-classification-using-multiclass-support-vector-machine-and-feature-subset-selection
#1
Debasmita Pradhan, Sudarsan Padhy, Biswajit Sahoo
Proteins are the macromolecules responsible for almost all biological processes in a cell. With the availability of large number of protein sequences from different sequencing projects, the challenge with the scientist is to characterize their functions. As the wet lab methods are time consuming and expensive, many computational methods such as FASTA, PSI-BLAST, DNA microarray clustering, and Nearest Neighborhood classification on protein-protein interaction network have been proposed. Support vector machine is one such method that has been used successfully for several problems such as protein fold recognition, protein structure prediction etc...
August 31, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28922997/how-social-and-refractory-is-the-social-psychological-refractory-period
#2
Peter Wühr, Herbert Heuer
The social psychological refractory period (PRP) effect refers to an increase in RT to the second of two successive stimuli when another person responds to the first stimulus (shared dual-task condition) rather than when a single person responds to both stimuli (individual dual-task condition). We investigated (a) whether a social PRP effect would occur without explicit instruction concerning task priority and (b) whether there are crosstalk effects in the shared dual-task situation. We observed a strong PRP effect together with a small crosstalk effect in the individual dual-task condition, but in the shared dual-task condition both effects were absent...
July 2017: Experimental Psychology
https://www.readbyqxmd.com/read/28913724/use-of-phytoproductivity-data-in-the-choice-of-native-plant-species-to-restore-a-degraded-coal-mining-site-amended-with-a-stabilized-industrial-organic-sludge
#3
Claudete G Chiochetta, Hela Toumi, Renata F S Böhm, Fernanda Engel, Gabriel Poyer-Radetski, Leonardo R Rörig, Fabrizio Adani, Claudemir M Radetski
Coal mining-related activities result in a degraded landscape and sites associated with large amounts of dumped waste material. The arid soil resulting from acid mine drainage affects terrestrial and aquatic ecosystems, and thus, site remediation programs must be implemented to mitigate this sequential deleterious processes. A low-cost alternative material to counterbalance the affected physico-chemical-microbiological aspects of the degraded soil is the amendment with low contaminated and stabilized industrial organic sludge...
September 14, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28858218/a-novel-workflow-to-enrich-and-isolate-patient-matched-epcam-high-and-epcam-low-negative-ctcs-enables-the-comparative-characterization-of-the-pik3ca-status-in-metastatic-breast-cancer
#4
Rita Lampignano, Liwen Yang, Martin H D Neumann, André Franken, Tanja Fehm, Dieter Niederacher, Hans Neubauer
Circulating tumor cells (CTCs), potential precursors of most epithelial solid tumors, are mainly enriched by epithelial cell adhesion molecule (EpCAM)-dependent technologies. Hence, these approaches may overlook mesenchymal CTCs, considered highly malignant. Our aim was to establish a workflow to enrich and isolate patient-matched EpCAM(high) and EpCAM(low/negative) CTCs within the same blood samples, and to investigate the phosphatidylinositol 3-kinase catalytic subunit alpha (PIK3CA) mutational status within single CTCs...
August 31, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28853469/construction-of-cuo-in2s3-zno-heterostructure-arrays-for-enhanced-photocatalytic-efficiency
#5
Yu-Cheng Chang, Jin-You Guo, Chien-Ming Chen, Hsin-Wei Di, Chao-Chun Hsu
Novel one-dimensional (1D) heterostructure arrays composed of CuO nanowire cores, intermediate In2S3 nanostructures, and ZnO nanorod sheaths (i.e. CuO/In2S3/ZnO heterostructure arrays) have been successfully synthesized by a multi-step process. First, single-crystalline CuO nanowires were directly grown on flexible Cu mesh substrates using a one-step annealing process under ambient conditions. Second, In2S3 nanostructures and ZnO nanorods were sequentially grown on the CuO nanowires by a two-step hydrothermal method at low reaction temperature...
September 14, 2017: Nanoscale
https://www.readbyqxmd.com/read/28840320/cre-lox-based-multiple-markerless-gene-disruption-in-the-genome-of-the-extreme-thermophile-thermus-thermophilus
#6
Yoichiro Togawa, Tatsuo Nunoshiba, Keiichiro Hiratsu
Markerless gene-disruption technology is particularly useful for effective genetic analyses of Thermus thermophilus (T. thermophilus), which have a limited number of selectable markers. In an attempt to develop a novel system for the markerless disruption of genes in T. thermophilus, we applied a Cre/lox system to construct a triple gene disruptant. To achieve this, we constructed two genetic tools, a loxP-htk-loxP cassette and cre-expressing plasmid, pSH-Cre, for gene disruption and removal of the selectable marker by Cre-mediated recombination...
August 24, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28840294/prediction-of-successful-shock-wave-lithotripsy-with-ct-a-phantom-study-using-texture-analysis
#7
Manoj Mannil, Jochen von Spiczak, Thomas Hermanns, Hatem Alkadhi, Christian D Fankhauser
OBJECTIVE: To apply texture analysis (TA) in computed tomography (CT) of urinary stones and to correlate TA findings with the number of required shockwaves for successful shock wave lithotripsy (SWL). MATERIALS AND METHODS: CT was performed on thirty-four urinary stones in an in vitro setting. Urinary stones underwent SWL and the number of required shockwaves for disintegration was recorded. TA was performed after post-processing for pixel spacing and image normalization...
August 24, 2017: Abdominal Radiology
https://www.readbyqxmd.com/read/28836368/an-asymmetric-pathway-to-dendrobine-by-a-transition-metal-catalyzed-cascade-process
#8
Yujin Lee, Elise M Rochette, Junyong Kim, David Y-K Chen
An asymmetric pathway to the caged tetracyclic pyrrolidine alkaloid, dendrobine, is reported. The successful synthetic strategy features a one-pot, sequential palladium-catalyzed enyne cycloisomerization and rhodium-catalyzed diene-assisted pyrrolidine formation by allylic CH activation. The developed transition-metal-catalyzed cascade process permits rapid access to the dendrobine core structure and circumvents the handling of labile intermediates. An intramolecular aldol condensation under carefully defined reaction conditions takes place with a concomitant detosylation, followed by reductive amine methylation, to afford a late-stage intermediate (previously identified by several prior dendrobine syntheses) in only 10 synthetic steps overall...
August 24, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28836232/diencephalic-pediatric-low-grade-glioma-harboring-the-braf-v600e-mutation-presenting-with-various-morphologies-in-sequential-biopsy-specimens
#9
Yukitomo Ishi, Kanako C Hatanaka, Shigeru Yamaguchi, Hiromi Fujita, Hiroaki Motegi, Hiroyuki Kobayashi, Shunsuke Terasaka, Kiyohiro Houkin
A 5-year-old boy underwent biopsy of an intra-axial calcified tumor in the hypothalamus, which was incidentally found. Based on the presence of ganglion-like cells combined with glial cell element, the pathological diagnosis was ganglioglioma. Because the tumor grew gradually in size over the next 2 years, he underwent chemotherapy with temozolomide. However, at 8 years of age, the boy developed hydrocephalus and the cystic lesion had re-grown. Endoscopic cyst fenestration and tumor biopsy was performed, and pathological diagnosis was tentatively oligodendroglioma based on the presence of tumor cells with a perinuclear halo...
August 23, 2017: Brain Tumor Pathology
https://www.readbyqxmd.com/read/28822464/using-simulation-to-assess-the-impact-of-triage-interruptions
#10
Kimberly D Johnson, Abeer Alhaj-Ali
INTRODUCTION: Interruptions are common in the emergency department and contribute to catastrophic errors. Care priorities and acuity levels are assigned during triage, meaning that mistakes and omissions during the triage process could have detrimental effects on patients. The purpose of this project was to assess the feasibility of investigating the impact of interruptions on triage and the decision-making process in a simulated setting. METHODS: A 2-phase, sequential exploratory mixed method design was used...
September 2017: Journal of Emergency Nursing: JEN: Official Publication of the Emergency Department Nurses Association
https://www.readbyqxmd.com/read/28807089/supramolecular-based-ultrasonic-assisted-dispersion-solidification-liquid-liquid-microextraction-of-copper-and-cobalt-prior-to-their-flame-atomic-absorption-spectrometry-determination
#11
Ardeshir Shokrollahi, Foroogh Ebrahimi
In the present work, a simple, efficient, and environmentally friendly method was proposed for the simultaneous preconcentration and determination of minute quantities of copper and cobalt in water samples and serum by a supramolecular-based ultrasonic-assisted dispersion solidification liquid–liquid microextraction (DSLLME) procedure coupled with flame atomic absorption spectrometry. The procedure is based on the DSLLME of copper and cobalt with decanoic acid–tetrahydrofuran supramolecular solvent (SUPRAS) in the presence of sodium diethyldithiocarbamate, as the complexing agent...
August 15, 2017: Journal of AOAC International
https://www.readbyqxmd.com/read/28807034/exosomes-from-embryonic-mesenchymal-stem-cells-alleviate-osteoarthritis-through-balancing-synthesis-and-degradation-of-cartilage-extracellular-matrix
#12
Yafei Wang, Dongsheng Yu, Zhiming Liu, Fang Zhou, Jun Dai, Bingbing Wu, Jing Zhou, Boon Chin Heng, Xiao Hui Zou, Hongwei Ouyang, Hua Liu
BACKGROUND: Mesenchymal stem cell therapy for osteoarthritis (OA) has been widely investigated, but the mechanisms are still unclear. Exosomes that serve as carriers of genetic information have been implicated in many diseases and are known to participate in many physiological processes. Here, we investigate the therapeutic potential of exosomes from human embryonic stem cell-induced mesenchymal stem cells (ESC-MSCs) in alleviating osteoarthritis (OA). METHODS: Exosomes were harvested from conditioned culture media of ESC-MSCs by a sequential centrifugation process...
August 14, 2017: Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/28805260/determination-of-carbon-isotope-enrichment-factors-of-cis-dce-after-precursor-amendment
#13
Simon Leitner, Thomas G Reichenauer, Andrea Watzinger
RATIONALE: Bacterial reductive dechlorination of the groundwater contaminant tetrachloroethene (PCE) involves the formation of lower chlorinated metabolites. Metabolites can be instantaneously formed and consumed in this sequential process; quantification and validation of their isotopic effects conventionally rely on separate laboratory microcosm studies. Here, we present an evaluation method enabling the determination of the carbon isotope enrichment factor (ε) for the intermediate cis-dichloroethene (cis-DCE) by a single laboratory microcosm study initially amending the precursor PCE only...
August 14, 2017: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/28803110/dynamics-of-microbial-activities-and-community-structures-in-activated-sludge-under-aerobic-starvation
#14
Wenlong Liu, Yongzhen Peng, Bin Ma, Linna Ma, Fangxu Jia, Xiyao Li
The knowledge of the effect of aerobic starvation on the functional bacterial activities and community structures is important for the recovery of nutrient removal in activated sludge system. Four aerobic starvation processes (3, 7, 14 and 30days) for nitrifiers and polyphosphate accumulating organisms (PAOs) were studied. The results showed that nitrifiers could utilize the released ammonium for growth during the first 7days of the aerobic starvation, and then gradually decayed. In the recovery period, the slower recovery ability of nitrite-oxidizing bacteria (NOB) than ammonium-oxidizing bacteria (AOB) contributed to the nitrite accumulation...
November 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28802715/elucidating-virus-entry-using-a-tetracysteine-tagged-virus
#15
REVIEW
Bjorn-Patrick Mohl, Polly Roy
Fluorescent tags constitute an invaluable tool in facilitating a deeper understanding of the mechanistic processes governing virus-host interactions. However, when selecting a fluorescent tag for in vivo imaging of cells, a number of parameters and aspects must be considered. These include whether the tag may affect and interfere with protein conformation or localization, cell toxicity, spectral overlap, photo-stability and background. Cumulatively, these constitute challenges to be overcome. Bluetongue virus (BTV), a member of the Orbivirus genus in the Reoviridae family, is a non-enveloped virus that is comprised of two architecturally complex capsids...
August 9, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28789690/first-year-medical-students-learning-style-preferences-and-their-correlation-with-performance-in-different-subjects-within-the-medical-course
#16
Daniel Hernández-Torrano, Syed Ali, Chee-Kai Chan
BACKGROUND: Students commencing their medical training arrive with different educational backgrounds and a diverse range of learning experiences. Consequently, students would have developed preferred approaches to acquiring and processing information or learning style preferences. Understanding first-year students' learning style preferences is important to success in learning. However, little is understood about how learning styles impact learning and performance across different subjects within the medical curriculum...
August 8, 2017: BMC Medical Education
https://www.readbyqxmd.com/read/28783460/engaging-parents-in-early-head-start-home-based-programs-how-do-home-visitors-do-this
#17
Caroline Shanti
Parental engagement is considered elemental to successful outcomes for parents and their children in early childhood home visiting programs. Engagement is that piece of parental involvement that refers to the working relationship between the parent and the home visitor. Multiple papers have called for research to pinpoint the ways in which home visitors work with parents to form these working relationships, and form partnerships to achieve positive outcomes. Analysis revealed that in individualizing their efforts to each family, home visitors follow semi-sequential steps in implementing engagement...
September 2017: Journal of Evidence-informed Social Work
https://www.readbyqxmd.com/read/28750535/evaluation-of-dna-methyltransferase-activity-and-inhibition-via-isothermal-enzyme-free-concatenated-hybridization-chain-reaction
#18
Qing Wang, Min Pan, Jie Wei, Xiaoqing Liu, Fuan Wang
Methyltransferase (MTase)-catalyzed DNA methylation plays a vital role in the biological epigenetic processes of key diseases and has attracted increasing attention, making the amplified detection of MTase activity of great significance in clinical disease diagnosis and treatment. Herein, we developed an isothermal, enzyme-free, and autonomous strategy for analyzing MTase activity based on concatenated hybridization chain reaction (C-HCR)-mediated Förster resonance energy transfer (FRET). In a typical C-HCR procedure without MTase (Dam), Y-shaped initiator DNA activates upstream HCR-1 to assemble a double-stranded DNA (dsDNA) copolymeric nanowire consisting of multiple tandem DNA trigger units that motivate downstream HCR-2 to successively bring a fluorophore donor/acceptor (FAM/TAMRA) pair into close proximity, leading to the generation of an amplified FRET readout signal...
July 28, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28721044/stimulated-phase-shift-acoustic-nanodroplets-enhance-vancomycin-efficacy-against-methicillin-resistant-staphylococcus-aureus-biofilms
#19
Hao Guo, Ziming Wang, Quanyin Du, Pan Li, Zhigang Wang, Aimin Wang
PURPOSE: Bacterial biofilms on the surface of prostheses are becoming a rising concern in managing prosthetic joint infections. The inherent resistant features of biofilms render traditional antimicrobial therapy unproductive and revision surgery outcomes uncertain. This situation has prompted the exploration of novel antimicrobial strategies. The synergy of ultrasound microbubbles and vancomycin has been proposed as an efficient alternative for biofilm eradication. The purpose of this study was to evaluate the anti-biofilm effect of stimulated phase-shift acoustic nanodroplets (NDs) combined with vancomycin...
2017: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/28719199/giant-pbse-cdse-cdse-quantum-dots-crystal-structure-defined-ultrastable-near-infrared-photoluminescence-from-single-nanocrystals
#20
Christina J Hanson, Nicolai F Hartmann, Ajay Singh, Xuedan Ma, William J I DeBenedetti, Joanna L Casson, John K Grey, Yves J Chabal, Anton V Malko, Milan Sykora, Andrei Piryatinski, Han Htoon, Jennifer A Hollingsworth
Toward a truly photostable PbSe quantum dot (QD), we apply the thick-shell or "giant" QD structural motif to this notoriously environmentally sensitive nanocrystal system. Namely, using a sequential application of two shell-growth techniques-partial-cation exchange and successive ionic layer adsorption and reaction (SILAR)-we are able to overcoat the PbSe QDs with sufficiently thick CdSe shells to impart new single-QD-level photostability, as evidenced by suppression of both photobleaching and blinking behavior...
August 16, 2017: Journal of the American Chemical Society
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