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https://www.readbyqxmd.com/read/28088762/the-super-n-motifs-model-a-novel-alignment-free-approach-for-representing-and-comparing-rna-secondary-structures
#1
Jean-Pierre Séhi Glouzon, Jean-Pierre Perreault, Shengrui Wang
MOTIVATION: Comparing ribonucleic acid (RNA) secondary structures of arbitrary size uncovers structural patterns that can provide a better understanding of RNA functions. However, performing fast and accurate secondary structure comparisons is challenging when we take into account the RNA configuration (i.e. linear or circular), the presence of pseudoknot and G-quadruplex (G4) motifs and the increasing number of secondary structures generated by high-throughput probing techniques. To address this challenge, we propose the super-n-motifs model based on a latent analysis of enhanced motifs comprising not only basic motifs but also adjacency relations...
January 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28088760/usp15-regulates-dynamic-protein-protein-interactions-of-the-spliceosome-through-deubiquitination-of-prp31
#2
Tanuza Das, Joon Kyu Park, Jinyoung Park, Eunji Kim, Michael Rape, Eunice EunKyeong Kim, Eun Joo Song
Post-translational modifications contribute to the spliceosome dynamics by facilitating the physical rearrangements of the spliceosome. Here, we report USP15, a deubiquitinating enzyme, as a regulator of protein-protein interactions for the spliceosome dynamics. We show that PRP31, a component of U4 snRNP, is modified with K63-linked ubiquitin chains by the PRP19 complex and deubiquitinated by USP15 and its substrate targeting factor SART3. USP15(SART3) makes a complex with USP4 and this ternary complex serves as a platform to deubiquitinate PRP31 and PRP3...
January 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28088748/a-dna-probe-based-on-phosphorescent-resonance-energy-transfer-for-detection-of-transgenic-35s-promoter-dna
#3
Jinzhi Lv, Yanming Miao, Jiajia Yang, Jin Qin, Dongxia Li, Guiqin Yan
A QDs-DNA nano-probe was made by combining Mn-doped ZnS room-temperature phosphorescence (RTP) quantum dots (QDs) and DNA. Then an RTP sensor for quantitative detection of genetically-modified mark sequence cauliflower mosaic virus 35S promoter (Ca MV 35S) DNA was built on basis of phosphorescent resonance energy transfer (PRET). The underlying principles were that a QDs-DNA water-soluble nano-probe was built by connecting single-strand DNA to the surfaces of QDs via a ligand exchange method. This probe had good RTP performance and could well identify Ca MV 35S...
January 7, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28088726/fabrication-of-highly-hydrophilic-filter-using-natural-and-hydrothermally-treated-mica-nanoparticles-for-efficient-waste-oil-water-separation
#4
Udara Bimendra Gunatilake, Jayasundera Bandara
For the effective oil/water separation, a novel superhydrophilic (underwater superoleophobic) filter is fabricated with the naturally and hydrothermally treated mica particles. To fabricate a double layered filter, hydrothermally treated mica particles were initially electrodeposited on a stainless steel mesh and a natural mica particles were sprayed on the first hydrothermally deposited mica layer. The double layered mica coated membrane showed superamphiphilic and superhydrophilic/superoleophobic (contact angle >159°) characteristics in air and underwater respectively...
January 12, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28088720/role-of-dissolved-mn-iii-in-transformation-of-organic-contaminants-non-oxidative-versus-oxidative-mechanisms
#5
Erdan Hu, Ya Zhang, Shuyan Wu, Jun Wu, Liyuan Liang, Feng He
Mn(III) is a strong oxidant for one electron transfer, which may be important in the transformation of organic contaminants during water/wastewater treatment and biogeochemical redox processes. This study explored the reaction mechanisms of dissolved Mn(III) with organics. The role of dissolved Mn(III) either as a catalyst or an oxidant in reactions with organics was recognized. Aquo and/or hydroxo (or free) Mn(III), generated from the bisulfite activated permanganate process, facilitated efficient N-dealkylation of atrazine via a β-elimination mechanism, resulting no net redox reaction...
January 7, 2017: Water Research
https://www.readbyqxmd.com/read/28088718/highly-efficient-inactivation-of-bacteria-found-in-drinking-water-using-chitosan-bentonite-composites-modelling-and-breakthrough-curve-analysis
#6
Sarah C Motshekga, Suprakas Sinha Ray
Disinfection of bacterially-contaminated drinking water requires a robust and effective technique and can be achieved by using an appropriate disinfectant material. The advanced use of nanomaterials is observed as an alternative and effective way for the disinfection process and water treatment as a whole. Hence, the inactivation of Escherichia coli (E. coli) using chitosan-Bentonite (Cts-Bent) composites was studied in a fixed bed column. Cts-Bent composites were synthesized using in situ cross-linking method using Bent-supported silver and zinc oxide nanoparticles...
January 3, 2017: Water Research
https://www.readbyqxmd.com/read/28088695/deep-metabolome-annotation-in-natural-products-research-towards-a-virtuous-cycle-in-metabolite-identification
#7
REVIEW
Pierre-Marie Allard, Grégory Genta-Jouve, Jean-Luc Wolfender
Natural products (NPs) research is changing and rapidly adopting cutting-edge tools, which radically transform the way to characterize extracts and small molecules. With the innovations in metabolomics, early integration of deep metabolome annotation information allows to efficiently guide the isolation of valuable NPs only and, in parallel, to generate massive metadata sets for the study of given extracts under various perspectives. This is the case for chemotaxonomy studies where common biosynthetic traits among species can be evidenced, but also for drug discovery purpose where such traits, in combination with bioactivity studies on extracts, may evidence bioactive molecules even before their isolation...
January 12, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28088691/stability-effect-of-cholesterol-poly-acrylic-acid-in-a-stimuli-responsive-polymer-liposome-complex-obtained-from-soybean-lecithin-for-controlled-drug-delivery
#8
M G Simões, P Alves, Manuela Carvalheiro, P N Simões
The development of polymer-liposome complexes (PLCs), in particular for biomedical applications, has grown significantly in the last decades. The importance of these studies comes from the emerging need in finding intelligent controlled release systems, more predictable, effective and selective, for applications in several areas, such as treatment and/or diagnosis of cancer, neurological, dermatological, ophthalmic and orthopedic diseases, gene therapy, cosmetic treatments, and food engineering. This work reports the development and characterization of a pH sensitive system for controlled release based on PLCs...
January 4, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28088668/near-infrared-light-triggered-drug-delivery-system-for-higher-efficacy-of-combined-chemo-photothermal-treatment
#9
Yi Chen, Haohuan Li, Yueyang Deng, Haifeng Sun, Xue Ke, Tianyuan Ci
: The combination of chemotherapy and photothermal therapy is a promising strategy for cancer treatment. In the present study, indocyanine green (ICG), a widely used near-infrared (NIR) dye in photothermal therapy, and chemotherapeutic drug-doxorubicin (DOX) were loaded within the nanoparticles of novel designed arylboronic ester and cholesterol modified hyaluronic acid (PPE-Chol1-HA), denoted as PCH-DI. We take advantage of reactive oxygen species (ROS) production capability of ICG and ROS-sensitivity of arylboronic ester to realize controllable drug release...
January 11, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28088667/cell-laden-hydrogels-for-osteochondral-and-cartilage-tissue-engineering
#10
REVIEW
Jingzhou Yang, Yu Shrike Zhang, Kan Yue, Ali Khademhosseini
: Despite tremendous advances in the field of regenerative medicine, it still remains challenging to repair the osteochondral interface and full-thickness articular cartilage defects. This inefficiency largely originates from the lack of appropriate tissue engineered artificial matrices that can replace the damaged regions and promote tissue regeneration. Hydrogels are emerging as a promising class of biomaterials for both soft and hard tissue regeneration. Many critical properties of hydrogels, such as mechanical stiffness, elasticity, water content, bioactivity, and degradation, can be rationally designed and conveniently tuned by proper selection of the material and chemistry...
January 11, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28088663/development-and-validation-of-a-sensitive-and-fast-uplc-ms-ms-method-for-simultaneous-determination-of-seven-bioactive-compounds-in-rat-plasma-after-oral-administration-of-guizhi-gancao-decoction
#11
Bin Ji, Limeng Zhuo, Bin Yang, Yang Wang, Lin Li, Miao Yu, Yunli Zhao, Zhiguo Yu
Rapid, sensitive, selective and accurate UPLC-MS/MS method was developed and fully validated for simultaneous determination of cinnamaldehyde, cinnamic acid, 2-methoxy cinnamic acid, glycyrrhizic acid, glycyrrhetinic acid, liquiritigenin and isoliquiritin in rat plasma after oral administration of Guizhi-gancao decoction. Plasma samples were processed with a simple protein precipitation technique using acetonitrile, followed by chromatographic separation using a Thermo Hypersil GOLD C18 column. A 11.0min linear gradient elution was used at a flow rate of 0...
January 9, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28088630/support-dependent-active-species-formation-for-cuo-catalysts-leading-to-efficient-pollutant-degradation-in-alkaline-conditions
#12
Yibing Li, Lianshuang Guo, Dekang Huang, Ali Jawad, Zhuqi Chen, Jiakuan Yang, Weidong Liu, Yan Shen, Mingkui Wang, Guochuan Yin
Redox metal ions play the crucial role in versatile advanced oxidation technologies, in which controlling the active species formation through catalyst design is one of the key challenges in oxidant utilization. This work describes an example of different active species formations in CuO-mediated degradation just because of supporting material differences. Although three CuO catalysts were prepared by similar procedures, it was found that CuO-MgO catalyst demonstrated high efficiency in phenol degradation with bicarbonate activated H2O2, in which the superoxide radical is crucial, while hydroxyl radical and singlet oxygen are ignorable...
December 31, 2016: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/28088617/assessing-physician-productivity-following-norwegian-hospital-reform-a-panel-and-data-envelopment-analysis
#13
Karl Arne Johannessen, Sverre A C Kittelsen, Terje P Hagen
BACKGROUND: Although health care reforms may improve efficiency at the macro level, less is known regarding their effects on the utilization of health care personnel. Following the 2002 Norwegian hospital reform, we studied the productivity of the physician workforce and the effect of personnel mix on this measure in all nineteen Norwegian hospitals from 2001 to 2013. METHODS: We used panel analysis and non-parametric data envelopment analysis (DEA) to study physician productivity defined as patient treatments per full-time equivalent (FTE) physician...
January 6, 2017: Social Science & Medicine
https://www.readbyqxmd.com/read/28088567/simple-fabrication-of-zeolitic-imidazolate-framework-zif-8-polymer-composite-beads-by-phase-inversion-method-for-efficient-oil-sorption
#14
Zahra Abbasi, Ezzatollah Shamsaei, Xi-Ya Fang, Bradley Ladewig, Huanting Wang
Zeolitic imidazolate framework ZIF-8 beads of 2-3mm in diameter were prepared using a simple one-step phase inversion method. The beads were fabricated by different amounts of ZIF-8 to polyether sulfone (PES) ratios. ZIF-8 played the role of an adsorbent while PES acted as a binder in the composite matrix to keep the ZIF-8 particles. Since ZIF-8 is highly hydrophobic, the beads floated on water and adsorbed oil droplets successfully. This efficient oil adsorption is attributed to the hydrophobicity and high surface area of ZIF-8 particles which can effectively adsorb oil droplets...
January 5, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28088565/rapid-microwave-assisted-growth-of-silver-nanoparticles-on-3d-graphene-networks-for-supercapacitor-application
#15
S Khamlich, T Khamliche, M S Dhlamini, M Khenfouch, B M Mothudi, M Maaza
Silver nanoparticles (AgNPs) grown on a three dimensional (3d) graphene networks (GNs) has been successfully prepared by an efficient and rapid microwave-assisted growth process to form GNs/AgNPs nanocomposite electrode materials for supercapacitor application. The 3d nature of the used GNs offers a unique architecture, which creates an efficient conduction networks and maximum utilization of space and interface, and acts as a conductive layer for the deposited AgNPs. The electrochemical performances of the fabricated electrode were evaluated by cyclic voltammetry (CV), galvanostatic charge/discharge and electrochemical impedance spectroscopy (EIS) tests...
January 7, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28088542/interaction-of-earthworms-microbe-facilitating-biofilm-dewaterability-performance-during-wasted-activated-sludge-reduction-and-stabilization
#16
Yadan Zheng, Meiyan Xing, Luziyu Cai, Tao Xiao, Yufan Lu, Jinzhou Jiang
Sludge dewaterability was chemically and morphologically explored during sewage sludge treatment by vermifiltration. The results, with a conventional biofilter (BF, no earthworms) as a control, demonstrated that the capillary suction time(CST) and specific resistance of filtration(SRF) of vermifilter (VF, with earthworms) treated sludge were 64.9±1.7s and (23.1±1.3)×10(12)m/kg,16.8% and 36.0% lower than that of the BF, respectively. Additionally, the VF could efficiently decompose loosely bound extracellular polymeric substances (LB-EPS), releasing more water trapped inside biofilm...
January 11, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28088540/multiplexed-site-specific-genome-engineering-for-overproducing-bioactive-secondary-metabolites-in-actinomycetes
#17
Lei Li, Guosong Zheng, Jun Chen, Mei Ge, Weihong Jiang, Yinhua Lu
Actinomycetes produce a large variety of pharmaceutically active compounds, yet production titers often require to be improved for discovery, development and large-scale manufacturing. Here, we describe a new technique, multiplexed site-specific genome engineering (MSGE) via the 'one integrase-multiple attB sites' concept, for the stable integration of secondary metabolite biosynthetic gene clusters (BGCs). Using MSGE, we achieved five-copy chromosomal integration of the pristinamycin II (PII) BGC in Streptomyces pristinaespiralis, resulting in the highest reported PII titers in flask and batch fermentations (2...
January 11, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28088527/navigation-in-the-electronic-health-record-a-review-of-the-safety-and-usability-literature
#18
REVIEW
Lisette C Roman, Jessica S Ancker, Stephen B Johnson, Yalini Senathirajah
OBJECTIVE: Inefficient navigation in electronic health records has been shown to increase users' cognitive load, which may increase potential for errors, reduce efficiency, and increase fatigue. However, navigation has received insufficient recognition and attention in the electronic health record (EHR) literature as an independent construct and contributor to overall usability. Our aims in this literature review were to (1) assess the prevalence of navigation-related topics within the EHR usability and safety research literature, (2) categorize types of navigation actions within the EHR, (3) capture relationships between these navigation actions and usability principles, and (4) collect terms and concepts related to EHR navigation...
January 11, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28088493/apoptosis-induced-by-the-methanol-extract-of-salvia-miltiorrhiza-bunge-in-non-small-cell-lung-cancer-through-pten-mediated-inhibition-of-pi3k-akt-pathway
#19
Yin-Tao Ye, Wei Zhong, Pei Sun, Dong Wang, Chen Wang, Li-Min Hu, Jun-Qiang Qian
ETHNOPHARMACOLOGICAL RELEVANCE: Salvia miltiorrhiza Bunge, a well-known traditional Chinese medicinal (TCM) plant, has been used to treat cardiovascular diseases since thousands of years. Many studies have reported that the active component tanshinones displayed a variety of biological activities: antithrombous, antiplatelet aggregation, antioxidant and antitumor promoting. But the mechanism of how the active components working still need to be clarified. The anti-tumor effect of compounds of tanshinone (CTN), the methanol extract of Salvia miltiorrhiza Bunge roots, was investigated...
January 11, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/28088486/pharmacological-targeting-of-adenosine-receptor-signaling
#20
REVIEW
Maria Peleli, Bertil Fredholm, Luis Sobrevia, Mattias Carlström
Adenosine receptor signaling plays important roles in normal physiology, but is also known to modulate the development or progression of several different diseases. The design of new, efficient, and safe pharmacological approaches to target the adenosine system may have considerable therapeutic potential, but is also associated with many challenges. This review summarizes the main challenges of adenosine receptor targeted treatment including tolerance, disease stage, cell type-specific effects, caffeine intake, adenosine level assessment and receptor distribution in vivo...
January 11, 2017: Molecular Aspects of Medicine
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