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https://www.readbyqxmd.com/read/28339747/deep-learning-for-pharmacovigilance-recurrent-neural-network-architectures-for-labeling-adverse-drug-reactions-in-twitter-posts
#1
Anne Cocos, Alexander G Fiks, Aaron J Masino
Objective: Social media is an important pharmacovigilance data source for adverse drug reaction (ADR) identification. Human review of social media data is infeasible due to data quantity, thus natural language processing techniques are necessary. Social media includes informal vocabulary and irregular grammar, which challenge natural language processing methods. Our objective is to develop a scalable, deep-learning approach that exceeds state-of-the-art ADR detection performance in social media...
February 22, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28338417/a-3d-tissue-printing-approach-for-validation-of-diffusion-tensor-imaging-in-skeletal-muscle
#2
David B Berry, Shangting You, John Warner, Lawrence R Frank, Shaochen Chen, Samuel R Ward
The ability to noninvasively assess skeletal muscle microstructure, which predicts function and disease, would be of significant clinical value. One method that holds this promise is diffusion tensor magnetic resonance imaging (DT-MRI), which is sensitive to the microscopic diffusion of water within tissues and has become ubiquitous in neuroimaging as a way of assessing neuronal structure and damage. However, its application to the assessment of changes in muscle microstructure associated with injury, pathology, or age remains poorly defined, because it is difficult to precisely control muscle microstructural features in vivo...
March 24, 2017: Tissue Engineering. Part A
https://www.readbyqxmd.com/read/28338000/cavity-filling-mutations-at-the-thyroxine-binding-site-dramatically-increase-transthyretin-stability-and-prevent-its-aggregation
#3
Ricardo Sant'Anna, Maria Rosário Almeida, Nathalia Varejāo, Pablo Gallego, Sebastian Esperante, Priscila Ferreira, Alda Pereira-Henriques, Fernando L Palhano, Mamede de Carvalho, Debora Foguel, David Reverter, Maria João Saraiva, Salvador Ventura
More than a hundred different Transthyretin (TTR) mutations are associated with fatal systemic amyloidoses. They destabilize the protein tetrameric structure and promote the extracellular deposition of TTR as pathological amyloid fibrils. So far, only mutations R104H and T119M have been shown to stabilize significantly TTR, acting as disease suppressors. We describe a novel A108V non-pathogenic mutation found in a Portuguese subject. This variant is more stable than wild type TTR both in vitro and in human plasma, a feature that prevents its aggregation...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28337951/true-atomic-scale-imaging-in-three-dimensions-a-review-of-the-rebirth-of-field-ion-microscopy
#4
Francois Vurpillot, Frédéric Danoix, Matthieu Gilbert, Sebastian Koelling, Michal Dagan, David N Seidman
This article reviews recent advances utilizing field-ion microscopy (FIM) to extract atomic-scale three-dimensional images of materials. This capability is not new, as the first atomic-scale reconstructions of features utilizing FIM were demonstrated decades ago. The rise of atom probe tomography, and the application of this latter technique in place of FIM has unfortunately severely limited further FIM development. Currently, the ubiquitous availability of extensive computing power makes it possible to treat and reconstruct FIM data digitally and this development allows the image sequences obtained utilizing FIM to be extremely valuable for many material science and engineering applications...
March 24, 2017: Microscopy and Microanalysis
https://www.readbyqxmd.com/read/28335993/biomaterials-innovation-for-next-generation-ex%C3%A2-vivo-immune-tissue-engineering
#5
REVIEW
Ankur Singh
Primary and secondary lymphoid organs are tissues that facilitate differentiation of B and T cells, leading to the induction of adaptive immune responses. These organs are present in the body from birth and are also recognized as locations where self-reactive B and T cells can be eliminated during the natural selection process. Many insights into the mechanisms that control the process of immune cell development and maturation in response to infection come from the analysis of various gene-deficient mice that lack some or all hallmark features of lymphoid tissues...
March 15, 2017: Biomaterials
https://www.readbyqxmd.com/read/28335253/soft-interaction-in-liposome-nanocarriers-for-therapeutic-drug-delivery
#6
REVIEW
Domenico Lombardo, Pietro Calandra, Davide Barreca, Salvatore Magazù, Mikhail A Kiselev
The development of smart nanocarriers for the delivery of therapeutic drugs has experienced considerable expansion in recent decades, with the development of new medicines devoted to cancer treatment. In this respect a wide range of strategies can be developed by employing liposome nanocarriers with desired physico-chemical properties that, by exploiting a combination of a number of suitable soft interactions, can facilitate the transit through the biological barriers from the point of administration up to the site of drug action...
June 25, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28333956/discriminating-between-hur-and-ttp-binding-sites-using-the-k-spectrum-kernel-method
#7
Shweta Bhandare, Debra S Goldberg, Robin Dowell
BACKGROUND: The RNA binding proteins (RBPs) human antigen R (HuR) and Tristetraprolin (TTP) are known to exhibit competitive binding but have opposing effects on the bound messenger RNA (mRNA). How cells discriminate between the two proteins is an interesting problem. Machine learning approaches, such as support vector machines (SVMs), may be useful in the identification of discriminative features. However, this method has yet to be applied to studies of RNA binding protein motifs. RESULTS: Applying the k-spectrum kernel to a support vector machine (SVM), we first verified the published binding sites of both HuR and TTP...
2017: PloS One
https://www.readbyqxmd.com/read/28332640/leptospirosis-in-domestic-animals-in-france-serological-results-from-1988-to-2007
#8
G André-Fontaine
Leptospirosis is a common infection in domestic animals. The microscopic agglutination test (MAT) is used for serological diagnosis. From 1988 to 2007, the Leptospira Medical and Molecular Bacteriology Laboratory at the Nantes National College of Veterinary Medicine, Food Science and Engineering used the MAT to test serum samples from more than 40,000 cattle, 40,000 pigs, 20,000 horses and 9,500 dogs. Five Leptospira serogroups were prominent, with specific variations within the four animal species: Icterohaemorrhagiae, Australis, Sejroë, Grippotyphosa and Autumnalis...
December 2016: Revue Scientifique et Technique
https://www.readbyqxmd.com/read/28330431/fabrication-and-characterization-of-biphasic-silk-fibroin-scaffolds-for-tendon-ligament-to-bone-tissue-engineering
#9
Sònia Font Tellado, Walter Bonani, Elizabeth Rosado Balmayor, Peter Föhr, Antonella Motta, Claudio Migliaresi, Martijn van Griensven
Tissue engineering is an attractive strategy for tendon/ligament-to-bone interface repair. The structure and extracellular matrix composition of the interface are complex and allow for a gradual mechanical stress transfer between tendons/ligaments and bone. Thus, scaffolds mimicking the structural features of the native interface may be able to better support functional tissue regeneration. In this study, we fabricated biphasic silk fibroin scaffolds designed to mimic the gradient in collagen molecule alignment present at the interface...
March 23, 2017: Tissue Engineering. Part A
https://www.readbyqxmd.com/read/28330374/recent-developments-in-the-use-of-tyrosinase-and-laccase-in-environmental-applications
#10
Sidy Ba, Vaidyanathan Vinoth Kumar
Our current global environmental challenges include the reduction of harmful chemicals and their derivatives. Bioremediation has been a key strategy to control the massive presence of chemicals in the environment. Enzymes including the phenoloxidases, laccases and tyrosinases, are increasingly being investigated as "green products" in the removal of many chemical contaminants in waters and soils. Both phenoloxidases are widespread in nature and attractive biocatalysts due to their ability to use readily available molecular oxygen as sole cofactor for their catalytic elimination of a large number of chemicals...
March 22, 2017: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/28329704/the-ifn-%C3%AE-ifn-%C3%AE-r1-il-10r%C3%AE-complex-reveals-structural-features-underlying-type-iii-ifn-functional-plasticity
#11
Juan L Mendoza, William M Schneider, Hans-Heinrich Hoffmann, Koen Vercauteren, Kevin M Jude, Anming Xiong, Ignacio Moraga, Tim M Horton, Jeffrey S Glenn, Ype P de Jong, Charles M Rice, K Christopher Garcia
Type III interferons (IFN-λs) signal through a heterodimeric receptor complex composed of the IFN-λR1 subunit, specific for IFN-λs, and interleukin-10Rβ (IL-10Rβ), which is shared by multiple cytokines in the IL-10 superfamily. Low affinity of IL-10Rβ for cytokines has impeded efforts aimed at crystallizing cytokine-receptor complexes. We used yeast surface display to engineer a higher-affinity IFN-λ variant, H11, which enabled crystallization of the ternary complex. The structure revealed that IL-10Rβ uses a network of tyrosine residues as hydrophobic anchor points to engage IL-10 family cytokines that present complementary hydrophobic binding patches, explaining its role as both a cross-reactive but cytokine-specific receptor...
March 21, 2017: Immunity
https://www.readbyqxmd.com/read/28328943/structurally-detailed-coarse-grained-model-for-sec-facilitated-co-translational-protein-translocation-and-membrane-integration
#12
Michiel J M Niesen, Connie Y Wang, Reid C Van Lehn, Thomas F Miller
We present a coarse-grained simulation model that is capable of simulating the minute-timescale dynamics of protein translocation and membrane integration via the Sec translocon, while retaining sufficient chemical and structural detail to capture many of the sequence-specific interactions that drive these processes. The model includes accurate geometric representations of the ribosome and Sec translocon, obtained directly from experimental structures, and interactions parameterized from nearly 200 μs of residue-based coarse-grained molecular dynamics simulations...
March 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28328197/dual-band-electrochromic-devices-based-on-nb-doped-tio2-nanocrystalline-electrodes
#13
Mariam Barawi, Luca De Trizio, Roberto Giannuzzi, Giulia Veramonti, Liberato Manna, Michele Manca
The reliable exploitation of localized surface plasmon resonance in transparent conductive oxides is being prospected to push the blooming of an emerging class of advanced dynamic windows, which offer the opportunity to selectively, and dynamically, control the intensity of the incoming thermal radiation without affecting visible transparency. In this view, Nb-doped TiO2 colloidal nanocrystals are particularly promising as they have a wide bandgap and their plasmonic features can be finely tailored across the near infrared region by varying the concentration of dopants...
March 22, 2017: ACS Nano
https://www.readbyqxmd.com/read/28326561/hemoxcell-a-new-oxygen-carrier-usable-as-an-additive-for-mesenchymal-stem-cell-culture-in-platelet-lysate-supplemented-media
#14
Fiona Le Pape, Lucie Cosnuau-Kemmat, Gaëlle Richard, Frédéric Dubrana, Claude Férec, Franck Zal, Elisabeth Leize, Pascal Delépine
Human mesenchymal stem cells (MSCs) are promising candidates for therapeutic applications such as tissue engineering. However, one of the main challenges is to improve oxygen supply to hypoxic areas to reduce oxygen gradient formation while preserving MSC differentiation potential and viability. For this purpose, a marine hemoglobin, HEMOXCell, was evaluated as an oxygen carrier for culturing human bone marrow MSCs in vitro for future three-dimensional culture applications. Impact of HEMOXCell on cell growth and viability was assessed in human platelet lysate (hPL)-supplemented media...
March 22, 2017: Artificial Organs
https://www.readbyqxmd.com/read/28324641/preparation-of-a-non-woven-poly-%C3%AE%C2%B5-caprolactone-fabric-with-partially-embedded-apatite-surface-for-bone-tissue-engineering-applications-by-partial-surface-melting-of-poly-%C3%AE%C2%B5-caprolactone-fibers
#15
In Ae Kim, Sang-Hoon Rhee
This paper describes a novel method for the preparation of a biodegradable non-woven poly(ε-caprolactone) fabric with a partially-embedded apatite surface designed for application as a scaffold material for bone tissue engineering. The non-woven poly(ε-caprolactone) fabric was generated by the electro-spinning technique and then apatite was coated in simulated body fluid after coating the PVA solution containing CaCl2 ·2H2 O. The apatite crystals were partially- or fully-embedded into the thermoplastic poly(ε-caprolactone) fibers by controlling the degree of poly(ε-caprolactone) fiber surface melting in a convection oven...
March 21, 2017: Journal of Biomedical Materials Research. Part A
https://www.readbyqxmd.com/read/28324629/electrospun-nerve-guide-scaffold-of-poly-%C3%AE%C2%B5-caprolactone-collagen-nano-bioglass-an-in-vitro-study-in-peripheral-nerve-tissue-engineering
#16
Forouzan Mohamadi, Somayeh Ebrahimi-Barough, Mohammad Reza Nourani, Mohammad Ali Derakhshan, Vahabodin Goodarzi, Mohammad Sadegh Nazockdast, Mehdi Farokhi, Roksana Tajerian, Reza Faridi Majidi, Jafar Ai
In among of various methods, nerve tissue engineering (NTE) is one of the applicable methods to reconstruct damaged nerve tissues. Electrospinning technique and biomaterials are often considered to fabricate fibrous tissue engineered conduits which have great similarity to the extracellular matrix on fiber structure. Polymer blending is one of the most effective methods for production of new materials with outstanding features. In this research, conduit structures as main part of the peripheral nerve regeneration based on polymer blend nanocomposites PCL/Collagen/NBG (poly (ε-caprolactone)/Collagen/nano bioglass) were manufactured by electrospinning technique...
March 21, 2017: Journal of Biomedical Materials Research. Part A
https://www.readbyqxmd.com/read/28324143/rapid-customised-operon-assembly-by-yeast-recombinational-cloning
#17
Michael A Liu, Johanna J Kenyon, Jason Lee, Peter R Reeves
We have developed a system called the Operon Assembly Protocol (OAP), which takes advantage of the homologous recombination DNA repair pathway in Saccharomyces cerevisiae to assemble full-length operons from a series of overlapping PCR products into a specially engineered yeast-Escherichia coli shuttle vector. This flexible, streamlined system can be used to assemble several operon clones simultaneously, and each clone can be expressed in the same E. coli tester strain to facilitate direct functional comparisons...
March 21, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28321439/overexpression-of-parkinson-s-disease-associated-mutation-lrrk2-g2019s-in-mouse-forebrain-induces-behavioral-deficits-and-%C3%AE-synuclein-pathology
#18
Yulan Xiong, Stewart Neifert, Senthilkumar S Karuppagounder, Jeannette N Stankowski, Byoung Dae Lee, Jonathan C Grima, Guanxing Chen, Han Seok Ko, Yunjong Lee, Debbie Swing, Lino Tessarollo, Ted M Dawson, Valina L Dawson
Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene have been identified as an unambiguous cause of late-onset, autosomal-dominant familial Parkinson's disease (PD) and LRRK2 mutations are the strongest genetic risk factor for sporadic PD known to date. A number of transgenic mice expressing wild-type or mutant LRRK2 have been described with varying degrees of LRRK2-related abnormalities and modest pathologies. None of these studies directly addressed the role of the kinase domain in the changes observed and none of the mice present with robust features of the human disease...
March 2017: ENeuro
https://www.readbyqxmd.com/read/28320939/decoupling-local-mechanics-from-large-scale-structure-in-modular-metamaterials
#19
Nan Yang, Jesse L Silverberg
A defining feature of mechanical metamaterials is that their properties are determined by the organization of internal structure instead of the raw fabrication materials. This shift of attention to engineering internal degrees of freedom has coaxed relatively simple materials into exhibiting a wide range of remarkable mechanical properties. For practical applications to be realized, however, this nascent understanding of metamaterial design must be translated into a capacity for engineering large-scale structures with prescribed mechanical functionality...
March 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28319854/extremely-thermophilic-energy-metabolisms-biotechnological-prospects
#20
REVIEW
Christopher T Straub, Benjamin M Zeldes, Gerrit J Schut, Michael Ww Adams, Robert M Kelly
New strategies for metabolic engineering of extremely thermophilic microorganisms to produce bio-based fuels and chemicals could leverage pathways and physiological features resident in extreme thermophiles for improved outcomes. Furthermore, very recent advances in genetic tools for these microorganisms make it possible for them to serve as metabolic engineering hosts. Beyond providing a higher temperature alternative to mesophilic platforms, exploitation of strategic metabolic characteristics of high temperature microorganisms grants new opportunities for biotechnological products...
March 16, 2017: Current Opinion in Biotechnology
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