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Pradipta Ranjan Rauta, Sarbani Ashe, Debasis Nayak, Bismita Nayak
Virulence-related outer membrane proteins (Omps) are expressed in bacteria (Gram-negative) such as V. cholerae and are vital to bacterial invasion in to eukaryotic cell and survival within macrophages that could be best candidate for development of vaccine against V. cholerae. Applying in silico approaches, the 3-D model of the Omp was developed using Swiss model server and validated byProSA and Procheck web server. The continuous stretch of amino acid sequences 26mer: RTRSNSGLLTWGDKQTITLEYGDPAL and 31mer: FFAGGDNNLRGYGYKSISPQDASGALTGAKY having B-cell binding sites were selected from sequence alignment after B cell epitopes prediction by BCPred and AAP prediction modules of BCPreds...
October 12, 2016: Computational Biology and Chemistry
Lindsay V Slater, Joseph M Hart
The squat is an assessment of lower extremity alignment during movement, however there is little information regarding altered joint kinetics during poorly performed squats. The purpose of this study was to examine changes in joint kinetics and power from altered knee alignment during a squat. Thirty participants completed squats while displacing the knee medially, anteriorly, and with neutral alignment (control). Sagittal and frontal plane torques at the ankle, knee, and hip were altered in the descending and ascending phase of the squat in both the medial and anterior malaligned squat compared to the control squat...
October 12, 2016: Journal of Electromyography and Kinesiology
Xingxing Zhou, Anneng Yang, Zhongbing Huang, Guangfu Yin, Ximing Pu, Juan Jin
Extracellular matrix (ECM) can promote peripheral nerve repair. In this study, a conductive fiber-film (CFF) with core-sheath structure and conductivity of ∼10Scm(-1) was prepared by electrospinning of aligned poly(l-lactide acid) (PLLA) fibers and electrochemical deposition of polypyrole (PPy) nanoparticles. Then the multiple components of ECM, including laminin, fibronectin and collagen, were coated on the surface of CFF by culturing and lysing L929 cells to fabricate the bioactive scaffold of ECM-linked CFF (ECM-CFF)...
October 11, 2016: Colloids and Surfaces. B, Biointerfaces
Nils Krietenstein, Megha Wal, Shinya Watanabe, Bongsoo Park, Craig L Peterson, B Franklin Pugh, Philipp Korber
Chromatin remodelers regulate genes by organizing nucleosomes around promoters, but their individual contributions are obfuscated by the complex in vivo milieu of factor redundancy and indirect effects. Genome-wide reconstitution of promoter nucleosome organization with purified proteins resolves this problem and is therefore a critical goal. Here, we reconstitute four stages of nucleosome architecture using purified components: yeast genomic DNA, histones, sequence-specific Abf1/Reb1, and remodelers RSC, ISW2, INO80, and ISW1a...
October 20, 2016: Cell
Johan Kreuger, Paul O'Callaghan
Here we report on a technical difficulty we encountered while optimizing genotyping strategies to identify mice derived from Exoc3l2tm1a(KOMP)Wtsi embryonic stem cells obtained from the Knockout Mouse Project Repository. The Exoc3l2tm1a(KOMP)Wtsi construct encodes a "knockout-first" design with loxP sites that confer conditional potential (KO1st). We designed primers that targeted wild-type sequences flanking the most downstream element of the construct, an 80 base pair synthetic loxP region, which BLAST alignment analysis reveals is an element common to over 10,000 conditional gene-targeting mouse models...
2016: PloS One
Luca Santini, Santiago Saura, Carlo Rondinini
One of the biggest challenges in large-scale conservation is quantifying connectivity at broad geographic scales and for a large set of species. Because connectivity analyses can be computationally intensive, and the planning process quite complex when multiple taxa are involved, assessing connectivity at large spatial extents for many species turns to be often intractable. Such limitation results in that conducted assessments are often partial by focusing on a few key species only, or are generic by considering a range of dispersal distances and a fixed set of areas to connect that are not directly linked to the actual spatial distribution or mobility of particular species...
2016: PloS One
Higinio Mora, Jerónimo M Mora-Pascual, Alberto García-García, Pablo Martínez-González
The Iterative Closest Point (ICP) algorithm is currently one of the most popular methods for rigid registration so that it has become the standard in the Robotics and Computer Vision communities. Many applications take advantage of it to align 2D/3D surfaces due to its popularity and simplicity. Nevertheless, some of its phases present a high computational cost thus rendering impossible some of its applications. In this work, it is proposed an efficient approach for the matching phase of the Iterative Closest Point algorithm...
2016: PloS One
Stephen Matthew Quinnan
Obtaining optimal results in the treatment of extraarticular distal tibia fractures can be challenging. Plate and screw and intramedullary fixation have proven to be effective treatments, but are associated with significant complication rates when used for open fractures and patient with severe medical comorbidities. External fixation is a third alternative that is less often employed, but provides a very effective means of treatment. Circular external fixation offers great flexibility in obtaining anatomic alignment and stable fixation for even the most challenging distal tibia fractures...
November 2016: Journal of Orthopaedic Trauma
Stefan Kramel, Greg A Voth, Saskia Tympel, Federico Toschi
We introduce a new particle shape which shows preferential rotation in three dimensional homogeneous isotropic turbulence. We call these particles chiral dipoles because they consist of a rod with two helices of opposite handedness, one at each end. 3D printing is used to fabricate these particles with a length in the inertial range and their rotations are tracked in a turbulent flow between oscillating grids. High aspect ratio chiral dipoles preferentially align with their long axis along the extensional eigenvectors of the strain rate tensor, and the helical ends respond to the extensional strain rate with a mean spinning rate that is nonzero...
October 7, 2016: Physical Review Letters
Zuojia Wang, Kan Yao, Min Chen, Hongsheng Chen, Yongmin Liu
Swift electrons moving closely parallel to a periodic grating produce far-field radiation of light, which is known as the Smith-Purcell effect. In this letter, we demonstrate that designer Babinet metasurfaces composed of C-aperture resonators offer a powerful control over the polarization state of the Smith-Purcell emission, which can hardly be achieved via traditional gratings. By coupling the intrinsically nonradiative energy bound at the source current sheet to the out-of-plane electric dipole and in-plane magnetic dipole of the C-aperture resonator, we are able to excite cross-polarized light thanks to the bianisotropic nature of the metasurface...
October 7, 2016: Physical Review Letters
Pravas Deria, Diego A Gómez-Gualdrón, Idan Hod, Randall Q Snurr, Joseph T Hupp, Omar K Farha
Catalytic activity for acyl transfer from N-acetylimidazole (NAI) to different pyridylcarbinol (PC) regioisomers (2-PC, 3-PC, and 4-PC) is demonstrated for a set of topologically diverse, zirconium-based (porphinato)zinc metal-organic frameworks (MOFs). The MOFs studied are PCN-222, MOF-525, and NU-902, which are based on the csq, ftw, and scu topologies, respectively. The experimentally obtained reaction kinetics are discussed in light of molecular modeling results. The catalytic activity is shown to vary across the series of MOFs due to the different extent to which each topology facilitates reactant preconcentration and alignment of PC and NAI via coordination to framework porphyrin sites (orientation effects)...
October 21, 2016: Journal of the American Chemical Society
Stephanie Heinzlmeir, Denis Kudlinzki, Sridhar Sreeramulu, Susan Klaeger, Santosh Lakshmi Gande, Verena Linhard, Mathias Wilhelm, Huichao Qiao, Dominic Helm, Benjamin Ruprecht, Krishna Saxena, Guillaume Médard, Harald Schwalbe, Bernhard Kuster
The receptor tyrosine kinase EPHA2 (Ephrin type-A receptor 2) plays important roles in oncogenesis, metastasis and treatment resistance yet therapeutic targeting, drug discovery or investigation of EPHA2 biology is hampered by the lack of appropriate inhibitors and structural information. Here, we used chemical proteomics to survey 235 clinical kinase inhibitors for their kinase selectivity and identified 24 drugs with sub-micromolar affinities for EPHA2. NMR-based conformational dynamics together with nine new co-crystal structures delineated drug-EPHA2 interactions in full detail...
October 21, 2016: ACS Chemical Biology
Colin G Murphy, Michel P Bonnin, Antoine H Desbiolles, Yannick Carrillon, Tarik Aїt Si Selmi
BACKGROUND: Varus inclination of the uncemented stem is not necessarily a technical error. The proximal femoral anatomy of hips with a coxa vara deformity frequently predisposes varus inclination. METHODS: We reviewed a series of 200 patients undergoing primary uncemented THA with the Corail® hip system. Preoperative data were based on patient demographics, diagnosis, and radiographic information (preoperative templating-CT measurements), and compared postoperative alignment for each stem and type of stem used...
October 15, 2016: Hip International: the Journal of Clinical and Experimental Research on Hip Pathology and Therapy
C Jason Wang, Skye H Cheng, Jen-You Wu, Yi-Ping Lin, Wen-Hsin Kao, Chia-Li Lin, Yin-Jou Chen, Shu-Ling Tsai, Feng-Yu Kao, Andrew T Huang
Importance: Value-driven payment system reform is a potential tool for aligning economic incentives with the improvement of quality and efficiency of health care and containment of cost. Such a payment system has not been researched satisfactorily in full-cycle cancer care. Objective: To examine the association of outcomes and medical expenditures with a bundled-payment pay-for-performance program for breast cancer in Taiwan compared with a fee-for-service (FFS) program...
October 20, 2016: JAMA Oncology
Marcello Marelli, Claudio Evangelisti, Maria Vittoria Diamanti, Vladimiro Dal Santo, Mariapia Pedeferri, Claudia Letizia Bianchi, Luca Schiavi, Alberto Strini
A new protocol to synthesize size-controlled Au nanoparticles (NPs) loaded onto vertically aligned anatase TiO2 nanotubes arrays (TNTAs) prepared by electrochemical anodization is reported. Ligand-free Au NPs (< 10 nm) were deposited onto anatase TNTAs supports, finely tuning the Au loading by controlling the immersion time of the support into metal vapor synthesis (MVS)-derived Au-acetone solutions. The Au/TNTAs composites were characterized by electron microscopies (SEM, (S)TEM), X-ray diffraction, X-ray photoelectron spectroscopy and UV-Vis spectroscopy...
October 21, 2016: ACS Applied Materials & Interfaces
Bruce Wen, Kirby R Campbell, Karissa Tilbury, Oleg Nadiarnykh, Molly A Brewer, Manish Patankar, Vikas Singh, Kevin W Eliceiri, Paul J Campagnola
Remodeling of the collagen architecture in the extracellular matrix (ECM) has been implicated in ovarian cancer. To quantify these alterations we implemented a form of 3D texture analysis to delineate the fibrillar morphology observed in 3D Second Harmonic Generation (SHG) microscopy image data of normal (1) and high risk (2) ovarian stroma, benign ovarian tumors (3), low grade (4) and high grade (5) serous tumors, and endometrioid tumors (6). We developed a tailored set of 3D filters which extract textural features in the 3D image sets to build (or learn) statistical models of each tissue class...
October 21, 2016: Scientific Reports
P Jauhar, P A Mossey, H Popat, J Seehra, P S Fleming
Background Undergraduate orthodontic teaching has been focused on developing an understanding of occlusal development in an effort to equip practitioners to make appropriate referrals for specialist-delivered care. However, there is a growing interest among general dentists in delivering more specialised treatments, including short-term orthodontic alignment. This study aimed to assess the levels of knowledge of occlusal problems among final year undergraduate dental students, as well as their interest in various orthodontics techniques and training...
October 21, 2016: British Dental Journal
Gaohua Zhu, Jun Liu, Qiye Zheng, Ruigang Zhang, Dongyao Li, Debasish Banerjee, David G Cahill
Thermal conductivity of two-dimensional (2D) materials is of interest for energy storage, nanoelectronics and optoelectronics. Here, we report that the thermal conductivity of molybdenum disulfide can be modified by electrochemical intercalation. We observe distinct behaviour for thin films with vertically aligned basal planes and natural bulk crystals with basal planes aligned parallel to the surface. The thermal conductivity is measured as a function of the degree of lithiation, using time-domain thermoreflectance...
October 21, 2016: Nature Communications
Mutlu Mete, Unal Sakoglu, Jeffrey S Spence, Michael D Devous, Thomas S Harris, Bryon Adinoff
BACKGROUND: Neuroimaging studies have yielded significant advances in the understanding of neural processes relevant to the development and persistence of addiction. However, these advances have not explored extensively for diagnostic accuracy in human subjects. The aim of this study was to develop a statistical approach, using a machine learning framework, to correctly classify brain images of cocaine-dependent participants and healthy controls. In this study, a framework suitable for educing potential brain regions that differed between the two groups was developed and implemented...
October 6, 2016: BMC Bioinformatics
Sujoy Roy, Brandon C Curry, Behrouz Madahian, Ramin Homayouni
BACKGROUND: The amount of scientific information about MicroRNAs (miRNAs) is growing exponentially, making it difficult for researchers to interpret experimental results. In this study, we present an automated text mining approach using Latent Semantic Indexing (LSI) for prioritization, clustering and functional annotation of miRNAs. RESULTS: For approximately 900 human miRNAs indexed in miRBase, text documents were created by concatenating titles and abstracts of MEDLINE citations which refer to the miRNAs...
October 6, 2016: BMC Bioinformatics
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