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https://www.readbyqxmd.com/read/28535189/predicting-accurate-contacts-in-thousands-of-pfam-domain-families-using-pconsc3
#1
Mirco Michel, Marcin J Skwark, David Menéndez Hurtado, Magnus Ekeberg, Arne Elofsson
Motivation: A fewyears ago it was shown that by using amaximumentropy approach to describe couplings between columns in a multiple sequence alignment it is possible to significantly increase the accuracy of residue contact predictions. For very large protein families with more than 1000 effective sequences the accuracy is sufficient to produce accurate models of proteins as well as complexes. Today, for about half of all Pfam domain families no structure is known, but unfortunately most of these families have at most a few hundred members, i...
May 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28534797/transition-icons-for-time-series-visualization-and-exploratory-analysis
#2
Paul Nickerson, Raheleh Baharloo, Amal A Wanigatunga, Todd D Manini, Patrick J Tighe, Parisa Rashidi
The modern healthcare landscape has seen the rapid emergence of techniques and devices which temporally monitor and record physiological signals. The prevalence of time series data within the healthcare field necessitates the development of methods which can analyze the data in order to draw meaningful conclusions. Time series behavior is notoriously difficult to intuitively understand due to its intrinsic high-dimensionality, which is compounded in the case of analyzing groups of time series collected from different patients...
May 16, 2017: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/28531976/synthesis-of-in-situ-formable-hydrogels-with-collagen-and-hyaluronan-through-facile-michael-addition
#3
Riwang Li, Zhengwei Cai, Zhiwen Li, Qian Zhang, Shuyun Zhang, Li Deng, Lu Lu, Lihua Li, Changren Zhou
To mimic the natural extracellular matrix (ECM) and to facilitate tissue regeneration, in-situ formable collagen/hyaluronan composite hydrogels were prepared by a facile approach via Michael addition reaction, with maleilated collagen (Col-MA) and thiol derivatized hyaluronan (HA-SH). The hydrogels were denoted as CHG-1, CHG-2, CHG-3 and CHG-4 by vinyl/free thiol molar ratio (f) of 1:1, 1:2, 1:3 and 1:4, respectively. Results showed that with decrease of the f values, the gelation time decreased from 43s to 15s, Young's modulus increased from 1671...
August 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28530008/field-strength-and-frequency-tunable-two-way-rotation-of-liquid-crystal-micro-particles-dispersed-in-a-liquid-crystal-host
#4
Koki Imamura, Hiroyuki Yoshida, Masanori Ozaki
Liquid crystal (LC) micro-particles are functional materials possessing anisotropies of LCs originating from their inner molecular alignment, and are fabricated by polymerizing pre-aligned rod-like molecules in the LC state. Here we demonstrate field strength and frequency tunable two-way rotation control of LC micro-particles in a LC host, and unravel its mechanism by theoretically calculating the contributing free energies. Cuboid-shaped micro-particles with inner molecular alignment along the long axis are fabricated via two-photon excited direct laser writing, and dispersed in a dual-frequency (DF) LC to be electrically driven by a voltage applied in the in-plane direction of the cell...
May 22, 2017: Soft Matter
https://www.readbyqxmd.com/read/28521059/pediatric-clival-chordoma-a-curable-disease-that-conforms-to-collins-law
#5
Marcio S Rassi, M Maher Hulou, Kaith Almefty, Wenya Linda Bi, Svetlana Pravdenkova, Ian F Dunn, Timothy R Smith, Ossama Al-Mefty
BACKGROUND: Skull base chordomas in children are extremely rare. Their course, management, and outcome have not been defined. OBJECTIVE: To describe the preeminent clinical and radiological features in a series of pediatric patients with skull base chordomas and analyze the outcome of a cohort who underwent uniform treatment. We emphasize predictors of overall survival and progression-free survival, which aligns with Collins' law for embryonal tumors. METHODS: Thirty-one patients with a mean age of 10...
May 17, 2017: Neurosurgery
https://www.readbyqxmd.com/read/28514169/engineering-interface-structure-to-improve-efficiency-and-stability-of-organometal-halide-perovskite-solar-cells
#6
Longbin Qiu, Luis K Ono, Yan Jiang, Matthew R Leyden, Sonia R Raga, Shenghao Wang, Yabing Qi
The rapid rise of power conversion efficiency (PCE) of low cost organometal halide perovskite solar cells suggests that these cells are a promising alternative to conventional photovoltaic technology. However, anomalous hysteresis and unsatisfactory stability hinder the industrialization of perovskite solar cells. Interface engineering is of importance for the fabrication of highly stable and hysteresis free perovskite solar cells. Here we report that a surface modification of the widely used TiO2 compact layer can give insight into interface interaction in perovskite solar cells...
May 17, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28505831/fast-switching-chiral-nematic-liquid-crystal-mode-with-polymer-sustained-twisted-vertical-alignment
#7
Kai-Han Chang, Vinay Joshi, Liang-Chy Chien
We demonstrate a fast-switching liquid-crystal mode with polymer-sustained twisted vertical alignment. By optimizing the polymerization condition, a polymer microstructure with controlled orientation is produced. The polymer microstructure not only synergistically suppresses the optical bounce during field-induced homeotropic-twist transition but also shortens the response time significantly. Theoretical analyses validate that the ground state free energy density is modified by the aligning field of the polymer microstructure, which affects the driving voltage of the device...
April 2017: Physical Review. E
https://www.readbyqxmd.com/read/28501956/an-in-vitro-evaluation-of-sagittal-alignment-in-the-cervical-spine-after-insertion-of-supraphysiologic-lordotic-implants
#8
Donald J Blaskiewicz, Jeffrey E Harris, Patrick P Han, Alexander W Turner, Gregory M Mundis
PURPOSE: Cervical spine malalignment can develop as a consequence of degenerative disc disease or following spinal surgery. When normal sagittal alignment of the spine is disrupted, further degeneration may occur adjacent to the deformity. The purpose of this study was to investigate changes in lordosis and sagittal alignment in the cervical spine after insertion of supraphysiologic lordotic implants. METHODS: Eight cadaveric cervical spines (Occiput-T1) were tested...
May 13, 2017: European Spine Journal
https://www.readbyqxmd.com/read/28494366/aligned-copper-nanowires-as-a-cut-and-paste-exclusive-electrochemical-transducer-for-free-enzyme-highly-selective-quantification-of-intracellular-hydrogen-peroxide-in-cisplatin-treated-cells
#9
Laura García-Carmona, María Moreno-Guzmán, Aida Martín, Selma Benito Martínez, Ana B Fernández-Martínez, María Cristina González, Javier Lucio-Cazaña, Alberto Escarpa
The role and reliable quantification of intracellular hydrogen peroxide during cancer therapy constitutes an unexplored and fascinating application. In this work, we report the fabrication of vertically aligned copper nanowires (v-CuNWs) using electrosynthesis on templates, and their application as a cut-and-paste exclusive and flexible electrochemical transducer. This easily adaptable electrodic platform is demonstrated for a fast, simple and free-enzyme selective quantification of intracellular hydrogen peroxide in Cisplatin-treated human renal HK-2 cells...
May 1, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28492203/assessment-of-tobacco-control-efforts-in-three-sub-saharan-african-countries
#10
Akindele O Adebiyi, Akinbode Oluwafemi
BACKGROUND: Tobacco industry's undermining of tobacco control goes on unabated in sub-Saharan African countries, especially in Kenya, Nigeria, and Uganda. The Framework Convention on Tobacco Control (FCTC) contains provisions aimed at curbing these activities. However, the level to which FCTC is implemented and the strength of each country's tobacco control law will determine its usefulness in this regard. We determined the implementation status and strength of tobacco control laws in Kenya, Nigeria, and Uganda...
January 2017: Nigerian Postgraduate Medical Journal
https://www.readbyqxmd.com/read/28490745/a-nanofabricated-monolithic-path-separated-electron-interferometer
#11
Akshay Agarwal, Chung-Soo Kim, Richard Hobbs, Dirk van Dyck, Karl K Berggren
Progress in nanofabrication technology has enabled the development of numerous electron optic elements for enhancing image contrast and manipulating electron wave functions. Here, we describe a modular, self-aligned, amplitude-division electron interferometer in a conventional transmission electron microscope. The interferometer consists of two 45-nm-thick silicon layers separated by 20 μm. This interferometer is fabricated from a single-crystal silicon cantilever on a transmission electron microscope grid by gallium focused-ion-beam milling...
May 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28481970/foldit-standalone-a-video-game-derived-protein-structure-manipulation-interface-using-rosetta
#12
Robert Kleffner, Jeff Flatten, Andrew Leaver-Fay, David Baker, Justin B Siegel, Firas Khatib, Seth Cooper
Summary: Foldit Standalone is an interactive graphical interface to the Rosetta molecular modeling package. In contrast to most command-line or batch interactions with Rosetta, Foldit Standalone is designed to allow easy, real-time, direct manipulation of protein structures, while also giving access to the extensive power of Rosetta computations. Derived from the user interface of the scientific discovery game Foldit (itself based on Rosetta), Foldit Standalone has added more advanced features and removed the competitive game elements...
May 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28476562/a-novel-alignment-free-method-to-classify-protein-folding-types-by-combining-spectral-graph-clustering-with-chou-s-pseudo-amino-acid-composition
#13
Pooja Tripathi, Paras N Pandey
The present work employs pseudo amino acid composition (PseAAC) for encoding the protein sequences in their numeric form. Later this will be arranged in the similarity matrix, which serves as input for spectral graph clustering method. Spectral methods are used previously also for clustering of protein sequences, but they uses pair wise alignment scores of protein sequences, in similarity matrix. The alignment score depends on the length of sequences, so clustering short and long sequences together may not good idea...
May 3, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28473948/purely-ligamentous-flexion-distraction-injury-in-a-five-year-old-child-treated-with-surgical-management
#14
Ryan M Schiedo, William Lavelle, Nathaniel R Ordway, Tarush Rustagi, Mike H Sun
Chance fractures by definition are a type of flexion-distraction injury with concomitant vertebral body fracture. Although uncommon in the pediatric population, they are associated with motor vehicle accidents and typically involve the thoraco-lumbar spine. Injury occurs when the spine rotates about a fixed axis, such as a lap belt. Our case reports the management of a five-year-old girl involved in a head-on collision who suffered a purely ligamentous flexion-distraction injury (Chance-type injury, without bone involvement) at the L2-L3 vertebral level...
April 3, 2017: Curēus
https://www.readbyqxmd.com/read/28472388/cafe-accelerated-alignment-free-sequence-analysis
#15
Yang Young Lu, Kujin Tang, Jie Ren, Jed A Fuhrman, Michael S Waterman, Fengzhu Sun
Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, $d_2^*$ and $d_2^S$ are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software, aCcelerated Alignment-FrEe sequence analysis (CAFE), for efficient calculation of 28 alignment-free dissimilarity measures...
May 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28472320/chimerscope-a-novel-alignment-free-algorithm-for-fusion-transcript-prediction-using-paired-end-rna-seq-data
#16
You Li, Tayla B Heavican, Neetha N Vellichirammal, Javeed Iqbal, Chittibabu Guda
The RNA-Seq technology has revolutionized transcriptome characterization not only by accurately quantifying gene expression, but also by the identification of novel transcripts like chimeric fusion transcripts. The 'fusion' or 'chimeric' transcripts have improved the diagnosis and prognosis of several tumors, and have led to the development of novel therapeutic regimen. The fusion transcript detection is currently accomplished by several software packages, primarily relying on sequence alignment algorithms...
May 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28470311/size-and-strain-tunable-band-alignment-of-black-blue-phosphorene-lateral-heterostructures
#17
Yan Li, Fei Ma
Single-element lateral heterostructures composed of black and blue phosphorene are not only free from lattice mismatch but also exhibit rich physical properties related to the seamlessly stitched interfaces, providing the building blocks for designing atomically thin devices. Using first-principles calculations, we investigate the influence of interface structure, size effect and strain engineering on the electronic structure, effective masses and band alignment of black-blue phosphorene lateral heterostructures...
May 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28464826/microtaboo-a-general-and-practical-solution-to-the-k-disjoint-problem
#18
Mohammed Al-Jaff, Eric Sandström, Manfred Grabherr
BACKGROUND: A common challenge in bioinformatics is to identify short sub-sequences that are unique in a set of genomes or reference sequences, which can efficiently be achieved by k-mer (k consecutive nucleotides) counting. However, there are several areas that would benefit from a more stringent definition of "unique", requiring that these sub-sequences of length W differ by more than k mismatches (i.e. a Hamming distance greater than k) from any other sub-sequence, which we term the k-disjoint problem...
May 2, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28455730/knee-abduction-affects-greater-magnitude-of-change-in-acl-and-mcl-strains-than-matched-internal-tibial-rotation-in-vitro
#19
Nathaniel A Bates, Rebecca J Nesbitt, Jason T Shearn, Gregory D Myer, Timothy E Hewett
BACKGROUND: Anterior cruciate ligament (ACL) injures incur over USD 2 billion in annual medical costs and prevention has become a topic of interest in biomechanics. However, literature conflicts persist over how knee rotations contribute to ACL strain and ligament injury. To maximize the efficacy of ACL injury prevention, the effects of underlying mechanics need to be better understood. QUESTIONS/PURPOSES: We applied robotically controlled, in vivo-derived kinematic stimuli to the knee to assess ligament biomechanics in a cadaver model...
April 28, 2017: Clinical Orthopaedics and related Research
https://www.readbyqxmd.com/read/28453288/photothermal-transport-of-dna-in-entropy-landscape-plasmonic-waveguides
#20
Cameron L C Smith, Anil H Thilsted, Jonas N Pedersen, Tomas H Youngman, Julia C Dyrnum, Nicolai A Michaelsen, Rodolphe Marie, Anders Kristensen
The ability to handle single, free molecules in lab-on-a-chip systems is key to the development of advanced biotechnologies. Entropic confinement offers passive control of polymers in nanofluidic systems by locally asserting a molecule's number of available conformation states through structured landscapes. Separately, a range of plasmonic configurations have demonstrated active manipulation of nano-objects by harnessing concentrated electric fields. The integration of these two independent techniques promises a range of sophisticated and complementary functions to handle, for example, DNA, but numerous difficulties, in particular, conflicting requirements of channel size, have prevented progress...
April 28, 2017: ACS Nano
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