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https://www.readbyqxmd.com/read/28646754/free-energy-analysis-of-cell-spreading
#1
Eóin McEvoy, Vikram S Deshpande, Patrick McGarry
In this study we present a steady-state adaptation of the thermodynamically motivated stress fiber (SF) model of Vigliotti et al. (2015). We implement this steady-state formulation in a non-local finite element setting where we also consider global conservation of the total number of cytoskeletal proteins within the cell, global conservation of the number of binding integrins on the cell membrane, and adhesion limiting ligand density on the substrate surface. We present a number of simulations of cell spreading in which we consider a limited subset of the possible deformed spread-states assumed by the cell in order to examine the hypothesis that free energy minimization drives the process of cell spreading...
June 7, 2017: Journal of the Mechanical Behavior of Biomedical Materials
https://www.readbyqxmd.com/read/28640821/noise-reduction-in-single-time-frame-optical-dna-maps
#2
Paola C Torche, Vilhelm Müller, Fredrik Westerlund, Tobias Ambjörnsson
In optical DNA mapping technologies sequence-specific intensity variations (DNA barcodes) along stretched and stained DNA molecules are produced. These "fingerprints" of the underlying DNA sequence have a resolution of the order one kilobasepairs and the stretching of the DNA molecules are performed by surface adsorption or nano-channel setups. A post-processing challenge for nano-channel based methods, due to local and global random movement of the DNA molecule during imaging, is how to align different time frames in order to produce reproducible time-averaged DNA barcodes...
2017: PloS One
https://www.readbyqxmd.com/read/28621540/accurate-prediction-of-the-hydration-free-energies-of-20-salts-through-adaptive-force-matching-and-the-proper-comparison-with-experimental-references
#3
Jicun Li, Feng Wang
Simple pair-wise potentials for five alkali ions and four halide ions were developed by only fitting to ab initio MP2 forces with the adaptive force matching (AFM) method. Without fitting to any experimental information, the AFM models predict the hydration free energies of all 10 fluoride and chloride salts formed by these ions within 1.5% of experimental reference. The predicted hydration free energies for the 10 bromide and iodide salts are within 5-6% of experimental references with the larger error likely due to the neglect of explicit treatment of polarization and charge transfer...
June 16, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28620411/vicar-an-adaptive-and-landmark-free-registration-of-time-lapse-image-data-from-microfluidics-experiments
#4
Georges Hattab, Jan-Philip Schlüter, Anke Becker, Tim W Nattkemper
In order to understand gene function in bacterial life cycles, time lapse bioimaging is applied in combination with different marker protocols in so called microfluidics chambers (i.e., a multi-well plate). In one experiment, a series of T images is recorded for one visual field, with a pixel resolution of 60 nm/px. Any (semi-)automatic analysis of the data is hampered by a strong image noise, low contrast and, last but not least, considerable irregular shifts during the acquisition. Image registration corrects such shifts enabling next steps of the analysis (e...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28619296/understanding-north-american-yoga-therapists-attitudes-skills-and-use-of-evidence-based-practice-a-cross-national-survey
#5
Marlysa Sullivan, Matthew Leach, James Snow, Steffany Moonaz
INTRODUCTION: Little is known about the adoption of evidence-based practice (EBP) by yoga therapists (YTs). OBJECTIVE: To determine the attitudes, skills, training, use, barriers and facilitators to the use of EBP amongst North American YTs DESIGN: Cross-sectional, descriptive survey METHODS: Self-identified YTs practicing in North America were invited to participate in an online survey. YT attitudes, skills, training, utilisation, barriers to use, and facilitators of EBP use were measured using the 84-item Evidence-Based practice Attitude and utilization SurvEy (EBASE)...
June 2017: Complementary Therapies in Medicine
https://www.readbyqxmd.com/read/28617677/ferroelectric-switching-of-band-alignments-in-lsmo-pzt-co-multiferroic-tunnel-junctions-an-ab-initio-study
#6
Mighfar Imam, Natasa Stojic, N Binggeli
Band alignments in ferroelectric tunnel junctions (FTJs) are expected to play a critical role in determining the charge transport across the tunneling barrier. In general, however, the interface band discontinuities and their polarization dependence are not well known in these systems. Using a first-principles density-functional-theory approach, we explore the ferroelectric polarization dependence of the band alignments in La0.7Sr0.3MnO3/PbZr0.2Ti0.8O3/Co (LSMO/PZT/Co) multiferroic tunnel junctions, for which recent experiments indicated an ON/OFF conductivity behavior upon switching the PZT ferroelectric polarization...
June 15, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28617580/progressive-stereo-locking-psl-a-residual-dipolar-coupling-based-force-field-method-for-determining-the-relative-configuration-of-natural-products-and-other-small-molecules
#7
Gabriel Cornilescu, René F Ramos Alvarenga, Thomas P Wyche, Tim S Bugni, Roberto R Gil, Claudia C Cornilescu, William M Westler, John L Markley, Charles D Schwieters
Establishing the relative configuration of a bioactive natural product represents the most challenging part in determining its structure. Residual dipolar couplings (RDCs) are sensitive probes of the relative spatial orientation of internuclear vectors. We adapted a force field structure calculation methodology to allow free sampling of both R and S configurations of the stereocenters of interest. The algorithm uses a floating alignment tensor in a simulated annealing protocol to identify the conformations and configurations that best fit experimental RDC and distance restraints (from NOE and J-coupling data)...
June 15, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28617225/a-greedy-alignment-free-distance-estimator-for-phylogenetic-inference
#8
Sharma V Thankachan, Sriram P Chockalingam, Yongchao Liu, Ambujam Krishnan, Srinivas Aluru
BACKGROUND: Alignment-free sequence comparison approaches have been garnering increasing interest in various data- and compute-intensive applications such as phylogenetic inference for large-scale sequences. While k-mer based methods are predominantly used in real applications, the average common substring (ACS) approach is emerging as one of the prominent alignment-free approaches. This ACS approach has been further generalized by some recent work, either greedily or exactly, by allowing a bounded number of mismatches in the common substrings...
June 7, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28617222/an-extensive-assessment-of-network-alignment-algorithms-for-comparison-of-brain-connectomes
#9
Marianna Milano, Pietro Hiram Guzzi, Olga Tymofieva, Duan Xu, Christofer Hess, Pierangelo Veltri, Mario Cannataro
BACKGROUND: Recently the study of the complex system of connections in neural systems, i.e. the connectome, has gained a central role in neurosciences. The modeling and analysis of connectomes are therefore a growing area. Here we focus on the representation of connectomes by using graph theory formalisms. Macroscopic human brain connectomes are usually derived from neuroimages; the analyzed brains are co-registered in the image domain and brought to a common anatomical space. An atlas is then applied in order to define anatomically meaningful regions that will serve as the nodes of the network - this process is referred to as parcellation...
June 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28612446/interconnected-ternary-min2s4-m-fe-co-ni-thiospinels-nanosheets-array-a-type-of-efficient-pt-free-counter-electrodes-for-the-dye-sensitized-solar-cells
#10
Wenjing Hou, Yaoming Xiao, Gaoyi Han
The ternary iron group thiospinels of metal diindium sulfides (MIn2S4, M = Fe, Co, Ni) with the vertically aligned nanosheets array structure are fabricated through in situ solvothermal method on F-doped tin oxide substrates, which are employed as one type of platinum (Pt) free counter electrodes (CEs) in the structure-dependent dye-sensitized solar cells (DSSCs). DSSC assembled with ternary CoIn2S4 CE achieves an photoelectric conversion efficiency (PCE) of 8.83%, outperforming than that of FeIn2S4 (7.18%) and NiIn2S4 (8...
June 13, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28612199/mri-guided-radiotherapy-for-head-and-neck-cancer-initial-clinical-experience
#11
A M Chen, S Hsu, J Lamb, Y Yang, N Agazaryan, M L Steinberg, D A Low, M Cao
PURPOSE: To report a single-institutional experience with the use of magnetic resonance imaging (MRI)-guided radiotherapy for cancers of the head and neck. MATERIALS AND METHODS: Between October 2014 and October 2016, 18 patients with newly diagnosed cancers of the head and neck were prospectively enrolled on an institutional registry trial investigating the feasibility and efficacy of external-beam radiotherapy delivered using on-board MRI. All patients had biopsy-proven evidence of malignancy, measurable disease, and the ability to provide consent...
June 13, 2017: Clinical & Translational Oncology
https://www.readbyqxmd.com/read/28610557/integration-of-quantitated-expression-estimates-from-polya-selected-and-rrna-depleted-rna-seq-libraries
#12
Stephen J Bush, Mary E B McCulloch, Kim M Summers, David A Hume, Emily L Clark
BACKGROUND: The availability of fast alignment-free algorithms has greatly reduced the computational burden of RNA-seq processing, especially for relatively poorly assembled genomes. Using these approaches, previous RNA-seq datasets could potentially be processed and integrated with newly sequenced libraries. Confounding factors in such integration include sequencing depth and methods of RNA extraction and selection. Different selection methods (typically, either polyA-selection or rRNA-depletion) omit different RNAs, resulting in different fractions of the transcriptome being sequenced...
June 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28607784/use-of-nonvascularized-autologous-fibular-strut-graft-in-the-treatment-of-major-bone-defect-after-periprosthetic-knee-fracture
#13
Vincenzo Giordano, Bruno Parilha Coutinho, Mateus Kenji Miyahira, Felipe Serrão Mendes de Souza, Ney Pecegueiro do Amaral
We present the case of a patient who suffered a comminuted supracondylar periprosthetic femur fracture. The patient was an 86-year-old lady who suffered a minor fall at home and presented at our hospital with a right comminuted distal femur fracture around a total knee arthroplasty. The patient was submitted to a cruciate-sacrificing total knee replacement 6 years before at the same institution. Despite severe metaphyseal fragmentation and short distal fragment, the prosthesis was stable; thus, open fracture reduction and stabilization with internal fixation were performed...
2017: Case Reports in Orthopedics
https://www.readbyqxmd.com/read/28606076/flocculating-performance-of-a-bioflocculant-produced-by-arthrobacter-humicola-in-sewage-waste-water-treatment
#14
Mayowa Oladele Agunbiade, Esta Van Heerden, Carolina H Pohl, Anofi Tom Ashafa
BACKGROUND: The discharge of poorly treated effluents into the environment has far reaching, consequential impacts on human and aquatic life forms. Thus, we evaluated the flocculating efficiency of our test bioflocculant and we report for the first time the ability of the biopolymeric flocculant produced by Arthrobacter humicola in the treatment of sewage wastewater. This strain was isolated from sediment soil sample at Sterkfontein dam in the Eastern Free State province of South Africa...
June 12, 2017: BMC Biotechnology
https://www.readbyqxmd.com/read/28605460/modmaps3d-an-interactive-webtool-for-the-quantification-and-3d-visualization-of-interrelationships-in-a-dataset-of-dna-sequences
#15
Rallis Karamichalis, Lila Kari
Summary: MoDMaps3D (Molecular Distance Maps 3D) is an alignment-free, fast, computationally lightweight webtool for computing and visualizing the interrelationships within any dataset of DNA sequences, based on pairwise comparisons between their oligomer compositions. MoDMaps3D is a general-purpose interactive webtool that is free of any requirements on sequence composition, position of the sequences in their respective genomes, presence or absence of similarity or homology, sequence length, or even sequence origin (biological or computer-generated)...
June 10, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28601994/radiologic-features-of-dropped-head-syndrome-in-the-overall-sagittal-alignment-of-the-spine
#16
Kazuki Hashimoto, Hiroshi Miyamoto, Terumasa Ikeda, Masao Akagi
PURPOSE: Dropped head syndrome (DHS) is a rare clinical entity which is defined as a chin-on-chest deformity in the standing or sitting position, resulting from sagittal imbalance of the cervical region. The purpose of the present study was to clarify the radiologic features of DHS in the overall sagittal alignment of the spine. We also investigated the changes in sagittal alignment after correction surgery for DHS. METHODS: Twenty DHS patients [1 male and 19 female, with an average age of 78...
June 10, 2017: European Spine Journal
https://www.readbyqxmd.com/read/28601942/anatomic-reconstruction-of-the-medial-patellofemoral-ligament-in-children-and-adolescents-using-a-pedicled-quadriceps-tendon-graft-shows-favourable-results-at-a-minimum-of-2-year-follow-up
#17
Manfred Nelitz, Jens Dreyhaupt, Sean Robert March Williams
PURPOSE: In adults, reconstruction of the medial patellofemoral ligament (MPFL) has shown good results. Treatment for recurrent patellar instability in children and adolescents with open growth plates, however, requires alternative MPFL reconstruction techniques. This study presents the outcomes of a minimally invasive technique for anatomic reconstruction of the MPFL in children using a pedicled superficial quadriceps tendon graft, hardware-free patellar graft attachment, and anatomic femoral fixation that spares the distal femoral physis...
June 10, 2017: Knee Surgery, Sports Traumatology, Arthroscopy: Official Journal of the ESSKA
https://www.readbyqxmd.com/read/28596612/alignment-of-liquid-crystals-by-polymers-with-residual-amounts-of-solvents
#18
Alexander M Parshin, Victor Y Zyryanov, Vasily F Shabanov
The homogeneous nematic layers in liquid crystal cells with treated surfaces are affected by orientational transitions in the electric, magnetic, or temperature fields. The liquid crystal structures formed on solid or liquid surfaces find limited application in identifying the liquid-crystal states by the textures observed in polarized light. The use of surfaces prepared from polymer solutions makes it possible to significantly broaden the range of application of the liquid crystal structures. We investigate the structures with the continuous transformation of the nematic director orientation from radial to planar, which were formed by the polycarbonate surface in the presence of different residual solvents...
June 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28587743/a-novel-alignment-free-vector-method-to-cluster-protein-sequences
#19
Lily He, Yongkun Li, Rong Lucy He, Stephen S-T Yau
Classification of protein are crucial topics in biology. The number of protein sequences stored in databases increases sharply in the past decade. Traditionally, comparison of protein sequences is usually carried out through multiple sequence alignment methods. However, these methods may be unsuitable for clustering of protein sequences when gene rearrangements occur such as in viral genomes. The computation is also very time-consuming for large datasets with long genomes. In this paper, based on three important biochemical properties of amino acids: the hydropathy index, polar requirement and chemical composition of the side chain, we propose a 24 dimensional feature vector describing the composition of amino acids in protein sequences...
June 3, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28587088/locali-calibration-free-systematic-localization-approach-for-indoor-positioning
#20
Muhammad Usman Ali, Soojung Hur, Yongwan Park
Recent advancements in indoor positioning systems are based on infrastructure-free solutions, aimed at improving the location accuracy in complex indoor environments without the use of specialized resources. A popular infrastructure-free solution for indoor positioning is a calibration-based positioning, commonly known as fingerprinting. Fingerprinting solutions require extensive and error-free surveys of environments to build radio-map databases, which play a key role in position estimation. Fingerprinting also requires random updates of the database, when there are significant changes in the environment or a decrease in the accuracy...
May 25, 2017: Sensors
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