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https://www.readbyqxmd.com/read/28521784/functional-regression-method-for-whole-genome-eqtl-epistasis-analysis-with-sequencing-data
#1
Kelin Xu, Li Jin, Momiao Xiong
BACKGROUND: Epistasis plays an essential rule in understanding the regulation mechanisms and is an essential component of the genetic architecture of the gene expressions. However, interaction analysis of gene expressions remains fundamentally unexplored due to great computational challenges and data availability. Due to variation in splicing, transcription start sites, polyadenylation sites, post-transcriptional RNA editing across the entire gene, and transcription rates of the cells, RNA-seq measurements generate large expression variability and collectively create the observed position level read count curves...
May 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28516387/a-diffusion-weighted-imaging-informed-continuum-model-of-the-rabbit-triceps-surae-complex
#2
M Alipour, K Mithraratne, J Fernandez
The NZ white rabbit is the animal of choice for much experimental work due to its muscular frame and similar response to human diseases, and is one of the few mammals that have had their genome sequenced. However, continuum-level computational models of rabbit muscle detailing fibre architecture are limited in the literature, especially the triceps surae complex (gastrocnemius, plantaris and soleus), which has similar biomechanics and translatable findings to the human. This study presents a geometrical model of the rabbit triceps surae informed with diffusion-weighted imaging (DWI)-based fibres...
May 18, 2017: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/28450168/tuning-complement-activation-and-pathway-through-controlled-molecular-architecture-of-dextran-chains-in-nanoparticle-corona
#3
Jean-Baptiste Coty, Elquio Eleamen Oliveira, Christine Vauthier
The understanding of complement activation by nanomaterials is a key to a rational design of safe and efficient nanomedicines. This work proposed a systematic study investigating how molecular design of nanoparticle coronas made of dextran impacts on mechanisms that trigger complement activation. The nanoparticles used for this work consisted of dextran-coated poly(isobutylcyanoacrylate) (PIBCA) nanoparticles have already been thoroughly characterized. Their different capacity to trigger complement activation established on the cleavage of the protein C3 was also already described making these nanoparticles good models to investigate the relation between the molecular feature of their corona and the mechanism by which they triggered complement activation...
April 24, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28449714/detecting-central-fixation-by-means-of-artificial-neural-networks-in-a-pediatric-vision-screener-using-retinal-birefringence-scanning
#4
Boris I Gramatikov
BACKGROUND: Reliable detection of central fixation and eye alignment is essential in the diagnosis of amblyopia ("lazy eye"), which can lead to blindness. Our lab has developed and reported earlier a pediatric vision screener that performs scanning of the retina around the fovea and analyzes changes in the polarization state of light as the scan progresses. Depending on the direction of gaze and the instrument design, the screener produces several signal frequencies that can be utilized in the detection of central fixation...
April 27, 2017: Biomedical Engineering Online
https://www.readbyqxmd.com/read/28439858/circular-chromosome-conformation-capture-in-plants
#5
Stefan Grob
The study of nuclear architecture promises novel insights into genome function and regulation. Hereby, quantitative methods based on chromosome conformation capture (3C) revolutionized the field, as they allow accurate and unbiased characterization of 3D genome organization of genomic regions of interest. The choice of the appropriate 3C derivate is crucial to acquire results suited for a specific research question. Circular 3C (4C) is the method of choice to study the genome-wide 3D architecture of a specific genomic region of interest...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28414531/a-system-architecture-for-efficient-transmission-of-massive-dna-sequencing-data
#6
Mahmut Şamİl Sağiroğlu, M Oğuzhan Külekcİ
The DNA sequencing data analysis pipelines require significant computational resources. In that sense, cloud computing infrastructures appear as a natural choice for this processing. However, the first practical difficulty in reaching the cloud computing services is the transmission of the massive DNA sequencing data from where they are produced to where they will be processed. The daily practice here begins with compressing the data in FASTQ file format, and then sending these data via fast data transmission protocols...
April 17, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28412442/human-brain-mapping-a-systematic-comparison-of-parcellation-methods-for-the-human-cerebral-cortex
#7
REVIEW
Salim Arslan, Sofia Ira Ktena, Antonios Makropoulos, Emma C Robinson, Daniel Rueckert, Sarah Parisot
The macro-connectome elucidates the pathways through which brain regions are structurally connected or functionally coupled to perform a specific cognitive task. It embodies the notion of representing and understanding all connections within the brain as a network, while the subdivision of the brain into interacting functional units is inherent in its architecture. As a result, the definition of network nodes is one of the most critical steps in connectivity network analysis. Although brain atlases obtained from cytoarchitecture or anatomy have long been used for this task, connectivity-driven methods have arisen only recently, aiming to delineate more homogeneous and functionally coherent regions...
April 13, 2017: NeuroImage
https://www.readbyqxmd.com/read/28408878/reward-based-motor-adaptation-mediated-by-basal-ganglia
#8
Taegyo Kim, Khaldoun C Hamade, Dmitry Todorov, William H Barnett, Robert A Capps, Elizaveta M Latash, Sergey N Markin, Ilya A Rybak, Yaroslav I Molkov
It is widely accepted that the basal ganglia (BG) play a key role in action selection and reinforcement learning. However, despite considerable number of studies, the BG architecture and function are not completely understood. Action selection and reinforcement learning are facilitated by the activity of dopaminergic neurons, which encode reward prediction errors when reward outcomes are higher or lower than expected. The BG are thought to select proper motor responses by gating appropriate actions, and suppressing inappropriate ones...
2017: Frontiers in Computational Neuroscience
https://www.readbyqxmd.com/read/28399374/role-of-hydrophobic-aromatic-residues-on-the-stability-of-double-wall-%C3%AE-sheet-structures-formed-by-a-triblock-peptide
#9
Beytullah Ozgur, Mehmet Sayar
Bioinspired self-assembling peptides serve as powerful building blocks in the manufacturing of nanomaterials with tailored features. Because of their ease of synthesis, biocompatibility, and tunable activity, this emerging branch of biomolecules has become very popular. The triblock peptide architecture designed by the Hartgerink group is a versatile system that allows control over its assembly and has been shown to demonstrate tunable bioactivity. Three main forces, Coulomb repulsion, hydrogen bonding and hydrophobicity act together to guide the triblock peptides' assembly into one-dimensional objects and hydrogels...
April 17, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28391054/breaking-the-rules-in-perceptual-information-integration
#10
Maxim A Bushmakin, Ami Eidels, Andrew Heathcote
We develop a broad theoretical framework for modelling difficult perceptual information integration tasks under different decision rules. The framework allows us to compare coactive architectures, which combine information before it enters the decision process, with parallel architectures, where logical rules combine independent decisions made about each perceptual source. For both architectures we test the novel hypothesis that participants break the decision rules on some trials, making a response based on only one stimulus even though task instructions require them to consider both...
June 2017: Cognitive Psychology
https://www.readbyqxmd.com/read/28389770/a-fast-genomic-selection-approach-for-large-genomic-data
#11
Hailan Liu, Guo-Bo Chen
We propose a novel computational method for genomic selection that combines identical-by-state (IBS)-based Haseman-Elston (HE) regression and best linear prediction (BLP), called HE-BLP. Genomic best linear unbiased prediction (GBLUP) has been widely used in whole-genome prediction for breeding programs. To determine the total genetic variance of a training population, a linear mixed model (LMM) should be solved via restricted maximum likelihood (REML), whose computational complexity is the cube of the sample size...
April 7, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28379693/influence-of-linker-flexibility-on-the-binding-affinity-of-bidentate-binders
#12
Miguel A Soler, Sara Fortuna
The design of responsive nanosensors typically relies on the availability of probes capable of capturing their target with high affinity and specificity. This can be achieved by coupling two or more binding units through a linker. In this work, we study the dependence on the binder architecture of the binding affinity between a target molecule and a semirigid bidentate binder. Using two different binder architectures, central-rigid and extreme-rigid, and modifying the length and the flexibility degree of the linker we generated 153 different architectures...
April 13, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28351758/the-mouse-cortical-meninges-are-the-site-of-immune-responses-to-many-different-pathogens-and-are-accessible-to-in-vivo-imaging
#13
REVIEW
Jonathan A Coles, Phillip J Stewart-Hutchinson, Elmarie Myburgh, James M Brewer
A wide range of viral and microbial infections are known to cause meningitis, and there is evidence that the meninges are the gateway to pathogenic invasion of the brain parenchyma. Hence observation of these regions has wide application to understanding host-pathogen interactions. Interactions between pathogens and cells of the immune response can be modified by changes in their environment, such as suppression of the flow of blood and lymph, and, particularly in the case of the meninges with their unsupported membranes, invasive dissection can alter the tissue architecture...
March 25, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28318235/unusual-tri-hexa-and-nonanuclear-cu-ii-cage-methylsilsesquioxanes-synthesis-structures-and-catalytic-activity-in-oxidations-with-peroxides
#14
Alexey N Bilyachenko, Alena N Kulakova, Mikhail M Levitsky, Artem A Petrov, Alexander A Korlyukov, Lidia S Shul'pina, Victor N Khrustalev, Pavel V Dorovatovskii, Anna V Vologzhanina, Ulyana S Tsareva, Igor E Golub, Ekaterina S Gulyaeva, Elena S Shubina, Georgiy B Shul'pin
Three types of unusual cagelike copper(II) methylsilsesquioxanes, namely, nona- [(MeSiO1.5)18(CuO)9] 1, hexa- [(MeSiO1.5)10(HO0.5)2(CuO)6(C12H8N2)2(MeSiO1.5)10(HO0.5)1.33(CH3COO0.5)0.67(CuO)6(C12H8N2)2] 2, [(MeSiO1.5)10(CuO)6(MeO0.5)2(C10H8N2)2] 3, and trinuclear [(MeSiO1.5)8(CuO)3(C10H8N2)2] 4, were obtained in 44%, 27%, 20%, and 16% yields, respectively. Nuclearity and structural fashion of products was controlled by the choice of solvent system and ligand, specifically assisting the assembling of cage. Structures of 1-4 were determined by single-crystal X-ray diffraction analysis...
March 20, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28304337/inertial-motion-capture-costume-design-study
#15
Agnieszka Szczęsna, Przemysław Skurowski, Ewa Lach, Przemysław Pruszowski, Damian Pęszor, Marcin Paszkuta, Janusz Słupik, Kamil Lebek, Mateusz Janiak, Andrzej Polański, Konrad Wojciechowski
The paper describes a scalable, wearable multi-sensor system for motion capture based on inertial measurement units (IMUs). Such a unit is composed of accelerometer, gyroscope and magnetometer. The final quality of an obtained motion arises from all the individual parts of the described system. The proposed system is a sequence of the following stages: sensor data acquisition, sensor orientation estimation, system calibration, pose estimation and data visualisation. The construction of the system's architecture with the dataflow programming paradigm makes it easy to add, remove and replace the data processing steps...
March 17, 2017: Sensors
https://www.readbyqxmd.com/read/28299680/application-of-a-nanostructured-enzymatic-biosensor-based-on-fullerene-and-gold-nanoparticles-to-polyphenol-detection
#16
Cristina Tortolini, Gabriella Sanzò, Riccarda Antiochia, Franco Mazzei, Gabriele Favero
Electrochemical biosensors provide an attractive means of analyzing the content of a biological sample due to the direct conversion of a biological event to an electronic signal. The signal transduction and the general performance of electrochemical biosensors are often determined by the surface architectures that connect the sensing element to the biological sample at the nanometer scale. The most common surface modification techniques, the various electrochemical transduction mechanisms, and the choice of the recognition receptor molecules all influence the ultimate sensitivity of the sensor...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28286164/changing-children-s-eating-behaviour-a-review-of-experimental-research
#17
REVIEW
Patricia DeCosta, Per Møller, Michael Bom Frøst, Annemarie Olsen
The interest in children's eating behaviours and how to change them has been growing in recent years. This review examines the following questions: What strategies have been used to change children's eating behaviours? Have their effects been experimentally demonstrated? And, are the effects transient or enduring? Medline and Cab abstract (Ovid) and Web of Science (Thomson Reuters) were used to identify the experimental studies. A total of 120 experimental studies were identified and they are presented grouped within these 11 topics; parental control, reward, social facilitation, cooking programs, school gardens, sensory education, availability and accessibility, choice architecture and nudging, branding and food packaging, preparation and serving style, and offering a choice...
June 1, 2017: Appetite
https://www.readbyqxmd.com/read/28284215/physiological-fidelity-or-model-parsimony-the-relative-performance-of-reverse-toxicokinetic-modeling-approaches
#18
Michael A Rowland, Edward J Perkins, Michael L Mayo
BACKGROUND: Physiologically-based toxicokinetic (PBTK) models are often developed to facilitate in vitro to in vivo extrapolation (IVIVE) using a top-down, compartmental approach, favoring architectural simplicity over physiological fidelity despite the lack of general guidelines relating model design to dynamical predictions. Here we explore the impact of design choice (high vs. low fidelity) on chemical distribution throughout an animal's organ system. RESULTS: We contrast transient dynamics and steady states of three previously proposed PBTK models of varying complexity in response to chemical exposure...
March 11, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28283532/molecular-architecture-of-the-n-type-atpase-rotor-ring-from-burkholderia-pseudomallei
#19
Sarah Schulz, Martin Wilkes, Deryck J Mills, Werner Kühlbrandt, Thomas Meier
The genome of the highly infectious bacterium Burkholderia pseudomallei harbors an atp operon that encodes an N-type rotary ATPase, in addition to an operon for a regular F-type rotary ATPase. The molecular architecture of N-type ATPases is unknown and their biochemical properties and cellular functions are largely unexplored. We studied the B. pseudomallei N1No-type ATPase and investigated the structure and ion specificity of its membrane-embedded c-ring rotor by single-particle electron cryo-microscopy. Of several amphiphilic compounds tested for solubilizing the complex, the choice of the low-density, low-CMC detergent LDAO was optimal in terms of map quality and resolution...
April 2017: EMBO Reports
https://www.readbyqxmd.com/read/28281241/decellularized-cryopreserved-allografts-as-off-the-shelf-allogeneic-alternative-for-heart-valve-replacement-in-vitro-assessment-before-clinical-translation
#20
Laura Iop, Adolfo Paolin, Paola Aguiari, Diletta Trojan, Elisa Cogliati, Gino Gerosa
Cryopreserved allogeneic conduits are the elective biocompatible choice among currently available substitutes for surgical replacement in end-stage valvulopathy. However, degeneration occurs in 15 years in adults or faster in children, due to recipient's immunological reactions to donor's antigens. Here, human aortic valves were decellularized by TRICOL, based on Triton X-100 and sodium cholate, and submitted to standard cryopreservation (TRICOL-human aortic valves (hAVs)). Tissue samples were analyzed to study the effects of the combined procedure on original valve architecture and donor's cell removal...
March 9, 2017: Journal of Cardiovascular Translational Research
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