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https://www.readbyqxmd.com/read/28724079/single-step-genomic-and-pedigree-genotype-%C3%A3-environment-interaction-models-for-predicting-wheat-lines-in-international-environments
#1
Paulino Pérez-Rodríguez, José Crossa, Jessica Rutkoski, Jesse Poland, Ravi Singh, Andrés Legarra, Enrique Autrique, Gustavo de Los Campos, Juan Burgueño, Susanne Dreisigacker
Genomic prediction models have been commonly used in plant breeding but only in reduced datasets comprising a few hundred genotyped individuals. However, pedigree information for an entire breeding population is frequently available, as are historical data on the performance of a large number of selection candidates. The single-step method extends the genomic relationship information from genotyped individuals to pedigree information from a larger number of phenotyped individuals in order to combine relationship information on all members of the breeding population...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28723959/a-novel-surveillance-approach-for-disaster-mental-health
#2
Oliver Gruebner, Sarah R Lowe, Martin Sykora, Ketan Shankardass, S V Subramanian, Sandro Galea
BACKGROUND: Disasters have substantial consequences for population mental health. Social media data present an opportunity for mental health surveillance after disasters to help identify areas of mental health needs. We aimed to 1) identify specific basic emotions from Twitter for the greater New York City area during Hurricane Sandy, which made landfall on October 29, 2012, and to 2) detect and map spatial temporal clusters representing excess risk of these emotions. METHODS: We applied an advanced sentiment analysis on 344,957 Twitter tweets in the study area over eleven days, from October 22 to November 1, 2012, to extract basic emotions, a space-time scan statistic (SaTScan) and a geographic information system (QGIS) to detect and map excess risk of these emotions...
2017: PloS One
https://www.readbyqxmd.com/read/28723940/modeling-the-dynamics-of-chromosomal-alteration-progression-in-cervical-cancer-a-computational-model
#3
Augusto Cabrera-Becerril, Cruz Vargas-De-León, Sergio Hernández, Pedro Miramontes, Raúl Peralta
Computational modeling has been applied to simulate the heterogeneity of cancer behavior. The development of Cervical Cancer (CC) is a process in which the cell acquires dynamic behavior from non-deleterious and deleterious mutations, exhibiting chromosomal alterations as a manifestation of this dynamic. To further determine the progression of chromosomal alterations in precursor lesions and CC, we introduce a computational model to study the dynamics of deleterious and non-deleterious mutations as an outcome of tumor progression...
2017: PloS One
https://www.readbyqxmd.com/read/28723913/prebiotic-selection-for-motifs-in-a-model-of-template-free-elongation-of-polymers-within-compartments
#4
Grant Kinsler, Sam Sinai, Nicholas Keone Lee, Martin A Nowak
The transition from prelife where self-replication does not occur, to life which exhibits self-replication and evolution, has been a subject of interest for many decades. Membranes, forming compartments, seem to be a critical component of this transition as they provide several concurrent benefits. They maintain localized interactions, generate electro-chemical gradients, and help in selecting cooperative functions as they arise. These functions pave the way for the emergence and maintenance of simple metabolic cycles and polymers...
2017: PloS One
https://www.readbyqxmd.com/read/28723906/genomic-prediction-with-parallel-computing-for-slaughter-traits-in-chinese-simmental-beef-cattle-using-high-density-genotypes
#5
Peng Guo, Bo Zhu, Lingyang Xu, Hong Niu, Zezhao Wang, Long Guan, Yonghu Liang, Hemin Ni, Yong Guo, Yan Chen, Lupei Zhang, Xue Gao, Huijiang Gao, Junya Li
Genomic selection has been widely used for complex quantitative trait in farm animals. Estimations of breeding values for slaughter traits are most important to beef cattle industry, and it is worthwhile to investigate prediction accuracies of genomic selection for these traits. In this study, we assessed genomic predictive abilities for average daily gain weight (ADG), live weight (LW), carcass weight (CW), dressing percentage (DP), lean meat percentage (LMP) and retail meat weight (RMW) using Illumina Bovine 770K SNP Beadchip in Chinese Simmental cattle...
2017: PloS One
https://www.readbyqxmd.com/read/28723903/automatic-analysis-and-3d-modelling-of-hi-c-data-using-tadbit-reveals-structural-features-of-the-fly-chromatin-colors
#6
François Serra, Davide Baù, Mike Goodstadt, David Castillo, Guillaume Filion, Marc A Marti-Renom
The sequence of a genome is insufficient to understand all genomic processes carried out in the cell nucleus. To achieve this, the knowledge of its three-dimensional architecture is necessary. Advances in genomic technologies and the development of new analytical methods, such as Chromosome Conformation Capture (3C) and its derivatives, provide unprecedented insights in the spatial organization of genomes. Here we present TADbit, a computational framework to analyze and model the chromatin fiber in three dimensions...
July 19, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28723311/visual-perceptual-learning-and-models
#7
Barbara Dosher, Zhong-Lin Lu
Visual perceptual learning through practice or training can significantly improve performance on visual tasks. Originally seen as a manifestation of plasticity in the primary visual cortex, perceptual learning is more readily understood as improvements in the function of brain networks that integrate processes, including sensory representations, decision, attention, and reward, and balance plasticity with system stability. This review considers the primary phenomena of perceptual learning, theories of perceptual learning, and perceptual learning's effect on signal and noise in visual processing and decision...
July 19, 2017: Annual Review of Vision Science
https://www.readbyqxmd.com/read/28723151/fusion-of-structure-and-ligand-based-methods-for-identification-of-novel-cdk2-inhibitors
#8
Priya Mahajan, Gousia Chashoo, Monika Gupta, Amit Kumar, Parvinder Pal Singh, Amit Nargotra
Cyclin dependent kinases plays a central role in cell cycle regulation which makes them a promising target with multifarious therapeutic potential. CDK2 regulates various events of the eukaryotic cell division cycle and the pharmacological evidences indicated that over expression of CDK2 causes abnormal cell-cycle regulation, which was directly associated with hyper proliferation of cancer cells. Therefore, CDK2 is regarded as a potential target molecule for anti-cancer medication. Thus to decline CDK2 activity by potential lead compounds has proved to be an effective treatment for cancer...
July 19, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28723080/an-orthogonal-multi-input-integration-system-to-control-gene-expression-in-escherichia-coli
#9
Fabio Annunziata, Antoni Matyjaszkiewicz, Gianfranco Fiore, Claire Grierson, Lucia Marucci, Mario di Bernardo, Nigel Savery
In many biotechnological applications, it is useful for gene expression to be regulated by multiple signals, as this allows the programming of complex behaviour. Here we implement, in Escherichia coli, a system that compares the concentration of two signal molecules, and tunes GFP expression proportionally to their relative abundance. The computation is performed via molecular titration between an orthogonal σ factor and its cognate anti-σ factor. We use mathematical modelling and experiments to show that the computation system is predictable and able to adapt GFP expression dynamically to a wide range of combinations of the two signals, and our model qualitatively captures most of these behaviours...
July 19, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28723067/structural-and-spectroscopic-properties-of-assemblies-of-self-replicating-peptide-macrocycles
#10
Pim W J M Frederix, Julien Idé, Yigit Altay, Gaël Schaeffer, Mathieu Surin, David Beljonne, Anna S Bondarenko, Thomas L C Jansen, Sijbren Otto, Siewert J Marrink
Self-replication at the molecular level is often seen as essential to the early origins of life. Recently a mechanism of self-replication has been discovered in which replicator self-assembly drives the process. We have studied one of the examples of such self-assembling self-replicating molecules to a high level of structural detail using a combination of computational and spectroscopic techniques. Molecular Dynamics simulations of self-assembled stacks of peptide-derived replicators provide insights into the structural characteristics of the system and serve as the basis for semi-empirical calculations of the UV/Vis, circular dichroism (CD) and infrared (IR) absorption spectra that reflect the chiral organization and peptide secondary structure of the stacks...
July 19, 2017: ACS Nano
https://www.readbyqxmd.com/read/28723065/advances-in-modeling-the-stability-of-non-covalent-complexes-in-charged-droplets-with-applications-in-esi-ms-experiments
#11
Styliani Consta, Mahmoud Sharawy, Myong In Oh, Anatoly Malevanets
Electrospray ionization mass spectrometry is used extensively to measure the equilibrium constant of non-covalent complexes. In this Perspective we attempt to present an accessible introduction to computational methodologies that can be applied to determine the stability of weak non-covalent complexes in their journey from bulk solution into the gaseous state. We demonstrate the usage of the methods on two typical examples of non-covalent complexes drawn from a broad class of nucleic acids and transient protein complexes found in aqueous droplets...
July 19, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28722651/ephrin-a-epha-specific-co-adaptation-as-a-novel-mechanism-in-topographic-axon-guidance
#12
Felix Fiederling, Markus Weschenfelder, Martin Fritz, Anne von Philipsborn, Martin Bastmeyer, Franco Weth
Genetic hardwiring during brain development provides computational architectures for innate neuronal processing. Thus, the paradigmatic chick retinotectal projection, due to its neighborhood preserving, topographic organization, establishes millions of parallel channels for incremental visual field analysis. Retinal axons receive targeting information from quantitative guidance cue gradients. Surprisingly, novel adaptation assays demonstrate that retinal growth cones robustly adapt towards ephrin-A/EphA forward and reverse signals, which provide the major mapping cues...
July 19, 2017: ELife
https://www.readbyqxmd.com/read/28722409/conformational-landscape-of-tri-n-butyl-phosphate-matrix-isolation-infrared-spectroscopy-and-systematic-computational-analysis
#13
Nagarajan Ramanathan, Kalyanasundaram Sundararajan, Kodumudi S Viswanathan
The conformations of tri-n-butyl phosphate (TBP) were studied using matrix isolation infrared spectroscopy and DFT calculations. TBP was trapped in a N2 matrix using both effusive and supersonic sources and its infrared spectra were recorded. The computational exploration of TBP is a very demanding problem to confront, due to the presence of a large multitude of conformations in TBP. To simplify the problem, computations were done on model compounds, dimethyl butyl phosphate (DMBP) and dibutyl methyl phosphate (DBMP), to systematically arrive at the conformations of TBP that are expected to contribute to its chemistry at room temperature...
July 19, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28722180/a-generic-tg-186-shielded-applicator-for-commissioning-model-based-dose-calculation-algorithms-for-high-dose-rate-192-ir-brachytherapy
#14
Yunzhi Ma, Javier Vijande, Facundo Ballester, Åsa Carlsson Tedgren, Domingo Granero, Annette Haworth, Firas Mourtada, Gabriel Paiva Fonseca, Kyveli Zourari, Panagiotis Papagiannis, Mark J Rivard, Frank André Siebert, Ron S Sloboda, Ryan Smith, Marc J P Chamberland, Rowan M Thomson, Frank Verhaegen, Luc Beaulieu
PURPOSE: A joint working group was created by the American Association of Physicists in Medicine (AAPM), the European Society for Radiotherapy and Oncology (ESTRO), and the Australasian Brachytherapy Group (ABG) with the charge, among others, to develop a set of well-defined test case plans and perform model-based dose calculation algorithms (MBDCA) dose calculations and comparisons. Its main goal is to facilitate a smooth transition from the AAPM Task Group No. 43 (TG-43) dose calculation formalism, widely being used in clinical practice for brachytherapy, to the one proposed by Task Group No...
July 19, 2017: Medical Physics
https://www.readbyqxmd.com/read/28722138/a-red-blood-cell-model-to-estimate-the-hemolysis-fingerprint-of-cardiovascular-devices
#15
Riccardo Toninato, Giuseppe Fadda, Francesca Maria Susin
One of the most relevant and open issues within cardiovascular prosthetic hemodynamic performance is a realistic quantification of the damage sustained by red blood cells (RBCs). Specifically, the optimal design of bileaflet mechanical heart valves (BMHVs) requires both low shear stresses along the leaflets and short particle resident times. This study approaches RBC damage estimation by developing a numerical model of RBCs and computing the damage sustained by a set of passive RBCs immersed within in vitro flows...
July 19, 2017: Artificial Organs
https://www.readbyqxmd.com/read/28721994/evaluation-of-marginal-and-internal-gaps-of-metal-ceramic-crowns-obtained-from-conventional-impressions-and-casting-techniques-with-those-obtained-from-digital-techniques
#16
Rathika Rai, S Arun Kumar, R Prabhu, Ranjani Thillai Govindan, Faiz Mohamed Tanveer
BACKGROUND: Accuracy in fit of cast metal restoration has always remained as one of the primary factors in determining the success of the restoration. A well-fitting restoration needs to be accurate both along its margin and with regard to its internal surface. AIM: The aim of the study is to evaluate the marginal fit of metal ceramic crowns obtained by conventional inlay casting wax pattern using conventional impression with the metal ceramic crowns obtained by computer-aided design and computer-aided manufacturing (CAD/CAM) technique using direct and indirect optical scanning...
May 2017: Indian Journal of Dental Research: Official Publication of Indian Society for Dental Research
https://www.readbyqxmd.com/read/28721722/pillar-5-arene-based-supramolecular-plasmonic-thin-films-for-label-free-quantitative-and-multiplex-sers-detection
#17
Verónica Montes García, Borja Gómez-González, Diego M Solís, Jose M Taboada, Norman Jiménez Otero, Jacobo de Uña-Álvarez, Fernando Obelleiro, Luis García-Río, Jorge Perez-Juste, Isabel Pastoriza-Santos
Novel plasmonic thin films based on electrostatic layer-by-layer (LbL) deposition of citrate-stabilized Au nanoparticles (NPs) and ammonium pillar[5]arene (AP[5]A) has been developed. The supramolecular-induced LbL assembly of the plasmonic nanoparticles yields to the formation of controlled hot-spots with uniform interparticle distances. At the same time this strategy allows to modulate the density and dimensions of the Au aggregates, and therefore the optical response, on the thin film with the number of AuNP-AP[5]A deposition cycles...
July 19, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28721549/an-expected-coverage-model-with-a-cutoff-priority-queue
#18
Soovin Yoon, Laura A Albert
Emergency medical services provide immediate care to patients with various types of needs. When the system is congested, the response to urgent emergency calls can be delayed. To address this issue, we propose a spatial Hypercube approximation model with a cutoff priority queue that estimates performance measures for a system where some servers are reserved exclusively for high priority calls when the system is congested. In the cutoff priority queue, low priority calls are not immediately served-they are either lost or entered into a queue-whenever the number of busy ambulances is equal to or greater than the cutoff...
July 19, 2017: Health Care Management Science
https://www.readbyqxmd.com/read/28721539/-computational-neuroanatomy-and-microstructure-imaging-using-magnetic-resonance-imaging
#19
REVIEW
S Mohammadi, N Weiskopf
BACKGROUND: Current computational neuroanatomy focuses on morphological measurements of the brain using standard magnetic resonance imaging (MRI) techniques. In comparison quantitative MRI (qMRI) typically provides a better tissue contrast and also greatly improves the sensitivity and specificity with respect to the microstructural characteristics of tissue. OBJECTIVE: Current methodological developments in qMRI are presented, which go beyond morphology because this provides standardized measurements of the microstructure of the brain...
July 18, 2017: Der Nervenarzt
https://www.readbyqxmd.com/read/28721495/diversity-and-survival-of-artificial-lifeforms-under-sedimentation-and-random-motion
#20
Nicolas Glade, Olivier Bastien, Pascal Ballet
Cellular automata are often used to explore the numerous possible scenarios of what could have occurred at the origins of life and before, during the prebiotic ages, when very simple molecules started to assemble and organise into larger catalytic or informative structures, or to simulate ecosystems. Artificial self-maintained spatial structures emerge in cellular automata and are often used to represent molecules or living organisms. They converge generally towards homogeneous stationary soups of still-life creatures...
July 18, 2017: Theory in Biosciences, Theorie in Den Biowissenschaften
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