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https://www.readbyqxmd.com/read/28108657/risearch2-suffix-array-based-large-scale-prediction-of-rna-rna-interactions-and-sirna-off-targets
#1
Ferhat Alkan, Anne Wenzel, Oana Palasca, Peter Kerpedjiev, Anders Frost Rudebeck, Peter F Stadler, Ivo L Hofacker, Jan Gorodkin
Intermolecular interactions of ncRNAs are at the core of gene regulation events, and identifying the full map of these interactions bears crucial importance for ncRNA functional studies. It is known that RNA-RNA interactions are built up by complementary base pairings between interacting RNAs and high level of complementarity between two RNA sequences is a powerful predictor of such interactions. Here, we present RIsearch2, a large-scale RNA-RNA interaction prediction tool that enables quick localization of potential near-complementary RNA-RNA interactions between given query and target sequences...
January 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28108601/phylogenomics-using-target-restricted-assembly-resolves-intra-generic-relationships-of-parasitic-lice-phthiraptera-columbicola
#2
Bret M Boyd, Julie M Allen, Nam Nguyen, Andrew D Sweet, Tandy Warnow, Michael D Shapiro, Scott M Villa, Sarah E Bush, Dale H Clayton, Kevin P Johnson
Parasitic "wing lice" (Phthiraptera: Columbicola) and their dove and pigeon hosts are a well-recognized model system for coevolutionary studies at the intersection of micro- and macroevolution. Selection on lice in microevolutionary time occurs as pigeons and doves defend themselves against lice by preening. In turn, behavioral and morphological adaptations of the lice improve their ability to evade host defense. Over macroevolutionary time wing lice tend to cospeciate with their hosts; yet, some species of Columbicola have switched to new host species...
January 19, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28108416/symptoms-and-the-body-taking-the-inferential-leap
#3
REVIEW
Omer Van den Bergh, Michael Witthöft, Sibylle Petersen, Richard J Brown
The relationship between the conscious experience of physical symptoms and indicators of objective physiological dysfunction is highly variable and depends on characteristics of the person, the context and their interaction. This relationship often breaks down entirely in the case of "medically unexplained" or functional somatic symptoms, violating the basic assumption in medicine that physical symptoms have physiological causes. In this paper, we describe the prevailing theoretical approach to this problem and review the evidence pertaining to it...
January 17, 2017: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/28108373/left-ventricle-segmentation-via-two-layer-level-sets-with-circular-shape-constraint
#4
Cong Yang, Weiguo Wu, Yuanqi Su, Shaoxiang Zhang
This paper proposes a circular shape constraint and a novel two-layer level set method for the segmentation of the left ventricle (LV) from short-axis magnetic resonance images without training any shape models. Since the shape of LV throughout the apex-base axis is close to a ring shape, we propose a circle fitting term in the level set framework to detect the endocardium. The circle fitting term imposes a penalty on the evolving contour from its fitting circle, and thereby handles quite well with issues in LV segmentation, especially the presence of outflow track in basal slices and the intensity overlap between TPM and the myocardium...
January 17, 2017: Magnetic Resonance Imaging
https://www.readbyqxmd.com/read/28108306/bone-remodeling-as-a-spatial-evolutionary-game
#5
Marc D Ryser, Kevin A Murgas
Bone remodeling is a complex process involving cell-cell interactions, biochemical signaling and mechanical stimuli. Early models of the biological aspects of remodeling were non-spatial and focused on the local dynamics at a fixed location in the bone. Several spatial extensions of these models have been proposed, but they generally suffer from two limitations: first, they are not amenable to analysis and are computationally expensive, and second, they neglect the role played by bone-embedded osteocytes. To address these issues, we developed a novel model of spatial remodeling based on the principles of evolutionary game theory...
January 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28107510/effect-of-the-crystal-environment-on-side-chain-conformational-dynamics-in-cyanovirin-n-investigated-through-crystal-and-solution-molecular-dynamics-simulations
#6
Logan S Ahlstrom, Ivan I Vorontsov, Jun Shi, Osamu Miyashita
Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure...
2017: PloS One
https://www.readbyqxmd.com/read/28107447/a-software-tool-for-estimation-of-burden-of-infectious-diseases-in-europe-using-incidence-based-disability-adjusted-life-years
#7
Edoardo Colzani, Alessandro Cassini, Daniel Lewandowski, Marie-Josee J Mangen, Dietrich Plass, Scott A McDonald, Alies van Lier, Juanita A Haagsma, Guido Maringhini, Alessandro Pini, Piotr Kramarz, Mirjam E Kretzschmar
The burden of disease framework facilitates the assessment of the health impact of diseases through the use of summary measures of population health such as Disability-Adjusted Life Years (DALYs). However, calculating, interpreting and communicating the results of studies using this methodology poses a challenge. The aim of the Burden of Communicable Disease in Europe (BCoDE) project is to summarize the impact of communicable disease in the European Union and European Economic Area Member States (EU/EEA MS)...
2017: PloS One
https://www.readbyqxmd.com/read/28107358/modeling-an-excitable-biosynthetic-tissue-with-inherent-variability-for-paired-computational-experimental-studies
#8
Tanmay A Gokhale, Jong M Kim, Robert D Kirkton, Nenad Bursac, Craig S Henriquez
To understand how excitable tissues give rise to arrhythmias, it is crucially necessary to understand the electrical dynamics of cells in the context of their environment. Multicellular monolayer cultures have proven useful for investigating arrhythmias and other conduction anomalies, and because of their relatively simple structure, these constructs lend themselves to paired computational studies that often help elucidate mechanisms of the observed behavior. However, tissue cultures of cardiomyocyte monolayers currently require the use of neonatal cells with ionic properties that change rapidly during development and have thus been poorly characterized and modeled to date...
January 20, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28107159/caring-for-the-trafficked-patient-ethical-challenges-and-recommendations-for-health-care-professionals
#9
Wendy L Macias-Konstantopoulos
Human trafficking is an egregious human rights violation with profound negative physical and psychological consequences, including communicable diseases, substance use disorders, and mental illnesses. The health needs of this population are multiple, complex, and influenced by past and present experiences of abuse, neglect, and exploitation. Effective health care services for trafficked patients require clinicians to consider individual patients' needs, wishes, goals, priorities, risks, and vulnerabilities as well as public health implications and even resource allocation...
January 1, 2017: AMA Journal of Ethics
https://www.readbyqxmd.com/read/28106432/time-to-go-beyond-triple-gauge-boson-coupling-interpretation-of-w-pair-production
#10
Zhengkang Zhang
W boson pair production processes at e^{+}e^{-} and pp colliders have been conventionally interpreted as measurements of WWZ and WWγ triple gauge couplings (TGCs). Such an interpretation is based on the assumption that new physics effects other than anomalous TGCs are negligible. While this "TGC dominance assumption" was well motivated and useful at LEP2 thanks to precision electroweak constraints, it is already challenged by recent LHC data. In fact, contributions from anomalous Z boson couplings that are allowed by electroweak precision data but neglected in LHC analyses, which are enhanced at high energy, can even dominate over those from the anomalous TGCs considered...
January 6, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28106418/spatiotemporal-dynamics-and-reliable-computations-in-recurrent-spiking-neural-networks
#11
Ryan Pyle, Robert Rosenbaum
Randomly connected networks of excitatory and inhibitory spiking neurons provide a parsimonious model of neural variability, but are notoriously unreliable for performing computations. We show that this difficulty is overcome by incorporating the well-documented dependence of connection probability on distance. Spatially extended spiking networks exhibit symmetry-breaking bifurcations and generate spatiotemporal patterns that can be trained to perform dynamical computations under a reservoir computing framework...
January 6, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28106310/mechanism-of-type-iii-protein-secretion-regulation-of-flha-conformation-by-a-functionally-critical-charged-residue-cluster
#12
Marc Erhardt, Paige Wheatley, Eun A Kim, Takanori Hirano, Yang Zhang, Mayukh K Sarkar, Kelly T Hughes, David F Blair
The bacterial flagellum contains a specialized secretion apparatus in its base that pumps certain protein subunits through the growing structure to their sites of installation beyond the membrane. A related apparatus functions in the injectisomes of gram-negative pathogens to export virulence factors into host cells. This mode of protein export is termed type-III secretion (T3S). Details of the T3S mechanism are unclear. It is energized by the proton gradient; here, a mutational approach was used to identify proton-binding groups that might function in transport...
January 20, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28105958/dmirnet-inferring-direct-microrna-mrna-association-networks
#13
Minsu Lee, HyungJune Lee
BACKGROUND: MicroRNAs (miRNAs) play important regulatory roles in the wide range of biological processes by inducing target mRNA degradation or translational repression. Based on the correlation between expression profiles of a miRNA and its target mRNA, various computational methods have previously been proposed to identify miRNA-mRNA association networks by incorporating the matched miRNA and mRNA expression profiles. However, there remain three major issues to be resolved in the conventional computation approaches for inferring miRNA-mRNA association networks from expression profiles...
December 5, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28105940/integrated-single-cell-data-analysis-reveals-cell-specific-networks-and-novel-coactivation-markers
#14
Shila Ghazanfar, Adam J Bisogni, John T Ormerod, David M Lin, Jean Y H Yang
BACKGROUND: Large scale single cell transcriptome profiling has exploded in recent years and has enabled unprecedented insight into the behavior of individual cells. Identifying genes with high levels of expression using data from single cell RNA sequencing can be useful to characterize very active genes and cells in which this occurs. In particular single cell RNA-Seq allows for cell-specific characterization of high gene expression, as well as gene coexpression. RESULTS: We offer a versatile modeling framework to identify transcriptional states as well as structures of coactivation for different neuronal cell types across multiple datasets...
December 5, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28105911/integrating-gene-set-analysis-and-nonlinear-predictive-modeling-of-disease-phenotypes-using-a-bayesian-multitask-formulation
#15
Mehmet Gönen
BACKGROUND: Identifying molecular signatures of disease phenotypes is studied using two mainstream approaches: (i) Predictive modeling methods such as linear classification and regression algorithms are used to find signatures predictive of phenotypes from genomic data, which may not be robust due to limited sample size or highly correlated nature of genomic data. (ii) Gene set analysis methods are used to find gene sets on which phenotypes are linearly dependent by bringing prior biological knowledge into the analysis, which may not capture more complex nonlinear dependencies...
December 13, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28105908/degreecox-a-network-based-regularization-method-for-survival-analysis
#16
André Veríssimo, Arlindo Limede Oliveira, Marie-France Sagot, Susana Vinga
BACKGROUND: Modeling survival oncological data has become a major challenge as the increase in the amount of molecular information nowadays available means that the number of features greatly exceeds the number of observations. One possible solution to cope with this dimensionality problem is the use of additional constraints in the cost function optimization. LASSO and other sparsity methods have thus already been successfully applied with such idea. Although this leads to more interpretable models, these methods still do not fully profit from the relations between the features, specially when these can be represented through graphs...
December 13, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28104897/optimal-flow-rate-sampling-designs-for-studies-with-extended-exhaled-nitric-oxide-analysis
#17
Noa Molshatzki, Sandrah Eckel
INTRODUCTION: The fractional concentration of exhaled nitric oxide (FeNO) is a biomarker of airway inflammation. Repeat FeNO maneuvers at multiple fixed exhalation flow rates (extended NO analysis) can be used to estimate parameters quantifying proximal and distal sources of NO in mathematical models of lower respiratory tract NO. A growing number of studies use extended NO analysis, but there is no official standard flow rate sampling protocol. In this paper, we provide information for study planning by deriving theoretically optimal flow rate sampling designs...
January 20, 2017: Journal of Breath Research
https://www.readbyqxmd.com/read/28104551/a-framework-for-analysis-of-linear-ultrasound-videos-to-detect-fetal-presentation-and-heartbeat
#18
M A Maraci, C P Bridge, R Napolitano, A Papageorghiou, J A Noble
Confirmation of pregnancy viability (presence of fetal cardiac activity) and diagnosis of fetal presentation (head or buttock in the maternal pelvis) are the first essential components of ultrasound assessment in obstetrics. The former is useful in assessing the presence of an on-going pregnancy and the latter is essential for labour management. We propose an automated framework for detection of fetal presentation and heartbeat from a predefined free-hand ultrasound sweep of the maternal abdomen. Our method exploits the presence of key anatomical sonographic image patterns in carefully designed scanning protocols to develop, for the first time, an automated framework allowing novice sonographers to detect fetal breech presentation and heartbeat from an ultrasound sweep...
January 10, 2017: Medical Image Analysis
https://www.readbyqxmd.com/read/28103436/directional-charge-carrier-transport-in-oriented-benzodithiophene-covalent-organic-framework-thin-films
#19
Dana D Medina, Michiel L Petrus, Askhat N Jumabekov, Johannes T Margraf, Simon Weinberger, Julian M Rotter, Timothy Clark, Thomas Bein
Charge carrier transport in oriented COF thin films is an important factor for realizing COF-based optoelectronic devices. We describe how highly oriented electron-donating BDT-COF thin films serve as a model system for a directed charge transport study. Oriented BDT-COF films were deposited on different electrodes with excellent control over film roughness and topology, allowing for high quality electrode-COF interfaces suitable for device fabrication. Hole-only devices were constructed to study the columnar hole-mobility of the BDT-COF films...
January 19, 2017: ACS Nano
https://www.readbyqxmd.com/read/28103280/formulation-general-features-and-global-calibration-of-a-bioenergetically-constrained-fishery-model
#20
David A Carozza, Daniele Bianchi, Eric D Galbraith
Human exploitation of marine resources is profoundly altering marine ecosystems, while climate change is expected to further impact commercially-harvested fish and other species. Although the global fishery is a highly complex system with many unpredictable aspects, the bioenergetic limits on fish production and the response of fishing effort to profit are both relatively tractable, and are sure to play important roles. Here we describe a generalized, coupled biological-economic model of the global marine fishery that represents both of these aspects in a unified framework, the BiOeconomic mArine Trophic Size-spectrum (BOATS) model...
2017: PloS One
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