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https://www.readbyqxmd.com/read/28334803/statistical-analysis-of-genetic-interactions-in-tn-seq-data
#1
Michael A DeJesus, Subhalaxmi Nambi, Clare M Smith, Richard E Baker, Christopher M Sassetti, Thomas R Ioerger
Tn-Seq is an experimental method for probing the functions of genes through construction of complex random transposon insertion libraries and quantification of each mutant's abundance using next-generation sequencing. An important emerging application of Tn-Seq is for identifying genetic interactions, which involves comparing Tn mutant libraries generated in different genetic backgrounds (e.g. wild-type strain versus knockout strain). Several analytical methods have been proposed for analyzing Tn-Seq data to identify genetic interactions, including estimating relative fitness ratios and fitting a generalized linear model...
February 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28328145/short-range-dispersal-maintains-a-volatile-marine-metapopulation-the-brown-alga-postelsia-palmaeformis
#2
Robert T Paine, Eric R Buhle, Simon A Levin, Peter Kareiva
The annual brown alga Postelsia palmaeformis is dependent for its survival on short-distance dispersal (SDD) where it is already established, as well as occasional long-distance colonization of novel sites. To quantify SDD, we transplanted Postelsia to sites lacking established plants within ≥10 m. The spatial distribution of the first naturally produced sporophyte generation was used to fit dispersal kernels in a hierarchical Bayesian framework. Mean dispersal distance within a year ranged from 0.16 to 0...
March 22, 2017: Ecology
https://www.readbyqxmd.com/read/28328016/a-tunable-3d-nanostructured-conductive-gel-framework-electrode-for-high-performance-lithium-ion-batteries
#3
Ye Shi, Jun Zhang, Andrea M Bruck, Yiman Zhang, Jing Li, Eric A Stach, Kenneth J Takeuchi, Amy C Marschilok, Esther S Takeuchi, Guihua Yu
This study develops a tunable 3D nanostructured conductive gel framework as both binder and conductive framework for lithium ion batteries. A 3D nanostructured gel framework with continuous electron pathways can provide hierarchical pores for ion transport and form uniform coatings on each active particle against aggregation. The hybrid gel electrodes based on a polypyrrole gel framework and Fe3 O4 nanoparticles as a model system in this study demonstrate the best rate performance, the highest achieved mass ratio of active materials, and the highest achieved specific capacities when considering total electrode mass, compared to current literature...
March 22, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28306246/the-self-assembled-hierarchical-interfaces-of-zno-nanotubes-graphene-heterostructures-for-efficient-room-temperature-hydrogen-sensors
#4
Deepa Kathiravan, Bohr-Ran Huang, Adhimoorthy Saravanan
Herein, we report the novel nanostructural interfaces of self-assembled hierarchical ZnO nanotubes/graphene (ZNTs/G) with three different growing times of ZNTs on graphene substrates (namely, SH1, SH2 and SH3). Each sample was fabricated with interdigitated electrodes to fabricate hydrogen sensors and their hydrogen sensing properties were comprehensively studied. The systematical investigation reveals that SH1 sensor exhibits an ultra-high sensor response even at low detection level of 10 ppm (14.3%) to 100 ppm (28...
March 17, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28302189/temporal-dynamics-of-rituals-in-obsessive-compulsive-disorder
#5
Robert W Bond, Stephen J Guastello, Andrea D Guastello
Obsessive-compulsive disorder (OCD) is characterized by obsessions, defined as intrusive and persistent thoughts, and compulsions, defined as repetitive ritualistic behaviors that attempt to neutralize the anxiety associated with the obsessions. The present study investigated the patterns of symptoms as they occur over time in order to generate new insights about the triggers to symptoms. Fourteen adult participants who met the DSM-5 criteria for OCD completed 7-day logbooks of daily activities including the times when they engaged in compulsive rituals...
April 2017: Nonlinear Dynamics, Psychology, and Life Sciences
https://www.readbyqxmd.com/read/28301512/adaptation-to-random-and-systematic-errors-comparison-of-amputee-and-non-amputee-control-interfaces-with-varying-levels-of-process-noise
#6
Reva E Johnson, Konrad P Kording, Levi J Hargrove, Jonathon W Sensinger
The objective of this study was to understand how people adapt to errors when using a myoelectric control interface. We compared adaptation across 1) non-amputee subjects using joint angle, joint torque, and myoelectric control interfaces, and 2) amputee subjects using myoelectric control interfaces with residual and intact limbs (five total control interface conditions). We measured trial-by-trial adaptation to self-generated errors and random perturbations during a virtual, single degree-of-freedom task with two levels of feedback uncertainty, and evaluated adaptation by fitting a hierarchical Kalman filter model...
2017: PloS One
https://www.readbyqxmd.com/read/28295213/using-the-national-cancer-data-base-for-quality-evaluation-to-assess-adherence-to-treatment-guidelines-for-nonmetastatic-inflammatory-breast-cancer
#7
Heather Y Lin, Isabelle Bedrosian, Gildy V Babiera, Simona F Shaitelman, Henry M Kuerer, Wendy A Woodward, Naoto T Ueno, Yu Shen
BACKGROUND: Guidelines for the treatment of nonmetastatic inflammatory breast cancer (IBC) using trimodality therapy (TT) (chemotherapy, surgery, and radiotherapy) have remained largely unchanged since 2000. However, many patients with nonmetastatic IBC do not receive TT. It is unknown how patient-level (PL) and facility-level (FL) factors contribute to TT use. METHODS: Using the National Cancer Data Base, patients with nonmetastatic IBC who underwent locoregional treatment from 2003 through 2011 were identified...
March 13, 2017: Cancer
https://www.readbyqxmd.com/read/28295207/human-gestation-associated-tissues-express-functional-cytosolic-nucleic-acid-sensing-pattern-recognition-receptors
#8
Aled H Bryant, Georgina E Menzies, Louis M Scott, Samantha Spencer-Harty, Lleucu B Davies, Rachel A Smith, Ruth H Jones, Catherine A Thornton
The role of viral infections in adverse pregnancy outcomes has gained interest in recent years. Innate immune pattern recognition receptors (PRRs) and their signalling pathways that yield a cytokine output in response to pathogenic stimuli have been postulated to link infection at the maternal-fetal interface and adverse pregnancy outcomes. The objective of this study was to investigate the expression and functional response of nucleic acid ligand responsive Toll-like receptors (TLR3, 7, 8 and 9), and retinoic acid-inducible gene 1 (RIG-I)-like receptors (RIG-I, MDA5 and LGP2) in human term gestation-associated tissues (placenta, choriodecidua and amnion) using an explant model...
March 13, 2017: Clinical and Experimental Immunology
https://www.readbyqxmd.com/read/28289564/binsanity-unsupervised-clustering-of-environmental-microbial-assemblies-using-coverage-and-affinity-propagation
#9
Elaina D Graham, John F Heidelberg, Benjamin J Tully
Metagenomics has become an integral part of defining microbial diversity in various environments. Many ecosystems have characteristically low biomass and few cultured representatives. Linking potential metabolisms to phylogeny in environmental microorganisms is important for interpreting microbial community functions and the impacts these communities have on geochemical cycles. However, with metagenomic studies there is the computational hurdle of 'binning' contigs into phylogenetically related units or putative genomes...
2017: PeerJ
https://www.readbyqxmd.com/read/28284213/mathematical-modelling-and-a-systems-science-approach-to-describe-the-role-of-cytokines-in-the-evolution-of-severe-dengue
#10
S D Pavithra Jayasundara, S S N Perera, Gathsaurie Neelika Malavige, Saroj Jayasinghe
BACKGROUND: Dengue causes considerable morbidity and mortality in Sri Lanka. Inflammatory mediators such as cytokines, contribute to its evolution from an asymptotic infection to severe forms of dengue. The majority of previous studies have analysed the association of individual cytokines with clinical disease severity. In contrast, we view evolution to Dengue Haemorrhagic Fever as the behaviour of a complex dynamic system. We therefore, analyse the combined effect of multiple cytokines that interact dynamically with each other in order to generate a mathematical model to predict occurrence of Dengue Haemorrhagic Fever...
March 11, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28278479/ovarcall-bayesian-mutation-calling-method-utilizing-overlapping-paired-end-reads
#11
Takuya Moriyama, Yuichi Shiraishi, Kenichi Chiba, Rui Yamaguchi, Seiya Imoto, Satoru Miyano
Detection of somatic mutations from tumor and matched normal sequencing data has become a standard approach in cancer research. Although a number of mutation callers have been developed, it is still difficult to detect mutations with low allele frequency even in exome sequencing. We expect that overlapping paired-end read information is effective for this purpose, but no mutation caller has modeled overlapping information statistically in a proper form in exome sequence data. Here, we develop a Bayesian hierarchical method, OVar- Call (https://github...
March 1, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28276439/structure-guided-mutagenesis-reveals-a-hierarchical-mechanism-of-parkin-activation
#12
Matthew Y Tang, Marta Vranas, Andrea I Krahn, Shayal Pundlik, Jean-François Trempe, Edward A Fon
Parkin and PINK1 function in a common pathway to clear damaged mitochondria. Parkin exists in an auto-inhibited conformation stabilized by multiple interdomain interactions. The binding of PINK1-generated phospho-ubiquitin and the phosphorylation of the ubiquitin-like (Ubl) domain of Parkin at Ser65 release its auto-inhibition, but how and when these events take place in cells remain to be defined. Here we show that mutations that we designed to activate Parkin by releasing the Repressor Element of Parkin (REP) domain, or by disrupting the interface between the RING0:RING2 domains, can completely rescue mutations in the Parkin Ubl that are defective in mitochondrial autophagy...
March 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28274799/diagnostic-accuracy-of-frax-in-predicting-the-10-year-risk-of-osteoporotic-fractures-using-the-usa-treatment-thresholds-a-systematic-review-and-meta-analysis
#13
Xuezhi Jiang, Morgan Gruner, Florence Trémollieres, Wojciech Pluskiewicz, Elisabeth Sornay-Rendu, Piotr Adamczyk, Peter F Schnatz
OBJECTIVES: The aim of this study was to conduct a systematic review and meta-analysis on the performance of the WHO's Fracture Risk Assessment (FRAX) instrument in predicting 10-year risk of Major Osteoporotic Fractures (MOF) and Hip Fractures (HF), using the USA treatment thresholds, in populations other than their derivation cohorts. DESIGN: EMBASE and MEDLINE database were searched with search engine PubMed and OVID as well as Google Scholar for the English-language literature from July 2008 to July 2016...
March 5, 2017: Bone
https://www.readbyqxmd.com/read/28263652/therapist-effects-and-the-impacts-of-therapy-nonattendance
#14
Henry Xiao, Jeffrey A Hayes, Louis G Castonguay, Andrew A McAleavey, Benjamin D Locke
Although dropout from psychotherapy has received substantial attention, the impacts of nonattendance on client outcome across a course of psychotherapy have not been well researched. All in-person psychotherapy treatments require clients to actually attend sessions to generate positive symptomatic results, and missed sessions have at least a time and financial cost. Furthermore, it is plausible that therapist differences exist for client attendance rates. The present study examined impacts of nonattendance, particularly early in a course of treatment, comparing the effects of canceled and no-showed appointments on overall symptom reduction and rate of change while accounting for therapist effects...
March 2017: Psychotherapy
https://www.readbyqxmd.com/read/28253256/a-mechanism-for-the-cortical-computation-of-hierarchical-linguistic-structure
#15
Andrea E Martin, Leonidas A A Doumas
Biological systems often detect species-specific signals in the environment. In humans, speech and language are species-specific signals of fundamental biological importance. To detect the linguistic signal, human brains must form hierarchical representations from a sequence of perceptual inputs distributed in time. What mechanism underlies this ability? One hypothesis is that the brain repurposed an available neurobiological mechanism when hierarchical linguistic representation became an efficient solution to a computational problem posed to the organism...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28252516/decellularization-of-the-porcine-ear-generates-a-biocompatible-nonimmunogenic-extracellular-matrix-platform-for-face-subunit-bioengineering
#16
Jérôme Duisit, Giuseppe Orlando, Donovan Debluts, Louis Maistriaux, Daela Xhema, Yann-Alex J de Bisthoven, Cesare Galli, Andrea Peloso, Catherine Behets, Benoît Lengelé, Pierre Gianello
OBJECTIVE: The purpose of this study was to assess whether perfusion-decellularization technology could be applied to facial grafts. BACKGROUND: Facial allotransplantation remains an experimental procedure. Regenerative medicine techniques allow fabrication of transplantable organs from an individual's own cells, which are seeded into extracellular matrix (ECM) scaffolds from animal or human organs. Therefore, we hypothesized that ECM scaffolds also can be created from facial subunits...
March 1, 2017: Annals of Surgery
https://www.readbyqxmd.com/read/28245947/a-novel-hierarchical-selective-ensemble-classifier-with-bioinformatics-application
#17
Leyi Wei, Shixiang Wan, Jiasheng Guo, Kelvin Kl Wong
Selective ensemble learning is a technique that selects a subset of diverse and accurate basic models in order to generate stronger generalization ability. In this paper, we proposed a novel learning algorithm that is based on parallel optimization and hierarchical selection (PTHS). Our novel feature selection method is based on maximize the sum of relevance and distance (MSRD) for solving the problem of high dimensionality. Specifically, we have a PTHS algorithm that employs parallel optimization and candidate model pruning based on k-means and a hierarchical selection framework...
February 25, 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/28245661/value-based-contracting-innovated-medicare-advantage-healthcare-delivery-and-improved-survival
#18
Aloke K Mandal, Gene K Tagomori, Randell V Felix, Scott C Howell
OBJECTIVES: In Medicare Advantage (MA) with its CMS Hierarchical Condition Categories (CMS-HCC) payment model, CMS reimburses private plans (Medicare Advantage Organizations [MAOs]) with prospective, monthly, health-based or risk-adjusted, capitated payments. The effect of this payment methodology on healthcare delivery remains debatable. How value-based contracting generates cost efficiencies and improves clinical outcomes in MA is studied. STUDY DESIGN: A difference in contracting arrangements between an MAO and 2 provider groups facilitated an intervention-control, preintervention-postintervention, difference-in-differences approach among statistically similar, elderly, community-dwelling MA enrollees within one metropolitan statistical area...
February 1, 2017: American Journal of Managed Care
https://www.readbyqxmd.com/read/28238168/learning-representation-hierarchies-by-sharing-visual-features-a-computational-investigation-of-persian-character-recognition-with-unsupervised-deep-learning
#19
Zahra Sadeghi, Alberto Testolin
In humans, efficient recognition of written symbols is thought to rely on a hierarchical processing system, where simple features are progressively combined into more abstract, high-level representations. Here, we present a computational model of Persian character recognition based on deep belief networks, where increasingly more complex visual features emerge in a completely unsupervised manner by fitting a hierarchical generative model to the sensory data. Crucially, high-level internal representations emerging from unsupervised deep learning can be easily read out by a linear classifier, achieving state-of-the-art recognition accuracy...
February 25, 2017: Cognitive Processing
https://www.readbyqxmd.com/read/28236748/should-metacognition-be-measured-by-logistic-regression
#20
Manuel Rausch, Michael Zehetleitner
Are logistic regression slopes suitable to quantify metacognitive sensitivity, i.e. the efficiency with which subjective reports differentiate between correct and incorrect task responses? We analytically show that logistic regression slopes are independent from rating criteria in one specific model of metacognition, which assumes (i) that rating decisions are based on sensory evidence generated independently of the sensory evidence used for primary task responses and (ii) that the distributions of evidence are logistic...
March 2017: Consciousness and Cognition
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