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hierarchical generative model

Sathyaseelan Subramaniam, Jacqueline Bober, Jennifer Chao, Shahriar Zehtabchi
BACKGROUND: Traditionally, emergency department (ED) physicians rely on their clinical examination to differentiate between cellulitis and abscess when evaluating skin and soft tissue infections (SSTI). Management of an abscess requires incision and drainage, whereas cellulitis generally requires a course of antibiotics. Misdiagnosis often results in unnecessary invasive procedures, sedations (for incision and drainage in pediatric patients), or a return ED visit for failed antibiotic therapy...
October 21, 2016: Academic Emergency Medicine: Official Journal of the Society for Academic Emergency Medicine
Dipankar Sahoo, Mihai Peterca, Emad Aqad, Benjamin E Partridge, Paul A Heiney, Robert Graf, Hans W Spiess, Xiangbing Zeng, Virgil Percec
Perylene bisimide derivatives (PBIs) are known to form only columnar or lamellar assemblies. There is no known example of a PBI self-assembling into a supramolecular sphere. Therefore, periodic and quasiperiodic arrays generated from spherical assemblies produced from PBIs are also not known. Here, a PBI functionalized at its imide groups with a second generation self-assembling dendron is reported to self-assemble into supramolecular spheres. These spheres self-organize in a body-centered cubic (BCC) periodic array, rarely encountered for self-assembling dendrons but often encountered in block copolymers...
October 19, 2016: Journal of the American Chemical Society
Leyou Zhang, Qing Wu, Yi Mu, Jingxia Zhang
As a new summarized record of an individual's medical data and information, Personal Health Record (PHR) can be accessible online. The owner can control fully his/her PHR files to be shared with different users such as doctors, clinic agents, and friends. However, in an open network environment like in the Cloud, these sensitive privacy information may be gotten by those unauthorized parties and users. In this paper, we consider how to achieve PHR data confidentiality and provide fine-grained access control of PHR files in the public Cloud based on Attribute Based Encryption(ABE)...
December 2016: Journal of Medical Systems
J Matthew Watson, Alexander Platzer, Anita Kazda, Svetlana Akimcheva, Sona Valuchova, Viktoria Nizhynska, Magnus Nordborg, Karel Riha
In plants, gametogenesis occurs late in development, and somatic mutations can therefore be transmitted to the next generation. Longer periods of growth are believed to result in an increase in the number of cell divisions before gametogenesis, with a concomitant increase in mutations arising due to replication errors. However, there is little experimental evidence addressing how many cell divisions occur before gametogenesis. Here, we measured loss of telomeric DNA and accumulation of replication errors in Arabidopsis with short and long life spans to determine the number of replications in lineages leading to gametes...
October 11, 2016: Proceedings of the National Academy of Sciences of the United States of America
Xiaochen Sun, Rohan Fernando, Jack Dekkers
BACKGROUND: Traditional genomic prediction models using multiple regression on single nucleotide polymorphisms (SNPs) genotypes exploit associations between genotypes of quantitative trait loci (QTL) and SNPs, which can be created by historical linkage disequilibrium (LD), recent co-segregation (CS) and pedigree relationships. Results from field data analyses show that prediction accuracy is usually much higher for individuals that are close relatives of the training population than for distantly related individuals...
October 11, 2016: Genetics, Selection, Evolution: GSE
A N Aggarwal, R Agarwal, I S Sehgal, S Dhooria, D Behera
OBJECTIVE: To determine the diagnostic accuracy of pleural fluid adenosine deaminase (ADA) in diagnosing tuberculous pleural effusion (TPE) among Indian patients using systematic review and meta-analysis. DESIGN: The PubMed, Embase, IndMED and Cochrane databases and other relevant publications were searched to identify Indian studies evaluating the sensitivity and specificity of ADA in diagnosing TPE. Pooled diagnostic accuracy measures and 95% confidence intervals (95%CI) were generated using a bivariate random-effects model, and examined using forest plots and hierarchical summary receiver operating characteristic (HSROC) curves...
October 2016: International Journal of Tuberculosis and Lung Disease
Dimitris A Pinotsis, Roman Loonis, Andre M Bastos, Earl K Miller, Karl J Friston
Neural rhythms or oscillations are ubiquitous in neuroimaging data. These spectral responses have been linked to several cognitive processes; including working memory, attention, perceptual binding and neuronal coordination. In this paper, we show how Bayesian methods can be used to finesse the ill-posed problem of reconstructing-and explaining-oscillatory responses. We offer an overview of recent developments in this field, focusing on (i) the use of MEG data and Empirical Bayes to build hierarchical models for group analyses-and the identification of important sources of inter-subject variability and (ii) the construction of novel dynamic causal models of intralaminar recordings to explain layer-specific activity...
October 7, 2016: Brain Topography
Yu Shrike Zhang, Andrea Arneri, Simone Bersini, Su-Ryon Shin, Kai Zhu, Zahra Goli-Malekabadi, Julio Aleman, Cristina Colosi, Fabio Busignani, Valeria Dell'Erba, Colin Bishop, Thomas Shupe, Danilo Demarchi, Matteo Moretti, Marco Rasponi, Mehmet Remzi Dokmeci, Anthony Atala, Ali Khademhosseini
Engineering cardiac tissues and organ models remains a great challenge due to the hierarchical structure of the native myocardium. The need of integrating blood vessels brings additional complexity, limiting the available approaches that are suitable to produce integrated cardiovascular organoids. In this work we propose a novel hybrid strategy based on 3D bioprinting, to fabricate endothelialized myocardium. Enabled by the use of our composite bioink, endothelial cells directly bioprinted within microfibrous hydrogel scaffolds gradually migrated towards the peripheries of the microfibers to form a layer of confluent endothelium...
December 2016: Biomaterials
Barun Mahata, Kaushik Biswas
Precise and targeted genome editing using Transcription Activator-Like Effector Endonucleases (TALENs) has been widely used and proven to be an extremely effective and specific knockout strategy in both cultured cells and animal models. The current chapter describes a protocol for the construction and generation of TALENs using serial and hierarchical digestion and ligation steps, and using the synthesized TALEN pairs to achieve locus-specific targeted gene editing in mammalian cell lines using a modified clonal selection strategy in an easy and cost-efficient manner...
2017: Methods in Molecular Biology
Michael Costanzo, Benjamin VanderSluis, Elizabeth N Koch, Anastasia Baryshnikova, Carles Pons, Guihong Tan, Wen Wang, Matej Usaj, Julia Hanchard, Susan D Lee, Vicent Pelechano, Erin B Styles, Maximilian Billmann, Jolanda van Leeuwen, Nydia van Dyk, Zhen-Yuan Lin, Elena Kuzmin, Justin Nelson, Jeff S Piotrowski, Tharan Srikumar, Sondra Bahr, Yiqun Chen, Raamesh Deshpande, Christoph F Kurat, Sheena C Li, Zhijian Li, Mojca Mattiazzi Usaj, Hiroki Okada, Natasha Pascoe, Bryan-Joseph San Luis, Sara Sharifpoor, Emira Shuteriqi, Scott W Simpkins, Jamie Snider, Harsha Garadi Suresh, Yizhao Tan, Hongwei Zhu, Noel Malod-Dognin, Vuk Janjic, Natasa Przulj, Olga G Troyanskaya, Igor Stagljar, Tian Xia, Yoshikazu Ohya, Anne-Claude Gingras, Brian Raught, Michael Boutros, Lars M Steinmetz, Claire L Moore, Adam P Rosebrock, Amy A Caudy, Chad L Myers, Brenda Andrews, Charles Boone
We generated a global genetic interaction network for Saccharomyces cerevisiae, constructing more than 23 million double mutants, identifying about 550,000 negative and about 350,000 positive genetic interactions. This comprehensive network maps genetic interactions for essential gene pairs, highlighting essential genes as densely connected hubs. Genetic interaction profiles enabled assembly of a hierarchical model of cell function, including modules corresponding to protein complexes and pathways, biological processes, and cellular compartments...
September 23, 2016: Science
Maninder Kaur, Om Silakari
The clinical efficacy of multiple kinase inhibitors has caught the interest of Pharmaceutical and Biotech researchers to develop potential drugs with multi-kinase inhibitory activity for complex diseases. In the present work, we attempted to identify dual inhibitors of. Syk and JAK3, keys players in immune signaling, by developing ideal pharmacophores integrating Ligand based pharmacophore models (LBPMs) and Structure based pharmacophore models (SBPMs), thereby projecting the optimum pharmacophoric required for inhibition of both the kinases...
September 28, 2016: Journal of Biomolecular Structure & Dynamics
Damien Maura, Ronen Hazan, Tomoe Kitao, Alicia E Ballok, Laurence G Rahme
Pseudomonas aeruginosa defies eradication by antibiotics and is responsible for acute and chronic human infections due to a wide variety of virulence factors. Currently, it is believed that MvfR (PqsR) controls the expression of many of these factors indirectly via the pqs and phnAB operons. Here we provide strong evidence that MvfR may also bind and directly regulate the expression of additional 35 loci across the P. aeruginosa genome, including major regulators and virulence factors, such as the quorum sensing (QS) regulators lasR and rhlR, and genes involved in protein secretion, translation, and response to oxidative stress...
September 28, 2016: Scientific Reports
Matt G Hall, Chris A Clark
PURPOSE: To investigate the sensitivity of diffusion-MR signal to microstructural change in muscle tissue associated with pathology, and recommend optimal acquisition parameters. METHODS: We employ Monte-Carlo simulation of diffusing spins in hierarchical tissue to generate synthetic diffusion-weighted signal curves over a wide range of scan parameters. Curves are analyzed using entropy-a measure of curve complexity. Entropy change between a baseline and various microstructural scenarios is investigated...
September 25, 2016: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
Thomas A G Risbridger, Daniel W Watkins, James P K Armstrong, Adam W Perriman, J L Ross Anderson, David J Fermin
The modification of protein surfaces employing cationic and anionic species enables the assembly of these biomaterials into highly sophisticated hierarchical structures. Such modifications can allow bioconjugates to retain or amplify their functionalities under conditions in which their native structure would be severely compromised. In this work, we assess the effect of this type of bioconjugation on the redox properties of two model heme proteins, that is, cytochrome c (CytC) and myoglobin (Mb). In particular, the work focuses on the sequential modification by 3-dimethylamino propylamine (DMAPA) and 4-nonylphenyl 3-sulfopropyl ether (S1) anionic surfactant...
October 3, 2016: Biomacromolecules
Olman Gomez, Heiko Neumann
A biologically inspired model architecture for inferring 3D shape from texture is proposed. The model is hierarchically organized into modules roughly corresponding to visual cortical areas in the ventral stream. Initial orientation selective filtering decomposes the input into low-level orientation and spatial frequency representations. Grouping of spatially anisotropic orientation responses builds sketch-like representations of surface shape. Gradients in orientation fields and subsequent integration infers local surface geometry and globally consistent 3D depth...
2016: PloS One
Saeed R Kheradpisheh, Masoud Ghodrati, Mohammad Ganjtabesh, Timothée Masquelier
View-invariant object recognition is a challenging problem that has attracted much attention among the psychology, neuroscience, and computer vision communities. Humans are notoriously good at it, even if some variations are presumably more difficult to handle than others (e.g., 3D rotations). Humans are thought to solve the problem through hierarchical processing along the ventral stream, which progressively extracts more and more invariant visual features. This feed-forward architecture has inspired a new generation of bio-inspired computer vision systems called deep convolutional neural networks (DCNN), which are currently the best models for object recognition in natural images...
2016: Frontiers in Computational Neuroscience
Facundo Costa, Hadj Batatia, Thomas Oberlin, Carlos D'Giano, Jean-Yves Tourneret
This paper deals with EEG source localization. The aim is to perform spatially coherent focal localization and recover temporal EEG waveforms, which can be useful in certain clinical applications. A new hierarchical Bayesian model is proposed with a multivariate Bernoulli Laplacian structured sparsity prior for brain activity. This distribution approximates a mixed ℓ20 pseudo norm regularization in a Bayesian framework. A partially collapsed Gibbs sampler is proposed to draw samples asymptotically distributed according to the posterior of the proposed Bayesian model...
September 15, 2016: NeuroImage
Laura N Medford-Davis, Rohan Shah, Danielle Kennedy, Emilie Becker
OBJECTIVES: The objective of this study was to determine characteristics associated with potentially preventable pediatric admissions as defined by the Agency for Healthcare Research and Quality. METHODS: The Texas Inpatient Public Use Data File, an administrative database of hospital admissions, identified 747 040 pediatric admissions ages 0 to 17 years to acute care facilities between 2005 and 2008. Potentially preventable admissions included 5 diagnoses: asthma, perforated appendicitis, diabetes, gastroenteritis, and urinary tract infection...
October 2016: Hospital Pediatrics
Berend Terluin, Niels Smits, Evelien P M Brouwers, Henrica C W de Vet
BACKGROUND: The Four-Dimensional Symptom Questionnaire (4DSQ) is a self-report questionnaire measuring distress, depression, anxiety and somatization with separate scales. The 4DSQ has extensively been validated in clinical samples, especially from primary care settings. Information about measurement properties and normative data in the general population was lacking. In a Dutch general population sample we examined the 4DSQ scales' structure, the scales' reliability and measurement invariance with respect to gender, age and education, the scales' score distributions across demographic categories, and normative data...
2016: Health and Quality of Life Outcomes
Tanvir R Faisal, Nicolay Hristozov, Tamara L Western, Alejandro Rey, Damiano Pasini
Plant petioles can be considered as hierarchical cellular structures, displaying geometric features defined at multiple length scales. Their macroscopic mechanical properties are the cumulative outcome of structural properties attained at each level of the structural hierarchy. This work appraises the compliance of a rhubarb stalk by determining the stalk's bending and torsional stiffness both computationally and experimentally. In our model, the irregular cross-sectional shape of the petiole and the layers of the constituent tissues are considered to evaluate the stiffness properties at the structural level...
September 14, 2016: Computer Methods in Biomechanics and Biomedical Engineering
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