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hierarchical generative model

Yibing Ma, Zhiguo Jiang, Haopeng Zhang, Fengying Xie, Yushan Zheng, Huaqiang Shi, Yu Zhao, Jun Shi
BACKGROUND AND OBJECTIVE: Content-based image retrieval is an effective method for histopathological image analysis. However, given a database of huge whole slide images (WSIs), acquiring appropriate region-of-interests (ROIs) for training is significant and difficult. Moreover, histopathological images can only be annotated by pathologists, resulting in the lack of labeling information. Therefore, it is an important and challenging task to generate ROIs from WSI and retrieve image with few labels...
June 2018: Computer Methods and Programs in Biomedicine
Y Kubota, B Kusumoto, T Shiono, W Ulrich
Species assembly patterns of local communities are shaped by the balance between multiple abiotic/biotic filters and dispersal that both select individuals from species pools at the regional scale. Knowledge regarding functional assembly can provide insight into the relative importance of the deterministic and stochastic processes that shape species assembly. We evaluated the hierarchical roles of the α niche and β niches by analyzing the influence of environmental filtering relative to functional traits on geographical patterns of tree species assembly in mid-latitude forests...
April 6, 2018: Oecologia
Stefan Sellman, Kimberly Tsao, Michael J Tildesley, Peter Brommesson, Colleen T Webb, Uno Wennergren, Matt J Keeling, Tom Lindström
Numerical models for simulating outbreaks of infectious diseases are powerful tools for informing surveillance and control strategy decisions. However, large-scale spatially explicit models can be limited by the amount of computational resources they require, which poses a problem when multiple scenarios need to be explored to provide policy recommendations. We introduce an easily implemented method that can reduce computation time in a standard Susceptible-Exposed-Infectious-Removed (SEIR) model without introducing any further approximations or truncations...
April 6, 2018: PLoS Computational Biology
Fang-Yu Lin, Pedro Eduardo Lopes, Edward D Harder, Benoît Roux, Alexander D MacKerell
Development of accurate force field parameters for molecular ions in the context of a polarizable energy function based on the classical Drude oscillator is a crucial step towards an accurate polarizable model for modeling and simulations of biological macromolecules. Towards this goal we have undertaken a hierarchical approach in which force field parameter optimization is initially performed for small molecules for which experimental data exists that serve as building blocks of macromolecular systems. Small molecules representative of the ionic moieties of biological macromolecules include the cationic ammonium and methyl substituted ammonium derivatives, imidazolium, guanidinium and methylguanidinium and the anionic acetate, phenolate and alkanethiolates...
April 6, 2018: Journal of Chemical Information and Modeling
Sang-Mok Choo, Byunghyun Ban, Jae Il Joo, Kwang-Hyun Cho
BACKGROUND: Controlling complex molecular regulatory networks is getting a growing attention as it can provide a systematic way of driving any cellular state to a desired cell phenotypic state. A number of recent studies suggested various control methods, but there is still deficiency in finding out practically useful control targets that ensure convergence of any initial network state to one of attractor states corresponding to a desired cell phenotype. RESULTS: To find out practically useful control targets, we introduce a new concept of phenotype control kernel (PCK) for a Boolean network, defined as the collection of all minimal sets of control nodes having their fixed state values that can generate all possible control sets which eventually drive any initial state to one of attractor states corresponding to a particular cell phenotype of interest...
April 5, 2018: BMC Systems Biology
Yongyi Wei, Zhan Mao, Zhengzhong Li, Fang Zhang, Hexing Li
Heterogeneous organometallic catalysts with well-defined active sites and hierarchical pores hold tremendous promise for efficient and eco-friendly chemical processes. However, the simple and scalable preparation of these materials remained difficult to date, which has hampered a more board application scope. Herein we reported a low cost, rapid and scalable aerosol-assisted assembly approach for the synthesis of well-defined PdDPP (PdCl2(PPh2(CH2)2) complex-containing benzene-bridged organosilica-based catalyst with hierarchically bimodal micro-macroporous structure...
April 4, 2018: ACS Applied Materials & Interfaces
Ozgur S Oguz, Zhehua Zhou, Stefan Glasauer, Dirk Wollherr
Human motor control is highly efficient in generating accurate and appropriate motor behavior for a multitude of tasks. This paper examines how kinematic and dynamic properties of the musculoskeletal system are controlled to achieve such efficiency. Even though recent studies have shown that the human motor control relies on multiple models, how the central nervous system (CNS) controls this combination is not fully addressed. In this study, we utilize an Inverse Optimal Control (IOC) framework in order to find the combination of those internal models and how this combination changes for different reaching tasks...
April 3, 2018: Scientific Reports
Robert Šket, Tadej Debevec, Susanne Kublik, Michael Schloter, Anne Schoeller, Boštjan Murovec, Katarina Vogel Mikuš, Damjan Makuc, Klemen Pečnik, Janez Plavec, Igor B Mekjavić, Ola Eiken, Zala Prevoršek, Blaž Stres
We explored the metagenomic, metabolomic and trace metal makeup of intestinal microbiota and environment in healthy male participants during the run-in (5 day) and the following three 21-day interventions: normoxic bedrest (NBR), hypoxic bedrest (HBR) and hypoxic ambulation (HAmb) which were carried out within a controlled laboratory environment (circadian rhythm, fluid and dietary intakes, microbial bioburden, oxygen level, exercise). The fraction of inspired O2 (Fi O2 ) and partial pressure of inspired O2 (Pi O2 ) were 0...
2018: Frontiers in Physiology
Yoshinobu Hagiwara, Masakazu Inoue, Hiroyoshi Kobayashi, Tadahiro Taniguchi
In this paper, we propose a hierarchical spatial concept formation method based on the Bayesian generative model with multimodal information e.g., vision, position and word information. Since humans have the ability to select an appropriate level of abstraction according to the situation and describe their position linguistically, e.g., "I am in my home" and "I am in front of the table," a hierarchical structure of spatial concepts is necessary in order for human support robots to communicate smoothly with users...
2018: Frontiers in Neurorobotics
Gabor Stefanics, Jakob Heinzle, András Attila Horváth, Klaas Enno Stephan
Predictive coding (PC) posits that the brain employs a generative model to infer the environmental causes of its sensory data and uses precision-weighted prediction errors (pwPE) to continuously update this model. While supported by much circumstantial evidence, experimental tests grounded in formal trial-by-trial predictions are rare. One partial exception are event-related potential (ERP) studies of the auditory mismatch negativity (MMN), where computational models have found signatures of pwPEs and related model-updating processes...
March 26, 2018: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
Adrian Quintero, Emmanuel Lesaffre
Hierarchical models are extensively used in pharmacokinetics and longitudinal studies. When the estimation is performed from a Bayesian approach, model comparison is often based on the deviance information criterion (DIC). In hierarchical models with latent variables, there are several versions of this statistic: the conditional DIC (cDIC) that incorporates the latent variables in the focus of the analysis and the marginalized DIC (mDIC) that integrates them out. Regardless of the asymptotic and coherency difficulties of cDIC, this alternative is usually used in Markov chain Monte Carlo (MCMC) methods for hierarchical models because of practical convenience...
March 26, 2018: Statistics in Medicine
Yan Wang, Biting Yu, Lei Wang, Chen Zu, David S Lalush, Weili Lin, Xi Wu, Jiliu Zhou, Dinggang Shen, Luping Zhou
Positron emission tomography (PET) is a widely used imaging modality, providing insight into both the biochemical and physiological processes of human body. Usually, a full dose radioactive tracer is required to obtain high-quality PET images for clinical needs. This inevitably raises concerns about potential health hazards. On the other hand, dose reduction may cause the increased noise in the reconstructed PET images, which impacts the image quality to a certain extent. In this paper, in order to reduce the radiation exposure while maintaining the high quality of PET images, we propose a novel method based on 3D conditional generative adversarial networks (3D c-GANs) to estimate the high-quality full-dose PET images from low-dose ones...
March 20, 2018: NeuroImage
Shabnam Sadeghi Esfahlani, Tommy Thompson, Ali Davod Parsa, Ian Brown, Silvia Cirstea
This paper proposes the use of a non-immersive virtual reality rehabilitation system "ReHabgame" developed using Microsoft Kinect™ and the Thalmic™ Labs Myo gesture control armband. The ReHabgame was developed based on two third-person video games that provide a feasible possibility of assessing postural control and functional reach tests. It accurately quantifies specific postural control mechanisms including timed standing balance, functional reach tests using real-time anatomical landmark orientation, joint velocity, and acceleration while end trajectories were calculated using an inverse kinematics algorithm...
February 2018: Heliyon
DanRong Hu, LiJuan Chen, Ying Qu, JinRong Peng, BingYang Chu, Kun Shi, Ying Hao, Lin Zhong, MengYao Wang, ZhiYong Qian
The combination of chemotherapy with photodynamic therapy (PDT) has attracted broad attention as it can overcome limitations of conventional chemo-treatment by using different modes of action. However, the efficacy of PDT to treat solid tumors is severely affected by hypoxia in tumors. Methods : In this study, we developed oxygen-generating theranostic nanoparticles (CDM NPs) by hierarchically assembling doxorubicin (DOX), chlorin e6 (Ce6) and colloidal manganese dioxide (MnO2 ) with poly (ε-caprolactone-co-lactide)-b-poly (ethylene glycol)-b-poly (ε-caprolactone-co-lactide) for treating breast cancer...
2018: Theranostics
Jonathan K Noel, Thomas F Babor, James J Grady
Aims: The current study was conducted to investigate how changes in the content of a social media ad, user engagement values associated with the ad and user-generated comments (UGCs) associated with the ad can influence the appeal (i.e. source appeal, informational appeal and emotional appeal) of a social media ad. Short summary: Facebook beer ads that violated the guidelines of a relevant marketing code were rated as more emotionally appealing compared to Facebook beer ads that did not violated the guidelines...
March 15, 2018: Alcohol and Alcoholism: International Journal of the Medical Council on Alcoholism
Lovjeet Singh, Pawan Rekha, Shri Chand
In order to find a better alternative of conventional aqueous ion-exchange method, several Cu/zeolite Y samples were synthesized by different routes and examined for the catalytic wet peroxide oxidation of quinoline aqueous solution in continuous fixed-bed reactor. The characterization of catalysts using ICPMS, XRD, N2 sorption, UV-vis DRS, FESEM and XPS techniques reveals the profound influence of preparation methods on synergy between copper-support interfaces. Aqueous ion-exchange (CuYAIE ) and wet-impregnation (CuYIMP ) methods promoted isolated Cu1+/2+ species; however, large crystallites of CuO were present on the external surface of precipitation-impregnation (CuYPI ) catalyst...
March 15, 2018: Journal of Environmental Management
Gen Li, Dereje Jima, Fred A Wright, Andrew B Nobel
BACKGROUND: Expression quantitative trait loci (eQTL) analysis identifies genetic markers associated with the expression of a gene. Most existing eQTL analyses and methods investigate association in a single, readily available tissue, such as blood. Joint analysis of eQTL in multiple tissues has the potential to improve, and expand the scope of, single-tissue analyses. Large-scale collaborative efforts such as the Genotype-Tissue Expression (GTEx) program are currently generating high quality data in a large number of tissues...
March 9, 2018: BMC Bioinformatics
Carla A Giambrone, Catherine P Cook-Cottone, Jessalyn E Klein
BACKGROUND: Concept mapping methodology was used to explore the perceived impact of practicing yoga with the Africa Yoga Project (AYP)-an organisation created to increase health and well-being by providing community-based yoga classes throughout Kenya. AYP's mission fit with theoretical models of well-being is discussed. Anecdotal evidence and initial qualitative research suggested the AYP meaningfully impacted adult students. METHODS: Of the hundreds of AYP's adult students, 56 and 82 students participated in Phases I and II, respectively...
March 2018: Applied Psychology. Health and Well-being
David P Medeiros
A central concern of generative grammar is the relationship between hierarchy and word order, traditionally understood as two dimensions of a single syntactic representation. A related concern is directionality in the grammar. Traditional approaches posit process-neutral grammars, embodying knowledge of language, put to use with infinite facility both for production and comprehension. This has crystallized in the view of Merge as the central property of syntax, perhaps its only novel feature. A growing number of approaches explore grammars with different directionalities, often with more direct connections to performance mechanisms...
2018: Frontiers in Psychology
Francisco Duarte, Bruno Martins, Cátia Sousa Pinto, Mário J Silva
We address the assignment of ICD-10 codes for causes of death by analyzing free-text descriptions in death certificates, together with the associated autopsy reports and clinical bulletins, from the Portuguese Ministry of Health. We leverage a deep neural network that combines word embeddings, recurrent units, and neural attention, for the generation of intermediate representations of the textual contents. The neural network also explores the hierarchical nature of the input data, by building representations from the sequences of words within individual fields, which are then combined according to the sequences of fields that compose the inputs...
February 26, 2018: Journal of Biomedical Informatics
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