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https://www.readbyqxmd.com/read/29053464/co-expression-network-approach-to-studying-the-effects-of-botulinum-neurotoxin-a
#1
Kavitha Mukund, Samuel R Ward, Richard L Lieber, Shankar Subramaniam
Botulinum Neurotoxin A (BoNT-A) is a potent neurotoxin with several clinical applications.The goal of this study was to utilize co-expression network theory to analyze temporal transcriptional data from skeletal muscle after BoNT-A treatment. Expression data for 2000 genes (extracted using a ranking heuristic) served as the basis for this analysis. Using weighted gene co-expression network analysis (WGCNA), we identified 19 co-expressed modules, further hierarchically clustered into 5 groups. Quantifying average expression and co-expression patterns across these groups revealed temporal aspects of muscle's response to BoNT-A...
October 16, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/29051528/induced-seismicity-closed-form-traffic-light-system-for-actuarial-decision-making-during-deep-fluid-injections
#2
A Mignan, M Broccardo, S Wiemer, D Giardini
The rise in the frequency of anthropogenic earthquakes due to deep fluid injections is posing serious economic, societal, and legal challenges to many geo-energy and waste-disposal projects. Existing tools to assess such problems are still inherently heuristic and mostly based on expert elicitation (so-called clinical judgment). We propose, as a complementary approach, an adaptive traffic light system (ATLS) that is function of a statistical model of induced seismicity. It offers an actuarial judgement of the risk, which is based on a mapping between earthquake magnitude and risk...
October 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29049521/can-measured-muscle-synergies-construct-unmeasured-muscle-excitations
#3
Nicholas A Bianco, Carolynn Patten, Benjamin J Fregly
Accurate prediction of muscle and joint contact forces during human movement could improve treatment planning for disorders such as osteoarthritis, stroke, Parkinson's disease, and cerebral palsy. Recent studies suggest that muscle synergies, a low-dimensional representation of a large set of muscle electromyographic (EMG) signals (henceforth called "muscle excitations"), may increase the uniqueness of muscle excitations predicted by optimization methods. This study explores the feasibility of using muscle synergy information extracted from eight muscle EMG signals (henceforth called "included" muscle excitations) to accurately construct muscle excitations from up to 16 additional EMG signals (henceforth called "excluded" muscle excitations)...
October 16, 2017: Journal of Biomechanical Engineering
https://www.readbyqxmd.com/read/29046743/post-processing-partitions-to-identify-domains-of-modularity-optimization
#4
William H Weir, Scott Emmons, Ryan Gibson, Dane Taylor, Peter J Mucha
We introduce the Convex Hull of Admissible Modularity Partitions (CHAMP) algorithm to prune and prioritize different network community structures identified across multiple runs of possibly various computational heuristics. Given a set of partitions, CHAMP identifies the domain of modularity optimization for each partition-i.e., the parameter-space domain where it has the largest modularity relative to the input set-discarding partitions with empty domains to obtain the subset of partitions that are "admissible" candidate community structures that remain potentially optimal over indicated parameter domains...
September 2017: Algorithms
https://www.readbyqxmd.com/read/29043020/secondary-invasion-when-invasion-success-is-contingent-on-other-invaders-altering-the-properties-of-recipient-ecosystems
#5
REVIEW
Luke S O'Loughlin, Peter T Green
Positive interactions between exotic species may increase ecosystem-level impacts and potentially facilitate the entry and spread of other exotic species. Invader-facilitated invasion success-"secondary invasion"-is a key conceptual aspect of the well-known invasional meltdown hypothesis, but remains poorly defined and empirically underexplored. Drawing from heuristic models and published empirical studies, we explore this form of "secondary invasion" and discuss the phenomenon within the recognized conceptual framework of the determinants of invasion success...
October 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29042585/compact-morphology-based-poly-metallic-nodule-delineation
#6
Timm Schoening, Daniel O B Jones, Jens Greinert
Poly-metallic nodules are a marine resource considered for deep sea mining. Assessing nodule abundance is of interest for mining companies and to monitor potential environmental impact. Optical seafloor imaging allows quantifying poly-metallic nodule abundance at spatial scales from centimetres to square kilometres. Towed cameras and diving robots acquire high-resolution imagery that allow detecting individual nodules and measure their sizes. Spatial abundance statistics can be computed from these size measurements, providing e...
October 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29041389/improved-tkm-tr-methods-for-papr-reduction-of-dco-ofdm-visible-light-communications
#7
Yongqiang Hei, Jiao Liu, Huaxi Gu, Wentao Li, Xiaochuan Xu, Ray T Chen
The dc-biased optical orthogonal frequency division multiplexing (DCO-OFDM) system is experimentally demonstrated as an appealing candidate in future visible light communication (VLC) system. However, the intrinsic high PAPR drawback that the DCO-OFDM system suffers from still needs to be addressed and few effective approach has been found so far. To deal with this problem, in this paper, the tone reservation (TR) technique based the time domain kernel matrix (TKM-TR) schemes for reducing the PAPR are studied and applied to DCO-OFDM system...
October 2, 2017: Optics Express
https://www.readbyqxmd.com/read/29036699/pain-related-acceptance-as-a-mediator-in-the-fear-avoidance-model-of-chronic-pain-a-preliminary-study
#8
Sophie Lykkegaard Ravn, Maria Louison Vang, Henrik Bjarke Vaegter, Tonny Elmose Andersen
Objective: The fear avoidance model has served as a popular, heuristic model in explaining the transition from acute to chronic pain. In addition, the significance of pain-related acceptance in chronic pain development and adjustment is underlined in a vast number of empirical studies. The objective of the current preliminary study was to investigate pain-related acceptance as a mediator within the key cognitive relationships proposed by the fear avoidance model of chronic pain. Materials and Methods: In a cross-sectional design, bodily pain, pain catastrophizing, fear avoidance beliefs, and pain-related acceptance were assessed by questionnaires in 125 chronic pain patients in a Danish multidisciplinary pain center...
September 23, 2017: Pain Medicine: the Official Journal of the American Academy of Pain Medicine
https://www.readbyqxmd.com/read/29035632/a-multi-objective-optimization-model-and-orthogonal-design-based-hybrid-heuristic-algorithm-for-regional-urban-mining-management-problems
#9
Hao Wu, Zhong Wan
In this paper, a multi-objective mixed-integer piecewise nonlinear programming model (MOMIPNLP) is built to formulate the management problem of urban mining system, where the decision variables are associated with buy-back pricing, choices of sites, transportation planning and adjustment of production capacity. Different from the existing approaches, the social negative effect, generated from structural optimization of the recycling system, is minimized in our model, as well as the total recycling profit and utility from environmental improvement are jointly maximized...
October 16, 2017: Journal of the Air & Waste Management Association
https://www.readbyqxmd.com/read/29035224/efficient-local-search-for-euclidean-path-difference-median-trees
#10
Alexey Markin, Oliver Eulenstein
Synthesizing large-scale phylogenetic trees is a fundamental problem in evolutionary biology. Median tree problems have evolved as a powerful tool to reconstruct such trees. Such problems seek a median tree for a given collection of input trees under some problem-specific tree distance. There has been an increased interest in the median tree problem for the classical path-difference distance between trees. While this problem is NP-hard, standard local search heuristics have been described that are based on solving a local search problem exactly...
October 16, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/29035210/inextensible-non-rigid-structure-from-motion-by-second-order-cone-programming
#11
Ajad Chhatkuli, Daniel Pizarro, Toby Collins, Adrien Bartoli
We present a global and convex formulation for the templateless 3D reconstruction of a deforming object with the perspective camera. We show for the first time how to construct a Second-Order Cone Programming (SOCP) problem for Non-Rigid Structure-from-Motion (NRSfM) using the Maximum-Depth Heuristic (MDH). In this regard, we deviate strongly from the general trend of using affine cameras and factorization-based methods to solve NRSfM, which do not perform well with complex nonlinear deformations. In MDH, the points' depths are maximized so that the distance between neighbouring points in camera space are upper bounded by the geodesic distance...
October 13, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/29034505/in-vivo-characterization-of-the-downfield-part-of-1-h-mr-spectra-of-human-brain-at-9-4-t-magnetization-exchange-with-water-and-relation-to-conventionally-determined-metabolite-content
#12
Nicole D Fichtner, Ioannis-Angelos Giapitzakis, Nikolai Avdievich, Ralf Mekle, Daniel Zaldivar, Anke Henning, Roland Kreis
PURPOSE: To perform exchange-rate measurements on the in vivo human brain downfield spectrum (5-10 ppm) at 9.4 T and to compare the variation in concentrations of the downfield resonances and of known upfield metabolites to determine potential peak labels. METHODS: Non-water-suppressed metabolite cycling was used in combination with an inversion transfer technique in two brain locations in healthy volunteers to measure the exchange rates and T1 values of exchanging peaks...
October 16, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/29034375/extracting-drug-drug-interactions-with-word-and-character-level-recurrent-neural-networks
#13
Ramakanth Kavuluru, Anthony Rios, Tung Tran
Drug-drug interactions (DDIs) are known to be responsible for nearly a third of all adverse drug reactions. Hence several current efforts focus on extracting signal from EMRs to prioritize DDIs that need further exploration. To this end, being able to extract explicit mentions of DDIs in free text narratives is an important task. In this paper, we explore recurrent neural network (RNN) architectures to detect and classify DDIs from unstructured text using the DDIExtraction dataset from the SemEval 2013 (task 9) shared task...
August 2017: IEEE International Conference on Healthcare Informatics IEEE International Conference on Healthcare Informatics
https://www.readbyqxmd.com/read/29033782/neural-correlates-of-direct-access-trading-in-a-real-stock-market-an-fmri-investigation
#14
GianMario Raggetti, Maria G Ceravolo, Lucrezia Fattobene, Cinzia Di Dio
Background: While financial decision making has been barely explored, no study has previously investigated the neural correlates of individual decisions made by professional traders involved in real stock market negotiations, using their own financial resources. Aim: We sought to detect how different brain areas are modulated by factors like age, expertise, psychological profile (speculative risk seeking or aversion) and, eventually, size and type (Buy/Sell) of stock negotiations, made through Direct Access Trading (DAT) platforms...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/29033145/a-novel-optimization-algorithm-for-mimo-hammerstein-model-identification-under-heavy-tailed-noise
#15
Qibing Jin, Hehe Wang, Qixin Su, Beiyan Jiang, Qie Liu
In this paper, we study the system identification of multi-input multi-output (MIMO) Hammerstein processes under the typical heavy-tailed noise. To the best of our knowledge, there is no general analytical method to solve this identification problem. Motivated by this, we propose a general identification method to solve this problem based on a Gaussian-Mixture Distribution intelligent optimization algorithm (GMDA). The nonlinear part of Hammerstein process is modeled by a Radial Basis Function (RBF) neural network, and the identification problem is converted to an optimization problem...
October 12, 2017: ISA Transactions
https://www.readbyqxmd.com/read/29031120/enabling-spontaneous-analogy-through-heuristic-change
#16
Thomas C Ormerod, James N MacGregor
Despite analogy playing a central role in theories of problem solving, learning and education, demonstrations of spontaneous analogical transfer are rare. Here, we present a theory of heuristic change for spontaneous analogical transfer, tested in four experiments that manipulated the experience of failure to solve a source problem prior to attempting a target problem. In Experiment 1, participants solved more source problems that contained an additional financial constraint designed to signal the inappropriateness of moves that maximized progress towards the goal...
October 11, 2017: Cognitive Psychology
https://www.readbyqxmd.com/read/29029962/answering-schr%C3%A3-dinger-s-question-a-free-energy-formulation
#17
REVIEW
Maxwell James Désormeau Ramstead, Paul Benjamin Badcock, Karl John Friston
The free-energy principle (FEP) is a formal model of neuronal processes that is widely recognised in neuroscience as a unifying theory of the brain and biobehaviour. More recently, however, it has been extended beyond the brain to explain the dynamics of living systems, and their unique capacity to avoid decay. The aim of this review is to synthesise these advances with a meta-theoretical ontology of biological systems called variational neuroethology, which integrates the FEP with Tinbergen's four research questions to explain biological systems across spatial and temporal scales...
September 20, 2017: Physics of Life Reviews
https://www.readbyqxmd.com/read/29028219/data-driven-finite-horizon-approximate-optimal-control-for-discrete-time-nonlinear-systems-using-iterative-hdp-approach
#18
Chaoxu Mu, Ding Wang, Haibo He
This paper presents a data-based finite-horizon optimal control approach for discrete-time nonlinear affine systems. The iterative adaptive dynamic programming (ADP) is used to approximately solve Hamilton-Jacobi-Bellman equation by minimizing the cost function in finite time. The idea is implemented with the heuristic dynamic programming (HDP) involved the model network, which makes the iterative control at the first step can be obtained without the system function, meanwhile the action network is used to obtain the approximate optimal control law and the critic network is utilized for approximating the optimal cost function...
October 10, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/29028204/identifying-condition-specific-modules-by-clustering-multiple-networks
#19
Xiaoke Ma, Penggang Sun, Guimin Qin
Condition-specific modules in multiple networks must be determined to reveal the underlying molecular mechanisms of diseases. Current algorithms exhibit limitations such as low accuracy and high sensitivity to the number of networks because these algorithms discover condition-specific modules in multiple networks by separating specificity and modularity of modules. To overcome these limitations, we characterize condition-specific module as a group of genes whose connectivity is strong in the corresponding network and weak in other networks; this strategy can accurately depict the topological structure of condition-specific modules...
October 10, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/29016972/biases-introduced-by-filtering-electronic-health-records-for-patients-with-complete-data
#20
Griffin M Weber, William G Adams, Elmer V Bernstam, Jonathan P Bickel, Kathe P Fox, Keith Marsolo, Vijay A Raghavan, Alexander Turchin, Xiaobo Zhou, Shawn N Murphy, Kenneth D Mandl
Objective: One promise of nationwide adoption of electronic health records (EHRs) is the availability of data for large-scale clinical research studies. However, because the same patient could be treated at multiple health care institutions, data from only a single site might not contain the complete medical history for that patient, meaning that critical events could be missing. In this study, we evaluate how simple heuristic checks for data "completeness" affect the number of patients in the resulting cohort and introduce potential biases...
November 1, 2017: Journal of the American Medical Informatics Association: JAMIA
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