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Constraint based modeling

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https://www.readbyqxmd.com/read/29150414/constraints-on-statistical-learning-across-species
#1
REVIEW
Chiara Santolin, Jenny R Saffran
Both human and nonhuman organisms are sensitive to statistical regularities in sensory inputs that support functions including communication, visual processing, and sequence learning. One of the issues faced by comparative research in this field is the lack of a comprehensive theory to explain the relevance of statistical learning across distinct ecological niches. In the current review we interpret cross-species research on statistical learning based on the perceptual and cognitive mechanisms that characterize the human and nonhuman models under investigation...
November 14, 2017: Trends in Cognitive Sciences
https://www.readbyqxmd.com/read/29150319/analytical-design-of-an-industrial-two-term-controller-for-optimal-regulatory-control-of-open-loop-unstable-processes-under-operational-constraints
#2
Rodrigue Tchamna, Moonyong Lee
This paper proposes a novel optimization-based approach for the design of an industrial two-term proportional-integral (PI) controller for the optimal regulatory control of unstable processes subjected to three common operational constraints related to the process variable, manipulated variable and its rate of change. To derive analytical design relations, the constrained optimal control problem in the time domain was transformed into an unconstrained optimization problem in a new parameter space via an effective parameterization...
November 14, 2017: ISA Transactions
https://www.readbyqxmd.com/read/29149173/trade-off-and-flexibility-in-the-dynamic-regulation-of-the-cullin-ring-ubiquitin-ligase-repertoire
#3
Ronny Straube, Meera Shah, Dietrich Flockerzi, Dieter A Wolf
Cullin-RING ubiquitin ligases (CRLs) catalyze the ubiquitylation of substrates many of which are degraded by the 26S proteasome. Their modular architecture enables recognition of numerous substrates via exchangeable substrate receptors that competitively bind to a cullin scaffold with high affinity. Due to the plasticity of these interactions there is ongoing uncertainty how cells maintain a flexible CRL repertoire in view of changing substrate loads. Based on a series of in vivo and in vitro studies, different groups proposed that the exchange of substrate receptors is mediated by a protein exchange factor named Cand1...
November 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29148432/a-singular-value-decomposition-linear-programming-svdlp-optimization-technique-for-circular-cone-based-robotic-radiotherapy
#4
Bin Liang, Yongbao Li, Wei Ran, Bin Guo, Xuang Xu, Bo Liu, Jiafeng Li, Qiuwen Wu, Fugen Zhou
With robot-controlled linac positioning, the robotic radiotherapy system such as CyberKnife significantly increases the freedom in radiation beam placement, but also imposes more challenges on treatment plan optimization. The resampling mechanism in vendor supplied treatment planning system (MultiPlan) could not fully explore the increased beam direction search space. Besides, a sparse treatment plan (using fewer beams) is desired to improve the treatment efficiency. This study proposes a singular value decomposition linear programming (SVDLP) optimization technique for circular collimator based robotic radiotherapy...
November 17, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/29147021/genome-scale-modeling-and-transcriptome-analysis-of-leuconostoc-mesenteroides-unravel-the-redox-governed-metabolic-states-in-obligate-heterofermentative-lactic-acid-bacteria
#5
Lokanand Koduru, Yujin Kim, Jeongsu Bang, Meiyappan Lakshmanan, Nam Soo Han, Dong-Yup Lee
Obligate heterofermentative lactic acid bacteria (LAB) are well-known for their beneficial health effects in humans. To delineate the incompletely characterized metabolism that currently limits their exploitation, at systems-level, we developed a genome-scale metabolic model of the representative obligate heterofermenting LAB, Leuconostoc mesenteroides (iLME620). Constraint-based flux analysis was then used to simulate several qualitative and quantitative phenotypes of L. mesenteroides, thereby evaluating the model validity...
November 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29142327/the-circumstellar-envelope-around-the-s-type-agb-star-w-aql-effects-of-an-eccentric-binary-orbit
#6
S Ramstedt, S Mohamed, W H T Vlemmings, T Danilovich, M Brunner, E De Beck, E M L Humphreys, M Lindqvist, M Maercker, H Olofsson, F Kerschbaum, G Quintana-Lacaci
Context: Recent observations at subarcsecond resolution, now possible also at submillimeter wavelengths, have shown intricate circumstellar structures around asymptotic giant branch (AGB) stars, mostly attributed to binary interaction. The results presented here are part of a larger project aimed at investigating the effects of a binary companion on the morphology of circumstellar envelopes (CSEs) of AGB stars. Aims: AGB stars are characterized by intense stellar winds that build CSEs around the stars...
September 21, 2017: Astronomy and Astrophysics
https://www.readbyqxmd.com/read/29141673/a-customized-fixation-plate-with-novel-structure-designed-by-topological-optimization-for-mandibular-angle-fracture-based-on-finite-element-analysis
#7
Yun-Feng Liu, Ying-Ying Fan, Xian-Feng Jiang, Dale A Baur
BACKGROUND: The purpose of this study was to design a customized fixation plate for mandibular angle fracture using topological optimization based on the biomechanical properties of the two conventional fixation systems, and compare the results of stress, strain and displacement distributions calculated by finite element analysis (FEA). METHODS: A three-dimensional (3D) virtual mandible was reconstructed from CT images with a mimic angle fracture and a 1 mm gap between two bone segments, and then a FEA model, including volume mesh with inhomogeneous bone material properties, three loading conditions and constraints (muscles and condyles), was created to design a customized plate using topological optimization method, then the shape of the plate was referenced from the stress concentrated area on an initial part created from thickened bone surface for optimal calculation, and then the plate was formulated as "V" pattern according to dimensions of standard mini-plate finally...
November 15, 2017: Biomedical Engineering Online
https://www.readbyqxmd.com/read/29134104/king-post-truss-as-a-motif-for-internal-structure-of-meta-material-with-controlled-elastic-properties
#8
Emilio Turco, Ivan Giorgio, Anil Misra, Francesco dell'Isola
One of the most interesting challenges in the modern theory of materials consists in the determination of those microstructures which produce, at the macro-level, a class of metamaterials whose elastic range is many orders of magnitude wider than the one exhibited by 'standard' materials. In dell'Isola et al. (2015 Zeitschrift für angewandte Mathematik und Physik66, 3473-3498. (doi:10.1007/s00033-015-0556-4)), it was proved that, with a pantographic microstructure constituted by 'long' micro-beams it is possible to obtain metamaterials whose elastic range spans up to an elongation exceeding 30%...
October 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/29134060/modelling-pyruvate-dehydrogenase-under-hypoxia-and-its-role-in-cancer-metabolism
#9
Filmon Eyassu, Claudio Angione
Metabolism is the only biological system that can be fully modelled at genome scale. As a result, metabolic models have been increasingly used to study the molecular mechanisms of various diseases. Hypoxia, a low-oxygen tension, is a well-known characteristic of many cancer cells. Pyruvate dehydrogenase (PDH) controls the flux of metabolites between glycolysis and the tricarboxylic acid cycle and is a key enzyme in metabolic reprogramming in cancer metabolism. Here, we develop and manually curate a constraint-based metabolic model to investigate the mechanism of pyruvate dehydrogenase under hypoxia...
October 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/29131359/conductance-based-profiling-of-nanopores-accommodating-fabrication-irregularities
#10
Y M Nuwan D Y Bandara, Jonathan W Nichols, Buddini Iroshika Karawdeniya, Jason R Dwyer
Solid-state nanopores are nanoscale channels through otherwise impermeable membranes. Single molecules or particles can be passed through electrolyte-filled nanopores by, e.g. electrophoresis, and then detected through the resulting physical displacement of ions within the nanopore. Nanopore size, shape, and surface chemistry must be carefully controlled, and on extremely challenging <10 nm-length scales. We previously developed a framework to characterize nanopores from the time-dependent changes in their conductance as they are being formed through solution-phase nanofabrication processes with the appeal of ease and accessibility...
November 13, 2017: Electrophoresis
https://www.readbyqxmd.com/read/29131199/positive-dwell-time-algorithm-with-minimum-equal-extra-material-removal-in-deterministic-optical-surfacing-technology
#11
Longxiang Li, Donglin Xue, Weijie Deng, Xu Wang, Yang Bai, Feng Zhang, Xuejun Zhang
In deterministic computer-controlled optical surfacing, accurate dwell time execution by computer numeric control machines is crucial in guaranteeing a high-convergence ratio for the optical surface error. It is necessary to consider the machine dynamics limitations in the numerical dwell time algorithms. In this paper, these constraints on dwell time distribution are analyzed, and a model of the equal extra material removal is established. A positive dwell time algorithm with minimum equal extra material removal is developed...
November 10, 2017: Applied Optics
https://www.readbyqxmd.com/read/29126820/blend-design-tools-for-medium-combustion-plants-mcp-firing-biomass-wastes
#12
I Ibarra, G Aragón, I Gómez, I Múgica, J González, J Rodríguez Maroto, E Rojas, D Sanz, R Ramos, R Escalada, E Borjabad, C Gutiérrez-Canas
A feasible alternative for agricultural or forestry waste management is the operation of a distributed network of sustainable Medium Combustion Plants (MCPs). However, one of the main factors that hinder its development is the propensity to operational problems derived from corrosion, slagging and fouling characteristics of both bottom and fly ashes. Therefore, a cost-effective approach for these multi-product MCP could be based on predictive tools for an optimal formulation of a fuel blend. This work focuses on the assessment of the ability of these methods to provide guidance for preventing ash-related operational problems and to provide fuel-blending rules...
November 7, 2017: Waste Management
https://www.readbyqxmd.com/read/29124777/coherence-in-the-visual-imagination
#13
Michael O Vertolli, Matthew A Kelly, Jim Davies
An incoherent visualization is when aspects of different senses of a word (e.g., the biological "mouse" vs. the computer "mouse") are present in the same visualization (e.g., a visualization of a biological mouse in the same image with a computer tower). We describe and implement a new model of creating contextual coherence in the visual imagination called Coherencer, based on the SOILIE model of imagination. We show that Coherencer is able to generate scene descriptions that are more coherent than SOILIE's original approach as well as a parallel connectionist algorithm that is considered competitive in the literature on general coherence...
November 10, 2017: Cognitive Science
https://www.readbyqxmd.com/read/29121406/multiple-mechanisms-of-early-plant-community-assembly-with-stochasticity-driving-the-process
#14
Bryndís Marteinsdóttir, Kristín Svavarsdóttir, Thóra Ellen Thórhallsdóttir
Initial plant establishment is one of the most critical phases in ecosystem development, where an early suite of physical (environmental filtering), biological (seed limitation, species interactions) and stochastic factors may affect successional trajectories and rates. While functional traits are commonly used to study processes that influence plant community assembly in late successional communities, few studies have applied them to primary succession. The objective here was to determine the importance of these factors in shaping early plant community assembly on a glacial outwash plain, Skeiðarársandur, in SE Iceland using a trait based approach...
November 9, 2017: Ecology
https://www.readbyqxmd.com/read/29120357/a-decentralized-compositional-framework-for-dependable-decision-process-in-self-managed-cyber-physical-systems
#15
Peng Zhou, Decheng Zuo, Kun-Mean Hou, Zhan Zhang
Cyber Physical Systems (CPSs) need to interact with the changeable environment under various interferences. To provide continuous and high quality services, a self-managed CPS should automatically reconstruct itself to adapt to these changes and recover from failures. Such dynamic adaptation behavior introduces systemic challenges for CPS design, advice evaluation and decision process arrangement. In this paper, a formal compositional framework is proposed to systematically improve the dependability of the decision process...
November 9, 2017: Sensors
https://www.readbyqxmd.com/read/29119499/an-integrative-approach-toward-biology-organisms-and-cancer
#16
Carlos Sonnenschein, Ana M Soto
Over the last two decades, we have challenged the hegemony of the somatic mutation theory of carcinogenesis (SMT) based on the lack of theoretical coherence of the premises adopted by its followers. We offered instead a theoretical alternative, the tissue organization field theory (TOFT), that is based on the premises that cancer is a tissue-based disease and that proliferation and motility is the default state of all cells. We went on to use a theory-neutral experimental protocol that simultaneously tested the TOFT and the SMT...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29118138/macroecological-factors-shape-local-scale-spatial-patterns-in-agriculturalist-settlements
#17
Tingting Tao, Sebastián Abades, Shuqing Teng, Zheng Y X Huang, Luís Reino, Bin J W Chen, Yong Zhang, Chi Xu, Jens-Christian Svenning
Macro-scale patterns of human systems ranging from population distribution to linguistic diversity have attracted recent attention, giving rise to the suggestion that macroecological rules shape the assembly of human societies. However, in which aspects the geography of our own species is shaped by macroecological factors remains poorly understood. Here, we provide a first demonstration that macroecological factors shape strong local-scale spatial patterns in human settlement systems, through an analysis of spatial patterns in agriculturalist settlements in eastern mainland China based on high-resolution Google Earth images...
November 15, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29117534/building-predictive-models-of-genetic-circuits-using-the-principle-of-maximum-caliber
#18
Taylor Firman, Gábor Balázsi, Kingshuk Ghosh
Learning the underlying details of a gene network is a major challenge in cellular and synthetic biology. We address this challenge by building a chemical kinetic model that utilizes information encoded in the stochastic protein expression trajectories typically measured in experiments. The applicability of the proposed method is demonstrated in an auto-activating genetic circuit, a common motif in natural and synthetic gene networks. Our approach is based on the principle of maximum caliber (MaxCal)-a dynamical analog of the principle of maximum entropy-and builds a minimal model using only three constraints: 1) protein synthesis, 2) protein degradation, and 3) positive feedback...
November 7, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29113934/validating-ehr-clinical-models-using-ontology-patterns
#19
Catalina Martínez-Costa, Stefan Schulz
Clinical models are artefacts that specify how information is structured in electronic health records (EHRs). However, the makeup of clinical models is not guided by any formal constraint beyond a semantically vague information model. We address this gap by advocating ontology design patterns as a mechanism that makes the semantics of clinical models explicit. This paper demonstrates how ontology design patterns can validate existing clinical models using SHACL. Based on the Clinical Information Modelling Initiative (CIMI), we show how ontology patterns detect both modeling and terminology binding errors in CIMI models...
November 4, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/29113398/combing-nlr-v20-and-mean-lung-dose-to-predict-radiation-induced-lung-injury-in-patients-with-lung-cancer-treated-with-intensity-modulated-radiation-therapy-and-chemotherapy
#20
Wen-Yan Pan, Chao Bian, Guan-Lian Zou, Cui-Ying Zhang, Ping Hai, Ren Zhao, Yan-Yang Wang
The purpose was to evaluate the predictive value of baseline neutrophil to lymphocyte ratio (NLR) level in the incidence of grade 3 or higher radiation induced lung injury (RILI) for lung cancer patients. A retrospectively analysis with 166 lung cancer patients was performed. All of the enrolled patients received chemoradiotherapy at our hospital between April 2014 and May 2016. The Cox proportional hazard model was used to identify the potential risk factors for RILI. In this cohort, the incidence of grade 3 or higher RILI was 23...
October 6, 2017: Oncotarget
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