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Constraint based modeling

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https://www.readbyqxmd.com/read/28338129/prediction-of-metabolic-fluxes-from-gene-expression-data-with-huber-penalty-convex-optimization-function
#1
Shao-Wu Zhang, Wang-Long Gou, Yan Li
As one of the critical parameters of a metabolic pathway, the metabolic flux in a metabolic network serves as an essential role in physiology and pathology. Constraint-based metabolic models are the widely used frameworks for predicting metabolic fluxes in genome-scale metabolic networks. Integrating the transcriptomic data into the constraint-based metabolic models can effectively predict context-specific fluxes across different conditions. However, these methods always need user-defined thresholds to identify the expression levels of metabolic genes or restrain the rate of biomass production, and the predictive results are sensitive to the thresholds...
March 24, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28336426/sar-simulations-safety
#2
Thomas M Fiedler, Mark E Ladd, Andreas K Bitz
At ultra-high fields, the assessment of radiofrequency (RF) safety presents several new challenges compared to low-field systems. Multi-channel RF transmit coils in combination with parallel transmit techniques produce time-dependent and spatially varying power loss densities in the tissue. Further, in ultra-high-field systems, localized field effects can be more pronounced due to a transition from the quasistationary to the electromagnetic field regime. Consequently, local information on the RF field is required for reliable RF safety assessment as well as for monitoring of RF exposure during MR examinations...
March 20, 2017: NeuroImage
https://www.readbyqxmd.com/read/28334697/constraint-based-stoichiometric-modelling-from-single-organisms-to-microbial-communities
#3
REVIEW
Willi Gottstein, Brett G Olivier, Frank J Bruggeman, Bas Teusink
Microbial communities are ubiquitously found in Nature and have direct implications for the environment, human health and biotechnology. The species composition and overall function of microbial communities are largely shaped by metabolic interactions such as competition for resources and cross-feeding. Although considerable scientific progress has been made towards mapping and modelling species-level metabolism, elucidating the metabolic exchanges between microorganisms and steering the community dynamics remain an enormous scientific challenge...
November 2016: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28334208/morphologically-constrained-spectral-unmixing-by-dictionary-learning-for-multiplex-fluorescence-microscopy
#4
Murad Megjhani, Pedro Correa de Sampaio, Julienne Leigh Carstens, Raghu Kalluri, Badrinath Roysam
Motivation: Current spectral unmixing methods for multiplex fluorescence microscopy have a limited ability to cope with high spectral overlap as they only analyze spectral information over individual pixels. Here, we present adaptive Morphologically Constrained Spectral Unmixing (MCSU) algorithms that overcome this limitation by exploiting morphological differences between sub-cellular structures, and their local spatial context. Results: The proposed method was effective at improving spectral unmixing performance by exploiting: (i) a set of dictionary-based models for object morphologies learned from the image data; and (ii) models of spatial context learned from the image data using a total variation algorithm...
March 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28333123/objective-video-quality-assessment-based-on-machine-learning-for-underwater-scientific-applications
#5
José-Miguel Moreno-Roldán, Miguel-Ángel Luque-Nieto, Javier Poncela, Pablo Otero
Video services are meant to be a fundamental tool in the development of oceanic research. The current technology for underwater networks (UWNs) imposes strong constraints in the transmission capacity since only a severely limited bitrate is available. However, previous studies have shown that the quality of experience (QoE) is enough for ocean scientists to consider the service useful, although the perceived quality can change significantly for small ranges of variation of video parameters. In this context, objective video quality assessment (VQA) methods become essential in network planning and real time quality adaptation fields...
March 23, 2017: Sensors
https://www.readbyqxmd.com/read/28332222/multinomial-additive-hazard-model-to-assess-the-disability-burden-using-cross-sectional-data
#6
Renata T C Yokota, Herman Van Oyen, Caspar W N Looman, Wilma J Nusselder, Martin Otava, Yimer Wasihun Kifle, Geert Molenberghs
Population aging is accompanied by the burden of chronic diseases and disability. Chronic diseases are among the main causes of disability, which is associated with poor quality of life and high health care costs in the elderly. The identification of which chronic diseases contribute most to the disability prevalence is important to reduce the burden. Although longitudinal studies can be considered the gold standard to assess the causes of disability, they are costly and often with restricted sample size. Thus, the use of cross-sectional data under certain assumptions has become a popular alternative...
March 23, 2017: Biometrical Journal. Biometrische Zeitschrift
https://www.readbyqxmd.com/read/28331463/a-gibbs-sampler-for-learning-dags
#7
Robert J B Goudie, Sach Mukherjee
We propose a Gibbs sampler for structure learning in directed acyclic graph (DAG) models. The standard Markov chain Monte Carlo algorithms used for learning DAGs are random-walk Metropolis-Hastings samplers. These samplers are guaranteed to converge asymptotically but often mix slowly when exploring the large graph spaces that arise in structure learning. In each step, the sampler we propose draws entire sets of parents for multiple nodes from the appropriate conditional distribution. This provides an efficient way to make large moves in graph space, permitting faster mixing whilst retaining asymptotic guarantees of convergence...
April 2016: Journal of Machine Learning Research: JMLR
https://www.readbyqxmd.com/read/28331186/disentangling-constraints-using-viability-evolution-principles-in-integrative-modeling-of-macromolecular-assemblies
#8
Giorgio Tamò, Andrea Maesani, Sylvain Träger, Matteo T Degiacomi, Dario Floreano, Matteo Dal Peraro
Predicting the structure of large molecular assemblies remains a challenging task in structural biology when using integrative modeling approaches. One of the main issues stems from the treatment of heterogeneous experimental data used to predict the architecture of native complexes. We propose a new method, applied here for the first time to a set of symmetrical complexes, based on evolutionary computation that treats every available experimental input independently, bypassing the need to balance weight components assigned to aggregated fitness functions during optimization...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28330348/learning-molecular-energies-using-localized-graph-kernels
#9
Grégoire Ferré, Terry Haut, Kipton Barros
Recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab initio calculations) and at speeds suitable for molecular dynamics simulation. Best performance is achieved when the known physical constraints are encoded in the machine learning models. For example, the atomic energy is invariant under global translations and rotations; it is also invariant to permutations of same-species atoms. Although simple to state, these symmetries are complicated to encode into machine learning algorithms...
March 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28328072/tensor-estimation-for-double-pulsed-diffusional-kurtosis-imaging
#10
Calvin B Shaw, Edward S Hui, Joseph A Helpern, Jens H Jensen
Double-pulsed diffusional kurtosis imaging (DP-DKI) represents the double diffusion encoding (DDE) MRI signal in terms of six-dimensional (6D) diffusion and kurtosis tensors. Here a method for estimating these tensors from experimental data is described. A standard numerical algorithm for tensor estimation from conventional (i.e. single diffusion encoding) diffusional kurtosis imaging (DKI) data is generalized to DP-DKI. This algorithm is based on a weighted least squares (WLS) fit of the signal model to the data combined with constraints designed to minimize unphysical parameter estimates...
March 22, 2017: NMR in Biomedicine
https://www.readbyqxmd.com/read/28327745/dynamics-of-miura-patterned-foldable-sheets-in-shear-flow
#11
Sarit Dutta, Michael D Graham
We study the dynamics of piecewise rigid sheets containing predefined crease lines in shear flow. The crease lines act like hinge joints along which the sheet may fold rigidly, i.e. without bending any other crease line. We choose the crease lines such that they tessellate the sheet into a two-dimensional array of parallelograms. Specifically, we focus on a particular arrangement of crease lines known as a Miura-pattern in the origami community. When all the hinges are fully open the sheet is planar, whereas when all are closed the sheet folds over itself to form a compact flat structure...
March 22, 2017: Soft Matter
https://www.readbyqxmd.com/read/28327538/error-analysis-and-calibration-method-of-a-multiple-field-of-view-navigation-system
#12
Shuai Shi, Kaichun Zhao, Zheng You, Chenguang Ouyang, Yongkui Cao, Zhenzhou Wang
The Multiple Field-of-view Navigation System (MFNS) is a spacecraft subsystem built to realize the autonomous navigation of the Spacecraft Inside Tiangong Space Station. This paper introduces the basics of the MFNS, including its architecture, mathematical model and analysis, and numerical simulation of system errors. According to the performance requirement of the MFNS, the calibration of both intrinsic and extrinsic parameters of the system is assumed to be essential and pivotal. Hence, a novel method based on the geometrical constraints in object space, called checkerboard-fixed post-processing calibration (CPC), is proposed to solve the problem of simultaneously obtaining the intrinsic parameters of the cameras integrated in the MFNS and the transformation between the MFNS coordinate and the cameras' coordinates...
March 22, 2017: Sensors
https://www.readbyqxmd.com/read/28327210/new-atom-probe-tomography-reconstruction-algorithm-for-multilayered-samples-beyond-the-hemispherical-constraint
#13
Nicolas Rolland, François Vurpillot, Sébastien Duguay, Baishakhi Mazumder, James S Speck, Didier Blavette
Accuracy of atom probe tomography measurements is strongly degraded by the presence of phases that have different evaporation fields. In particular, when there are perpendicular interfaces to the tip axis in the specimen, layers thicknesses are systematically biased and the resolution is degraded near the interfaces. Based on an analytical model of field evaporated emitter end-form, a new algorithm dedicated to the 3D reconstruction of multilayered samples was developed. Simulations of field evaporation of bilayer were performed to evaluate the effectiveness of the new algorithm...
March 22, 2017: Microscopy and Microanalysis
https://www.readbyqxmd.com/read/28325918/robust-analysis-of-fluxes-in-genome-scale-metabolic-pathways
#14
Michael MacGillivray, Amy Ko, Emily Gruber, Miranda Sawyer, Eivind Almaas, Allen Holder
Constraint-based optimization, such as flux balance analysis (FBA), has become a standard systems-biology computational method to study cellular metabolisms that are assumed to be in a steady state of optimal growth. The methods are based on optimization while assuming (i) equilibrium of a linear system of ordinary differential equations, and (ii) deterministic data. However, the steady-state assumption is biologically imperfect, and several key stoichiometric coefficients are experimentally inferred from situations of inherent variation...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28323824/local-structure-preserving-sparse-coding-for-infrared-target-recognition
#15
Jing Han, Jiang Yue, Yi Zhang, Lianfa Bai
Sparse coding performs well in image classification. However, robust target recognition requires a lot of comprehensive template images and the sparse learning process is complex. We incorporate sparsity into a template matching concept to construct a local sparse structure matching (LSSM) model for general infrared target recognition. A local structure preserving sparse coding (LSPSc) formulation is proposed to simultaneously preserve the local sparse and structural information of objects. By adding a spatial local structure constraint into the classical sparse coding algorithm, LSPSc can improve the stability of sparse representation for targets and inhibit background interference in infrared images...
2017: PloS One
https://www.readbyqxmd.com/read/28323161/seeg-dipole-source-localization-based-on-an-empirical-bayesian-approach-taking-into-account-forward-model-uncertainties
#16
S Le Cam, R Ranta, V Caune, G Korats, L Koessler, L Maillard, V Louis-Dorr
Electromagnetic brain source localization consists in the inversion of a forward model based on a limited number of potential measurements. A wide range of methods has been developed to regularize this severely ill-posed problem and to reduce the solution space, imposing spatial smoothness, anatomical constraint or sparsity of the activated source map. This last criteria, based on physiological assumptions stating that in some particular events (e.g., epileptic spikes, evoked potential) few focal area of the brain are simultaneously actives, has gained more and more interest...
March 17, 2017: NeuroImage
https://www.readbyqxmd.com/read/28322914/computer-aided-prediction-of-extent-of-motor-recovery-following-constraint-induced-movement-therapy-in-chronic-stroke
#17
Sarah Hulbert George, Mohammad Hossein Rafiei, Lynne Gauthier, Alexandra Borstad, John A Buford, Hojjat Adeli
Constraint-induced movement therapy (CI therapy) is a well-researched intervention for treatment of upper limb function. Overall, CI therapy yields clinically meaningful improvements in speed of task completion and greatly increases use of the more affected upper extremity for daily activities. However, individual improvements vary widely. It has been suggested that intrinsic feedback from somatosensation may influence motor recovery from CI therapy. To test this hypothesis, an enhanced probabilistic neural network (EPNN) prognostic computational model was developed to identify which baseline characteristics predict extent of motor recovery, as measured by the Wolf Motor Function Test (WMFT)...
March 17, 2017: Behavioural Brain Research
https://www.readbyqxmd.com/read/28320315/comparative-transcriptome-analyses-of-flower-development-in-four-species-of-achimenes-gesneriaceae
#18
Wade R Roberts, Eric H Roalson
BACKGROUND: Flowers have an amazingly diverse display of colors and shapes, and these characteristics often vary significantly among closely related species. The evolution of diverse floral form can be thought of as an adaptive response to pollination and reproduction, but it can also be seen through the lens of morphological and developmental constraints. To explore these interactions, we use RNA-seq across species and development to investigate gene expression and sequence evolution as they relate to the evolution of the diverse flowers in a group of Neotropical plants native to Mexico-magic flowers (Achimenes, Gesneriaceae)...
March 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28318825/riparian-erosion-vulnerability-model-based-on-environmental-features
#19
Alejandra Botero-Acosta, Maria L Chu, Jorge A Guzman, Patrick J Starks, Daniel N Moriasi
Riparian erosion is one of the major causes of sediment and contaminant load to streams, degradation of riparian wildlife habitats, and land loss hazards. Land and soil management practices are implemented as conservation and restoration measures to mitigate the environmental problems brought about by riparian erosion. This, however, requires the identification of vulnerable areas to soil erosion. Because of the complex interactions between the different mechanisms that govern soil erosion and the inherent uncertainties involved in quantifying these processes, assessing erosion vulnerability at the watershed scale is challenging...
March 16, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28300378/comparison-of-linear-and-nonlinear-programming-approaches-for-worst-case-dose-and-minmax-robust-optimization-of-intensity-modulated-proton-therapy-dose-distributions
#20
Maryam Zaghian, Wenhua Cao, Wei Liu, Laleh Kardar, Sharmalee Randeniya, Radhe Mohan, Gino Lim
Robust optimization of intensity-modulated proton therapy (IMPT) takes uncertainties into account during spot weight optimization and leads to dose distributions that are resilient to uncertainties. Previous studies demonstrated benefits of linear programming (LP) for IMPT in terms of delivery efficiency by considerably reducing the number of spots required for the same quality of plans. However, a reduction in the number of spots may lead to loss of robustness. The purpose of this study was to evaluate and compare the performance in terms of plan quality and robustness of two robust optimization approaches using LP and nonlinear programming (NLP) models...
March 2017: Journal of Applied Clinical Medical Physics
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