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Constraint based modeling

Giorgio Di Gessa, Laurie Corna, Debora Price, Karen Glaser
Background: despite an increasing proportion of older people working beyond State Pension Age (SPA), little is known about neither the motivations for this decision nor whether, and to what extent, working beyond SPA affects quality of life (QoL). Methods: QoL was measured using the CASP-19 scale. Respondents in paid work beyond SPA were distinguished based on whether they reported financial constraints as the main reason for continuing in work. Linear regression models were used to assess the associations between paid work beyond SPA and CASP-19 scores among men aged 65-74 and women aged 60-69 (n = 2,502) cross-sectionally and over time using Wave 4 and Wave 7 of the English Longitudinal Study of Ageing...
January 10, 2018: Age and Ageing
T Aumann, C A Bertulani, F Schindler, S Typel
An experimentally constrained equation of state of neutron-rich matter is fundamental for the physics of nuclei and the astrophysics of neutron stars, mergers, core-collapse supernova explosions, and the synthesis of heavy elements. To this end, we investigate the potential of constraining the density dependence of the symmetry energy close to saturation density through measurements of neutron-removal cross sections in high-energy nuclear collisions of 0.4 to 1 GeV/nucleon. We show that the sensitivity of the total neutron-removal cross section is high enough so that the required accuracy can be reached experimentally with the recent developments of new detection techniques...
December 29, 2017: Physical Review Letters
Chen-Guang Liu, Zhi-Yang Li, Yue Hao, Juan Xia, Feng-Wu Bai, Muhammad Aamer Mehmood
Flocculation plays an important role in the immobilized fermentation of biofuels and biochemicals. It is essential to understand the flocculation phenomenon at physical and molecular scale; however, flocs can't be studied directly due to fragile nature. Hence, the present study was focused on the morphological specificities of yeast flocs formation and sedimentation via the computer simulation by a single floc growth model, based on Diffusion-Limited Aggregation (DLA) model. The impact of shear force, adsorption, and cell propagation on porosity and floc size was systematically illustrated...
January 12, 2018: Biotechnology Journal
Yves Surrel
Camera-based optical metrology crucially relies on a proper identification of intrinsic (optical center position) and extrinsic (camera position) parameters of the used camera. A novel approach for processing phase data from multiple views of a target grid is presented, allowing these identifications within a pinhole camera model. First, the homography associated with the perspective distortion of each grid image is accurately identified using a phase-locking loop. Then, the affine transform for each view is determined, with the constraint of an identical set of intrinsic camera parameters...
January 1, 2018: Applied Optics
Yi Yu, Yonggang Wu, Binqi Hu, Xinglong Liu
The dispatching of hydro-thermal system is a nonlinear programming problem with multiple constraints and high dimensions and the solution techniques of the model have been a hotspot in research. Based on the advantage of that the artificial bee colony algorithm (ABC) can efficiently solve the high-dimensional problem, an improved artificial bee colony algorithm has been proposed to solve DHTS problem in this paper. The improvements of the proposed algorithm include two aspects. On one hand, local search can be guided in efficiency by the information of the global optimal solution and its gradient in each generation...
2018: PloS One
Haofeng Zhang, Li Liu, Yang Long, Ling Shao
In order to achieve efficient similarity searching, hash functions are designed to encode images into low-dimensional binary codes with the constraint that similar features will have a short distance in the projected Hamming space. Recently, deep learning-based methods have become more popular, and outperform traditional non-deep methods. However, without label information, most state-of-the-art unsupervised deep hashing (DH) algorithms suffer from severe performance degradation for unsupervised scenarios. One of the main reasons is that the ad-hoc encoding process cannot properly capture the visual feature distribution...
April 2018: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
Purushottam D Dixit, Ken Dill
Rate processes are often modeled using Markov State Models (MSM). Suppose you know a prior MSM, and then learn that your prediction of some particular observable rate is wrong. What is the best way to correct the whole MSM? For example, molecular dynamics simulations of protein folding may sample many microstates, possibly giving correct pathways through them, while also giving the wrong overall folding rate, when compared to experiment. Here, we describe Caliber Corrected Markov Modeling (C2M2): an approach based on the principle of maximum entropy for updating a Markov model by imposing state- and trajectory-based constraints...
January 11, 2018: Journal of Chemical Theory and Computation
Shun Asami, Daisuke Kiga, Akihiko Konagaya
BACKGROUND: Drug development considering individual varieties among patients becomes crucial to improve clinical development success rates and save healthcare costs. As a useful tool to predict individual phenomena and correlations among drug characteristics and individual varieties, recently, whole-body physiologically based pharmacokinetic (WB- PBPK) models are getting more attention. WB-PBPK models generally have a lot of drug-related parameters that need to be estimated, and the estimations are difficult because the observed data are limited...
December 21, 2017: BMC Systems Biology
Marcel Weiß, Sebastian E Ahnert
The mapping between biological genotypes and phenotypes plays an important role in evolution, and understanding the properties of this mapping is crucial to determine the outcome of evolutionary processes. One of the most striking properties observed in several genotype-phenotype (GP) maps is the positive correlation between the robustness and evolvability of phenotypes. This implies that a phenotype can be strongly robust against mutations and at the same time evolvable to a diverse range of alternative phenotypes...
January 2018: Journal of the Royal Society, Interface
Yuta Sakurai, Yutaka Hori
Model-guided design has become a standard approach to engineering biomolecular circuits in synthetic biology. However, the stochastic nature of biomolecular reactions is often overlooked in the design process. As a result, cell-cell heterogeneity causes unexpected deviation of biocircuit behaviours from model predictions and requires additional iterations of design-build-test cycles. To enhance the design process of stochastic biocircuits, this paper presents a computational framework to systematically specify the level of intrinsic noise using well-defined metrics of statistics and design highly heterogeneous biocircuits based on the specifications...
January 2018: Journal of the Royal Society, Interface
Autoosa Salari, Marco A Navarro, Mirela Milescu, Lorin S Milescu
To understand how ion channels and other proteins function at the molecular and cellular levels, one must decrypt their kinetic mechanisms. Sophisticated algorithms have been developed that can be used to extract kinetic parameters from a variety of experimental data types. However, formulating models that not only explain new data, but are also consistent with existing knowledge, remains a challenge. Here, we present a two-part study describing a mathematical and computational formalism that can be used to enforce prior knowledge into the model using constraints...
January 10, 2018: Journal of General Physiology
Marco A Navarro, Autoosa Salari, Mirela Milescu, Lorin S Milescu
Kinetic mechanisms predict how ion channels and other proteins function at the molecular and cellular levels. Ideally, a kinetic model should explain new data but also be consistent with existing knowledge. In this two-part study, we present a mathematical and computational formalism that can be used to enforce prior knowledge into kinetic models using constraints. Here, we focus on constraints that quantify the behavior of the model under certain conditions, and on constraints that enforce arbitrary parameter relationships...
January 10, 2018: Journal of General Physiology
Philippos Garefalakis, Fritz Schlunegger
Large sediment fluxes from mountain belts have the potential to cause megafans to prograde into the neighbouring sedimentary basins. These mechanisms have been documented based from numerical modelling and stratigraphic records. However, little attention has been focused on inferring temporal changes in the concentrations of supplied sediment from coarse-grained deposits. Here, we extract changes of this variable in the field from a Late Oligocene, c. 4 km-thick suite of fluvial conglomerates situated in the North Alpine foreland basin, which evolved in response to the tectonic and erosional history of the Alps...
January 9, 2018: Scientific Reports
Thomas Tessonnier, Andrea Mairani, Wenjing Chen, Paola Sala, Francesco Cerutti, Alfredo Ferrari, Thomas Haberer, Jürgen Debus, Katia Parodi
BACKGROUND: Due to their favorable physical and biological properties, helium ion beams are increasingly considered a promising alternative to proton beams for radiation therapy. Hence, this work aims at comparing in-silico the treatment of brain and ocular meningiomas with protons and helium ions, using for the first time a dedicated Monte Carlo (MC) based treatment planning engine (MCTP) thoroughly validated both in terms of physical and biological models. METHODS: Starting from clinical treatment plans of four patients undergoing proton therapy with a fixed relative biological effectiveness (RBE) of 1...
January 9, 2018: Radiation Oncology
Francine Piubeli, Manuel Salvador, Montserrat Argandoña, Joaquín J Nieto, Vicente Bernal, Jose M Pastor, Manuel Cánovas, Carmen Vargas
BACKGROUND: The halophilic bacterium Chromohalobacter salexigens is a natural producer of ectoines, compatible solutes with current and potential biotechnological applications. As production of ectoines is an osmoregulated process that draws away TCA intermediates, bacterial metabolism needs to be adapted to cope with salinity changes. To explore and use C. salexigens as cell factory for ectoine(s) production, a comprehensive knowledge at the systems level of its metabolism is essential...
January 9, 2018: Microbial Cell Factories
Sara Bernardi, Annachiara Colombi, Marco Scianna
In this article, we present a microscopic discrete mathematical model describing collective dynamics of a bee swarm. More specifically, each bee is set to move according to individual strategies and social interactions, the former involving the desire to reach a target destination, the latter accounting for repulsive/attractive stimuli and for alignment processes. The insects tend in fact to remain sufficiently close to the rest of the population, while avoiding collisions, and they are able to track and synchronize their movement to the flight of a given set of neighbors within their visual field...
January 2, 2018: Computers in Biology and Medicine
Tadeusz L Ogorzalek, Greg L Hura, Adam Belsom, Kathryn H Burnett, Andriy Kryshtafovych, John A Tainer, Juri Rappsilber, Susan E Tsutakawa, Krzysztof Fidelis
Experimental data offers empowering constraints for structure prediction. These constraints can be used to filter equivalently scored models or more powerfully within optimization functions toward prediction. In CASP12, Small Angle X-ray Scattering (SAXS) and Cross-Linking Mass Spectrometry (CLMS) data, measured on an exemplary set of novel fold targets, were provided to the CASP community of protein structure predictors. As HT, solution-based techniques, SAXS and CLMS can efficiently measure states of the full-length sequence in its native solution conformation and assembly...
January 4, 2018: Proteins
Grace C Huang, Gila Kriegel, Carolyn Wheaton, Scot Sternberg, Kenneth Sands, Jeremy Richards, Katherine Johnston, Mark Aronson
BACKGROUND: Diagnostic errors result in preventable morbidity and mortality. The outpatient setting may be at increased risk, where time constraints, the indolent nature of outpatient complaints and single decision-maker practice models predominate. METHODS: We developed a self-administered diagnostic pause to address diagnostic error. Clinicians (physicians and nurse practitioners) in an academic primary care setting received the tool if they were seeing urgent care patients who had previously been seen in the past two weeks in urgent care...
January 6, 2018: BMJ Quality & Safety
Chang-Yu Hsieh, Jianshu Cao
We use the "generalized hierarchical equation of motion" proposed in Paper I [C.-Y. Hsieh and J. Cao, J. Chem. Phys. 148, 014103 (2018)] to study decoherence in a system coupled to a spin bath. The present methodology allows a systematic incorporation of higher-order anharmonic effects of the bath in dynamical calculations. We investigate the leading order corrections to the linear response approximations for spin bath models. Two kinds of spin-based environments are considered: (1) a bath of spins discretized from a continuous spectral density and (2) a bath of localized nuclear or electron spins...
January 7, 2018: Journal of Chemical Physics
Shichao Chen, Yizheng Zhu
In quantitative phase imaging, sensitivity is a key measure of system reproducibility. Despite continuous experimental breakthroughs in achieving highly sensitive detection, in-depth studies of theoretical constraints on sensitivity are inadequate and comparisons between different techniques are difficult. In this paper, we introduce the method to evaluate the sensitivity of phase shifting interferometry which is a major category of quantitative phase imaging techniques. The method discusses in detail several key concepts of sensitivity evaluation, including a general three-level evaluation framework, a complete interference signal model, Cramér-Rao bound and algorithm sensitivity, algorithm and system efficiencies, as well as energy efficiency of an algorithm...
January 3, 2018: Methods: a Companion to Methods in Enzymology
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