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Constraint based modeling

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https://www.readbyqxmd.com/read/28722659/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
#1
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...
July 6, 2017: Oncotarget
https://www.readbyqxmd.com/read/28722541/nox-emission-calculations-for-bulk-carriers-by-using-engine-power-probabilities-as-weighting-factors
#2
Chih-Wen Cheng, Jian Hua, Daw-Shang Hwang
An important marine pollution issue identified by the International Maritime Organization is NOx emissions; however, the stipulated method for determining the NOx certification value does not reflect the actual high emission factors of slow-speed two-stroke diesel engines over long-term slow steaming. In this study, an accurate method is presented for calculating the NOx emission factors and total amount of NOx emissions by using the actual power probabilities of the diesel engines in four types of bulk carriers...
July 19, 2017: Journal of the Air & Waste Management Association
https://www.readbyqxmd.com/read/28720699/cellular-trade-offs-and-optimal-resource-allocation-during-cyanobacterial-diurnal-growth
#3
Alexandra-M Reimers, Henning Knoop, Alexander Bockmayr, Ralf Steuer
Cyanobacteria are an integral part of Earth's biogeochemical cycles and a promising resource for the synthesis of renewable bioproducts from atmospheric CO2 Growth and metabolism of cyanobacteria are inherently tied to the diurnal rhythm of light availability. As yet, however, insight into the stoichiometric and energetic constraints of cyanobacterial diurnal growth is limited. Here, we develop a computational framework to investigate the optimal allocation of cellular resources during diurnal phototrophic growth using a genome-scale metabolic reconstruction of the cyanobacterium Synechococcus elongatus PCC 7942...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28718326/cns-anticancer-drug-discovery-and-development-2016-conference-insights
#4
Victor A Levin, Lauren E Abrey, Timothy P Heffron, Peter J Tonge, Arvin C Dar, William A Weiss, James M Gallo
CNS Anticancer Drug Discovery and Development November 2016, AZ, USA The 2016 second CNS Anticancer Drug Discovery and Development Conference addressed diverse viewpoints about why new drug discovery/development focused on CNS cancers has been sorely lacking. Despite more than 70,000 individuals in the USA being diagnosed with a primary brain malignancy and 151,669-286,486 suffering from metastatic CNS cancer, in 1999, temozolomide was the last drug approved by the US FDA as an anticancer agent for high-grade gliomas...
July 18, 2017: CNS Oncology
https://www.readbyqxmd.com/read/28717933/a-novel-ms-cleavable-azo-cross-linker-for-peptide-structure-analysis-by-free-radical-initiated-peptide-sequencing-frips
#5
Claudio Iacobucci, Christoph Hage, Mathias Schäfer, Andrea Sinz
The chemical cross-linking/mass spectrometry (MS) approach is a growing research field in structural proteomics that allows gaining insights into protein conformations. It relies on creating distance constraints between cross-linked amino acid side chains that can further be used to derive protein structures. Currently, the most urgent task for designing novel cross-linking principles is an unambiguous and automated assignment of the created cross-linked products. Here, we introduce the homobifunctional, amine-reactive, and water soluble cross-linker azobisimidoester (ABI) as a prototype of a novel class of cross-linkers...
July 17, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28716400/direct-identification-of-generalized-prandtl-ishlinskii-model-inversion-for-asymmetric-hysteresis-compensation
#6
Young-Rae Ko, Yoonkyu Hwang, Minji Chae, Tae-Hyoung Kim
In this study, we present an identification-based direct construction of the inverse generalized Prandtl-Ishlinskii (P-I) model to facilitate inverse model-based feedforward compensation of asymmetric hysteresis nonlinearities. Compared with the derivation of the inverse model analytically from a generalized P-I model, this direct modeling approach has the following advantages. First, direct inverse model identification is formulated as a nonlinear optimization problem, which is not subject to the constraint condition on the generalized P-I model's threshold and density functions, where this is indispensable for the analytical model inversion procedure...
July 14, 2017: ISA Transactions
https://www.readbyqxmd.com/read/28714886/non-convex-sparse-and-low-rank-based-robust-subspace-segmentation-for-data-mining
#7
Wenlong Cheng, Mingbo Zhao, Naixue Xiong, Kwok Tai Chui
Parsimony, including sparsity and low-rank, has shown great importance for data mining in social networks, particularly in tasks such as segmentation and recognition. Traditionally, such modeling approaches rely on an iterative algorithm that minimizes an objective function with convex l₁-norm or nuclear norm constraints. However, the obtained results by convex optimization are usually suboptimal to solutions of original sparse or low-rank problems. In this paper, a novel robust subspace segmentation algorithm has been proposed by integrating lp-norm and Schatten p-norm constraints...
July 15, 2017: Sensors
https://www.readbyqxmd.com/read/28713807/the-development-of-a-postgraduate-orthopaedic-manual-therapy-residency-program-in-nairobi-kenya
#8
Shala Cunningham, Richard Jackson, Daniel Kangutu Muli, Joni McFelea
INTRODUCTION: There are very few opportunities for long-term, comprehensive postgraduate education in developing countries because of fiscal and human resource constraints. Therefore, physiotherapists have little opportunity following graduation to advance their skills through the improvement of clinical reasoning and treatment planning and application. BACKGROUND: To address the need for sustainable advanced instruction in physiotherapy within the country, a postgraduate Residency program was initiated in Nairobi, Kenya in 2012...
2017: Frontiers in Public Health
https://www.readbyqxmd.com/read/28713681/the-use-of-tcp-based-eud-to-rank-and-compare-lung-radiotherapy-plans-in-silico-study-to-evaluate-the-correlation-between-tcp-with-physical-quality-indices
#9
Abdulhamid Chaikh, Jacques Balosso
BACKGROUND: To apply the equivalent uniform dose (EUD) radiobiological model to estimate the tumor control probability (TCP) scores for treatment plans using different radiobiological parameter settings, and to evaluate the correlation between TCP and physical quality indices of the treatment plans. METHODS: Ten radiotherapy treatment plans for lung cancer were generated. The dose distributions were calculated using anisotropic analytical algorithm (AAA). Dose parameters and quality indices derived from dose volume histograms (DVH) for target volumes were evaluated...
June 2017: Translational Lung Cancer Research
https://www.readbyqxmd.com/read/28710856/quantitative-intracellular-flux-modeling-and-applications-in-biotherapeutic-development-and-production-using-cho-cell-cultures
#10
REVIEW
Zhuangrong Huang, Dong-Yup Lee, Seongkyu Yoon
Chinese hamster ovary (CHO) cells have been widely used for producing many recombinant therapeutic proteins. Constraint-based modeling, such as flux balance analysis (FBA) and metabolic flux analysis (MFA), has been developing rapidly for the quantification of intracellular metabolic flux distribution at a systematic level. Such methods would produce detailed maps of flows through metabolic networks, which contribute significantly to better understanding of metabolism in cells. Although these approaches have been extensively established in microbial systems, their application to mammalian cells is sparse...
July 15, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28710266/specificity-of-subtilin-mediated-activation-of-histidine-kinase-spak
#11
Christoph Geiger, Tobias Spieß, Sophie Marianne Korn, Peter Kötter, Karl-Dieter Entian
Autoinduction via two-component systems is a widespread regulatory mechanism that senses environmental and metabolic changes. Although the lantibiotics nisin and subtilin are closely related and share the same lanthionine ring structure, they autoinduce their biosynthesis in a highly specific manner. Subtilin can only activate the two-component system SpaRK of Bacillus subtilis, whereas nisin activates solely the two-component system NisRK of Lactococcus lactis To identify components that determine the specificity of subtilin autoinduction, several variants of the respective lantibiotic were analyzed for their autoinduction capacity...
July 14, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28709406/using-structural-equation-modeling-for-network-meta-analysis
#12
Yu-Kang Tu, Yun-Chun Wu
BACKGROUND: Network meta-analysis overcomes the limitations of traditional pair-wise meta-analysis by incorporating all available evidence into a general statistical framework for simultaneous comparisons of several treatments. Currently, network meta-analyses are undertaken either within the Bayesian hierarchical linear models or frequentist generalized linear mixed models. Structural equation modeling (SEM) is a statistical method originally developed for modeling causal relations among observed and latent variables...
July 14, 2017: BMC Medical Research Methodology
https://www.readbyqxmd.com/read/28709326/curvature-driven-stability-of-defects-in-nematic-textures-over-spherical-disks
#13
Xiuqing Duan, Zhenwei Yao
Stabilizing defects in liquid-crystal systems is crucial for many physical processes and applications ranging from functionalizing liquid-crystal textures to recently reported command of chaotic behaviors of active matters. In this work, we perform analytical calculations to study the curvature-driven stability mechanism of defects based on the isotropic nematic disk model that is free of any topological constraint. We show that in a growing spherical disk covering a sphere the accumulation of curvature effect can prevent typical +1 and +1/2 defects from forming boojum textures where the defects are repelled to the boundary of the disk...
June 2017: Physical Review. E
https://www.readbyqxmd.com/read/28709274/coherence-of-biochemical-oscillations-is-bounded-by-driving-force-and-network-topology
#14
Andre C Barato, Udo Seifert
Biochemical oscillations are prevalent in living organisms. Systems with a small number of constituents cannot sustain coherent oscillations for an indefinite time because of fluctuations in the period of oscillation. We show that the number of coherent oscillations that quantifies the precision of the oscillator is universally bounded by the thermodynamic force that drives the system out of equilibrium and by the topology of the underlying biochemical network of states. Our results are valid for arbitrary Markov processes, which are commonly used to model biochemical reactions...
June 2017: Physical Review. E
https://www.readbyqxmd.com/read/28708562/non-model-based-control-of-a-wheeled-vehicle-pulling-two-trailers-to-provide-early-powered-mobility-and-driving-experiences
#15
David A Sanders Td Vr
Non-model-based control of a wheeled vehicle pulling two trailers is presented. It is a fun train for disabled children consisting of a locomotive and two carriages. The fun train has afforded opportunities for both disabled and able bodied young people to share an activity and has provided early driving experiences for disabled children; it has introduced them to assistive and powered mobility. The train is a nonlinear system and subject to nonholonomic kinematic constraints so that position and state depend on the path taken to get there...
July 12, 2017: IEEE Transactions on Neural Systems and Rehabilitation Engineering
https://www.readbyqxmd.com/read/28708554/distance-metric-learning-via-iterated-support-vector-machines
#16
Wangmeng Zuo, Faqiang Wang, David Zhang, Liang Lin, Yuchi Huang, Deyu Meng, Lei Zhang
Distance metric learning aims to learn from the given training data a valid distance metric, with which the similarity between data samples can be more effectively evaluated for classification. Metric learning is often formulated as a convex or nonconvex optimization problem, while most existing methods are based on customized optimizers and become inefficient for large scale problems. In this paper, we formulate metric learning as a kernel classification problem with the positive semi-definite constraint, and solve it by iterated training of support vector machines (SVMs)...
July 11, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28708545/multi-gait-recognition-based-on-attribute-discovery
#17
Xin Chen, Jian Weng, Wei Lu, Jiaming Xu
Gait recognition is an important topic in biometrics. Current works primarily focus on recognizing a single person's walking gait. However, a person's gait will change when they walk with other people. How to recognize the gait of multiple people walking is still a challenging problem. This paper proposes an attribute discovery model in a max-margin framework to recognize a person based on gait while walking with multiple people. First, human graphlets are integrated into a tracking-bydetection method to obtain a person's complete silhouette...
July 12, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28705224/more-than-just-a-gut-feeling-constraint-based-genome-scale-metabolic-models-for-predicting-functions-of-human-intestinal-microbes
#18
REVIEW
Kees C H van der Ark, Ruben G A van Heck, Vitor A P Martins Dos Santos, Clara Belzer, Willem M de Vos
The human gut is colonized with a myriad of microbes, with substantial interpersonal variation. This complex ecosystem is an integral part of the gastrointestinal tract and plays a major role in the maintenance of homeostasis. Its dysfunction has been correlated to a wide array of diseases, but the understanding of causal mechanisms is hampered by the limited amount of cultured microbes, poor understanding of phenotypes, and the limited knowledge about interspecies interactions. Genome-scale metabolic models (GEMs) have been used in many different fields, ranging from metabolic engineering to the prediction of interspecies interactions...
July 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28704959/cross-deployment-networking-and-systematic-performance-analysis-of-underwater-wireless-sensor-networks
#19
Zhengxian Wei, Min Song, Guisheng Yin, Hongbin Wang, Xuefei Ma, Houbing Song
Underwater wireless sensor networks (UWSNs) have become a new hot research area. However, due to the work dynamics and harsh ocean environment, how to obtain an UWSN with the best systematic performance while deploying as few sensor nodes as possible and setting up self-adaptive networking is an urgent problem that needs to be solved. Consequently, sensor deployment, networking, and performance calculation of UWSNs are challenging issues, hence the study in this paper centers on this topic and three relevant methods and models are put forward...
July 12, 2017: Sensors
https://www.readbyqxmd.com/read/28704489/a-two-stage-approach-to-the-depot-shunting-driver-assignment-problem-with-workload-balance-considerations
#20
Jiaxi Wang, Manfred Gronalt, Yan Sun
Due to its environmentally sustainable and energy-saving characteristics, railway transportation nowadays plays a fundamental role in delivering passengers and goods. Emerged in the area of transportation planning, the crew (workforce) sizing problem and the crew scheduling problem have been attached great importance by the railway industry and the scientific community. In this paper, we aim to solve the two problems by proposing a novel two-stage optimization approach in the context of the electric multiple units (EMU) depot shunting driver assignment problem...
2017: PloS One
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