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Constraint based modeling

Juan Carlos López Alfonso, Shireen Parsai, Nikhil Joshi, Andrew Godley, Chirag Shah, Shlomo A Koyfman, Jimmy J Caudell, Clifton D Fuller, Heiko Enderling, Jacob G Scott
PURPOSE: Intensity modulated radiation therapy (IMRT) has allowed optimization of three-dimensional spatial radiation dose distributions permitting target coverage while reducing normal tissue toxicity. However, radiation-induced normal tissue toxicity is a major contributor to patients' quality of life and often a dose-limiting factor in the definitive treatment of cancer with radiation therapy. We propose the next logical step in the evolution of IMRT using canonical radiobiological principles, optimizing the temporal dimension through which radiation therapy is delivered to further reduce radiation-induced toxicity by increased time for normal tissue recovery...
May 22, 2018: Medical Physics
Brett M Burton, Kedar K Aras, Wilson W Good, Jess D Tate, Brian Zenger, Rob S MacLeod
The biophysical basis for electrocardiographic evaluation of myocardial ischemia stems from the notion that ischemic tissues develop, with relative uniformity, along the endocardial aspects of the heart. These injured regions of subendocardial tissue give rise to intramural currents that lead to ST segment deflections within electrocardiogram (ECG) recordings. The concept of subendocardial ischemic regions is often used in clinical practice, providing a simple and intuitive description of ischemic injury; however, such a model grossly oversimplifies the presentation of ischemic disease-inadvertently leading to errors in ECG-based diagnoses...
May 21, 2018: Annals of Biomedical Engineering
Carlos Platero, Lin Lin, M Carmen Tobar
Hippocampal atrophy measures from magnetic resonance imaging (MRI) are powerful tools for monitoring Alzheimer's disease (AD) progression. In this paper, we introduce a longitudinal image analysis framework based on robust registration and simultaneous hippocampal segmentation and longitudinal marker classification of brain MRI of an arbitrary number of time points. The framework comprises two innovative parts: a longitudinal segmentation and a longitudinal classification step. The results show that both steps of the longitudinal pipeline improved the reliability and the accuracy of the discrimination between clinical groups...
May 21, 2018: Neuroinformatics
Michael Scheunemann, Siobhan M Brady, Zoran Nikoloski
Plant organs consist of multiple cell types that do not operate in isolation, but communicate with each other to maintain proper functions. Here, we extract models specific to three developmental stages of eight root cell types or tissue layers in Arabidopsis thaliana based on a state-of-the-art constraint-based modeling approach with all publicly available transcriptomics and metabolomics data from this system to date. We integrate these models into a multi-cell root model which we investigate with respect to network structure, distribution of fluxes, and concordance to transcriptomics and proteomics data...
May 21, 2018: Scientific Reports
Olivier Le Polain de Waroux, W John Edmunds, Kensuke Takahashi, Koya Ariyoshi, E Kim Mulholland, David Goldblatt, Yoon Hong Choi, Dang Duc Anh, Lay Myint Yoshida, Stefan Flasche
Although catch-up campaigns (CCs) at the introduction of pneumococcal conjugate vaccines (PCVs) may accelerate their impact, supply constraints may limit their benefit if the need for additional PCV doses results in introduction delay. We studied the impact of PCV13 introduction with and without CC in Nha Trang, Vietnam - a country that has not yet introduced PCV - through a dynamic transmission model. We modelled the impact on carriage and invasive pneumococcal disease (IPD) of routine vaccination (RV) only and that of RV with CCs targeting <1y olds (CC1), <2y olds (CC2) and <5y olds (CC5)...
May 21, 2018: Human Vaccines & Immunotherapeutics
Maarten Lambrecht, Daniëlle B P Eekers, Claire Alapetite, Neil G Burnet, Valentin Calugaru, Ida E M Coremans, Piero Fossati, Morten Høyer, Johannes A Langendijk, Alejandra Méndez Romero, Frank Paulsen, Ana Perpar, Laurette Renard, Dirk de Ruysscher, Beate Timmermann, Pavel Vitek, Damien C Weber, Hiske L van der Weide, Gillian A Whitfield, Ruud Wiggenraad, Erik Roelofs, Petra Witt Nyström, Esther G C Troost
PURPOSE: For unbiased comparison of different radiation modalities and techniques, consensus on delineation of radiation sensitive organs at risk (OARs) and on their dose constraints is warranted. Following the publication of a digital, online atlas for OAR delineation in neuro-oncology by the same group, we assessed the brain OAR-dose constraints in a follow-up study. METHODS: We performed a comprehensive search to identify the current papers on OAR dose constraints for normofractionated photon and particle therapy in PubMed, Ovid Medline, Cochrane Library, Embase and Web of Science...
May 17, 2018: Radiotherapy and Oncology: Journal of the European Society for Therapeutic Radiology and Oncology
Bin He, Yi Guan, Rui Dai
Deep learning research on relation classification has achieved solid performance in the general domain. This study proposes a convolutional neural network (CNN) architecture with a multi-pooling operation for medical relation classification on clinical records and explores a loss function with a category-level constraint matrix. Experiments using the 2010 i2b2/VA relation corpus demonstrate these models, which do not depend on any external features, outperform previous single-model methods and our best model is competitive with the existing ensemble-based method...
May 16, 2018: Artificial Intelligence in Medicine
Tobias B Alter, Lars M Blank, Birgitta E Ebert
To date, several independent methods and algorithms exist for exploiting constraint-based stoichiometric models to find metabolic engineering strategies that optimize microbial production performance. Optimization procedures based on metaheuristics facilitate a straightforward adaption and expansion of engineering objectives, as well as fitness functions, while being particularly suited for solving problems of high complexity. With the increasing interest in multi-scale models and a need for solving advanced engineering problems, we strive to advance genetic algorithms, which stand out due to their intuitive optimization principles and the proven usefulness in this field of research...
May 16, 2018: Metabolites
Francesco Cavraro, Giulia Gheno, Renzo Ganzerla, Matteo Zucchetta, Piero Franzoi, Stefano Malavasi
Display of bright and striking color patterns is a widespread way of communication in many animal species. Carotenoid-based coloration accounts for most of the bright yellow, orange, and red displays in invertebrates, fish, amphibians, reptiles, and birds, being widely considered a signal of individual health. This type of coloration is under the influence of several factors, such as sexual selection, predator pressure, pigment availability, and light transmission. Fish offer numerous examples of visual communication by means of color patterns...
May 2018: Ecology and Evolution
Firas Hamze, Darryl C Jacob, Andrew J Ochoa, Dilina Perera, Wenlong Wang, Helmut G Katzgraber
We present a methodology for generating Ising Hamiltonians of tunable complexity and with a priori known ground states based on a decomposition of the model graph into edge-disjoint subgraphs. The idea is illustrated with a spin-glass model defined on a cubic lattice, where subproblems, whose couplers are restricted to the two values {-1,+1}, are specified on unit cubes and are parametrized by their local degeneracy. The construction is shown to be equivalent to a type of three-dimensional constraint-satisfaction problem known as the tiling puzzle...
April 2018: Physical Review. E
Md Zulfikar Ali, Ned S Wingreen, Ranjan Mukhopadhyay
We introduce a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutational algorithm, and apply the model to study neutral drift in networks that yield oscillatory dynamics. Starting with a functional core module, random evolutionary drift increases network complexity even in the absence of specific selective pressures. Surprisingly, we uncover a hidden order in sequence space that gives rise to long-term evolutionary memory, implying strong constraints on network evolution due to the topology of accessible sequence space...
April 2018: Physical Review. E
F J Fattoyev, J Piekarewicz, C J Horowitz
The historical first detection of a binary neutron star merger by the LIGO-Virgo Collaboration [B. P. Abbott et al., Phys. Rev. Lett. 119, 161101 (2017)PRLTAO0031-900710.1103/PhysRevLett.119.161101] is providing fundamental new insights into the astrophysical site for the r process and on the nature of dense matter. A set of realistic models of the equation of state (EOS) that yield an accurate description of the properties of finite nuclei, support neutron stars of two solar masses, and provide a Lorentz covariant extrapolation to dense matter are used to confront its predictions against tidal polarizabilities extracted from the gravitational-wave data...
April 27, 2018: Physical Review Letters
Narges Moradtalab, Markus Weinmann, Frank Walker, Birgit Höglinger, Uwe Ludewig, Guenter Neumann
Low soil temperature in spring is a major constraint for the cultivation of tropical and subtropical crops in temperate climates, associated with inhibition of root growth and activity, affecting early growth and frequently plant performance and final yield. This study was initiated to investigate the physiological base of cold-protective effects induced by supplementation with silicon (Si), widely recommended as a stress-protective mineral nutrient. Maize was used as a cold-sensitive model plant, exposed to chilling stress and low root-zone temperature (RZT) during early growth in a lab to field approach...
2018: Frontiers in Plant Science
Falu Weng, Mingxin Liu, Weijie Mao, Yuanchun Ding, Feifei Liu
The problem of sampled-data-based vibration control for structural systems with finite-time state constraint and sensor outage is investigated in this paper. The objective of designing controllers is to guarantee the stability and anti-disturbance performance of the closed-loop systems while some sensor outages happen. Firstly, based on matrix transformation, the state-space model of structural systems with sensor outages and uncertainties appearing in the mass, damping and stiffness matrices is established...
May 10, 2018: ISA Transactions
Daniel Toth, Shun Miao, Tanja Kurzendorfer, Christopher A Rinaldi, Rui Liao, Tommaso Mansi, Kawal Rhode, Peter Mountney
PURPOSE: In cardiac interventions, such as cardiac resynchronization therapy (CRT), image guidance can be enhanced by involving preoperative models. Multimodality 3D/2D registration for image guidance, however, remains a significant research challenge for fundamentally different image data, i.e., MR to X-ray. Registration methods must account for differences in intensity, contrast levels, resolution, dimensionality, field of view. Furthermore, same anatomical structures may not be visible in both modalities...
May 12, 2018: International Journal of Computer Assisted Radiology and Surgery
Guillermo Ruiz, Eduard Ramon, Jaime García, Federico M Sukno, Miguel A González Ballester
The use of 3D imaging has increased as a practical and useful tool for plastic and aesthetic surgery planning. Specifically, the possibility of representing the patient breast anatomy in a 3D shape and simulate aesthetic or plastic procedures is a great tool for communication between surgeon and patient during surgery planning. For the purpose of obtaining the specific 3D model of the breast of a patient, model-based reconstruction methods can be used. In particular, 3D morphable models (3DMM) are a robust and widely used method to perform 3D reconstruction...
May 2, 2018: Medical Image Analysis
Alireza Moradzadeh, Mohammad H Motevaselian, Sikandar Y Mashayak, Narayana R Aluru
We develop coarse-grained force fields (CGFFs) for computationally efficient and accurate molecular simulation of imidazolium-based ionic liquids (ILs). To obtain CGFF parameters, we employ a systematic coarse-graining approach based on the relative entropy (RE) method to reproduce not only the structure but also the thermodynamic properties of the reference all-atom molecular model. Our systematic coarse-graining approach adds a constraint to the RE minimization using Lagrange Multiplier in order to reproduce thermodynamic properties such as pressure...
May 11, 2018: Journal of Chemical Theory and Computation
Ulas Cikla, Balkan Sahin, Sahin Hanalioglu, Azam S Ahmed, David Niemann, Mustafa K Baskaya
OBJECTIVE Cerebrovascular bypass surgery is a challenging yet important neurosurgical procedure that is performed to restore circulation in the treatment of carotid occlusive diseases, giant/complex aneurysms, and skull base tumors. It requires advanced microsurgical skills and dedicated training in microsurgical techniques. Most available training tools, however, either lack the realism of the actual bypass surgery (e.g., artificial vessel, chicken wing models) or require special facilities and regulations (e...
May 11, 2018: Journal of Neurosurgery
Jing Li, Xiaoyun Tong, Jinjia Wang
Features and interaction between features of liver disease is of great significance for the classification of liver disease. Based on least absolute shrinkage and selection operator (LASSO) and interaction LASSO, the generalized interaction LASSO model is proposed in this paper for liver disease classification and compared with other methods. Firstly, the generalized interaction logistic classification model was constructed and the LASSO penalty constraints were added to the interactive model parameters. Then the model parameters were solved by an efficient alternating directions method of multipliers (ADMM) algorithm...
June 1, 2017: Sheng Wu Yi Xue Gong Cheng Xue za Zhi, Journal of Biomedical Engineering, Shengwu Yixue Gongchengxue Zazhi
Chloé Quignot, Julien Rey, Jinchao Yu, Pierre Tufféry, Raphaël Guerois, Jessica Andreani
Computational protein docking is a powerful strategy to predict structures of protein-protein interactions and provides crucial insights for the functional characterization of macromolecular cross-talks. We previously developed InterEvDock, a server for ab initio protein docking based on rigid-body sampling followed by consensus scoring using physics-based and statistical potentials, including the InterEvScore function specifically developed to incorporate co-evolutionary information in docking. InterEvDock2 is a major evolution of InterEvDock which allows users to submit input sequences - not only structures - and multimeric inputs and to specify constraints for the pairwise docking process based on previous knowledge about the interaction...
May 8, 2018: Nucleic Acids Research
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