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Constraint based modeling

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https://www.readbyqxmd.com/read/28934480/hydroxyl-radical-footprinting-combined-with-molecular-modeling-identifies-unique-features-of-dna-conformation-and-nucleosome-positioning
#1
Alexey K Shaytan, Hua Xiao, Grigoriy A Armeev, Carl Wu, David Landsman, Anna R Panchenko
Nucleosomes are the most abundant protein-DNA complexes in eukaryotes that provide compaction of genomic DNA and are implicated in regulation of transcription, DNA replication and repair. The details of DNA positioning on the nucleosome and the DNA conformation can provide key regulatory signals. Hydroxyl-radical footprinting (HRF) of protein-DNA complexes is a chemical technique that probes nucleosome organization in solution with a high precision unattainable by other methods. In this work we propose an integrative modeling method for constructing high-resolution atomistic models of nucleosomes based on HRF experiments...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28933350/locally-linear-constraint-based-optimization-model-for-material-decomposition
#2
Qian Wang, Yining Zhu, Hengyong Yu
Dual spectral computed tomography (DSCT) has a superior material distinguishability than the conventional single spectral computed tomography (SSCT). However, the decomposition process is an illposed problem, which is sensitive to noise. Thus, the decomposed image quality is degraded, and the corresponding signal-to-noise ratio (SNR) is much lower than that of directly reconstructed image of SSCT. In this work, we establish a locally linear relationship between the decomposed results of DSCT and SSCT. Based on this constraint, we propose an optimization model for DSCT and develop an iterative method with image guided filtering...
September 21, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28932740/tapping-the-vast-potential-of-the-data-deluge-in-small-scale-food-animal-production-businesses-challenges-to-near-real-time-data-analysis-and-interpretation
#3
Flavie Vial, Andrew Tedder
Food-animal production businesses are part of a data-driven ecosystem shaped by stringent requirements for traceability along the value chain and the expanding capabilities of connected products. Within this sector, the generation of animal health intelligence, in particular, in terms of antimicrobial usage, is hindered by the lack of a centralized framework for data storage and usage. In this Perspective, we delimit the 11 processes required for evidence-based decisions and explore processes 3 (digital data acquisition) to 10 (communication to decision-makers) in more depth...
2017: Frontiers in Veterinary Science
https://www.readbyqxmd.com/read/28927019/worst-case-energy-efficiency-maximization-in-a-5g-massive-mimo-noma-system
#4
Sunil Chinnadurai, Poongundran Selvaprabhu, Yongchae Jeong, Xueqin Jiang, Moon Ho Lee
In this paper, we examine the robust beamforming design to tackle the energy efficiency (EE) maximization problem in a 5G massive multiple-input multiple-output (MIMO)-non-orthogonal multiple access (NOMA) downlink system with imperfect channel state information (CSI) at the base station. A novel joint user pairing and dynamic power allocation (JUPDPA) algorithm is proposed to minimize the inter user interference and also to enhance the fairness between the users. This work assumes imperfect CSI by adding uncertainties to channel matrices with worst-case model, i...
September 18, 2017: Sensors
https://www.readbyqxmd.com/read/28926580/simple-yet-effective-historical-proximity-variables-improve-the-species-distribution-models-for-invasive-giant-hogweed-heracleum-mantegazzianum-s-l-in-poland
#5
Piotr Mędrzycki, Ingeborga Jarzyna, Artur Obidziński, Barbara Tokarska-Guzik, Zofia Sotek, Piotr Pabjanek, Adam Pytlarczyk, Izabela Sachajdakiewicz
Species distribution models are scarcely applicable to invasive species because of their breaking of the models' assumptions. So far, few mechanistic, semi-mechanistic or statistical solutions like dispersal constraints or propagule limitation have been applied. We evaluated a novel quasi-semi-mechanistic approach for regional scale models, using historical proximity variables (HPV) representing a state of the population in a given moment in the past. Our aim was to test the effects of addition of HPV sets of different minimal recentness, information capacity and the total number of variables on the quality of the species distribution model for Heracleum mantegazzianum on 116000 km2 in Poland...
2017: PloS One
https://www.readbyqxmd.com/read/28922127/jointly-learning-structured-analysis-discriminative-dictionary-and-analysis-multiclass-classifier
#6
Zhao Zhang, Weiming Jiang, Jie Qin, Li Zhang, Fanzhang Li, Min Zhang, Shuicheng Yan
In this paper, we propose an analysis mechanism-based structured analysis discriminative dictionary learning (ADDL) framework. The ADDL seamlessly integrates ADDL, analysis representation, and analysis classifier training into a unified model. The applied analysis mechanism can make sure that the learned dictionaries, representations, and linear classifiers over different classes are independent and discriminating as much as possible. The dictionary is obtained by minimizing a reconstruction error and an analytical incoherence promoting term that encourages the subdictionaries associated with different classes to be independent...
September 14, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28922118/a-fast-gradient-method-for-nonnegative-sparse-regression-with-self-dictionary
#7
Nicolas Gillis, Robert Luce
A nonnegative matrix factorization (NMF) can be computed efficiently under the separability assumption, which asserts that all the columns of the given input data matrix belong to the cone generated by a (small) subset of them. The provably most robust methods to identify these conic basis columns are based on nonnegative sparse regression and self dictionaries, and require the solution of large-scale convex optimization problems. In this paper we study a particular nonnegative sparse regression model with self dictionary...
September 18, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28919103/alterations-of-musculoskeletal-models-for-a-more-accurate-estimation-of-lower-limb-joint-contact-forces-during-normal-gait-a-systematic-review
#8
REVIEW
F Moissenet, L Modenese, R Dumas
Musculoskeletal modelling is a methodology used to investigate joint contact forces during a movement. High accuracy in the estimation of the hip or knee joint contact forces can be obtained with subject-specific models. However, construction of subject-specific models remains time consuming and expensive. The purpose of this systematic review of the literature was to identify what alterations can be made on generic (i.e. literature-based, without any subject-specific measurement other than body size and weight) musculoskeletal models to obtain a better estimation of the joint contact forces...
September 1, 2017: Journal of Biomechanics
https://www.readbyqxmd.com/read/28918679/relating-the-proton-relative-biological-effectiveness-to-tumor-control-and-normal-tissue-complication-probabilities-assuming-interpatient-variability-in-%C3%AE-%C3%AE
#9
Harald Paganetti
BACKGROUND: Proton therapy uses a constant relative biological effectiveness (RBE) of 1.1. The use of variable RBE values has been suggested but is currently not feasible due to uncertainties. The impact of variable RBE has solely been studied using dosimetric indices. This work elucidates the impact of RBE variations on tumor control and normal tissue complication probabilities (TCP/NTCP). METHODS: Models to estimate TCP and NTCP were used in combination with an empirical proton RBE model...
September 18, 2017: Acta Oncologica
https://www.readbyqxmd.com/read/28915815/designing-an-implementation-intervention-with-the-behaviour-change-wheel-for-health-provider-smoking-cessation-care-for-australian-indigenous-pregnant-women
#10
Gillian S Gould, Yael Bar-Zeev, Michelle Bovill, Lou Atkins, Maree Gruppetta, Marilyn J Clarke, Billie Bonevski
BACKGROUND: Indigenous smoking rates are up to 80% among pregnant women: prevalence among pregnant Australian Indigenous women was 45% in 2014, contributing significantly to the health gap for Indigenous Australians. We aimed to develop an implementation intervention to improve smoking cessation care (SCC) for pregnant Indigenous smokers, an outcome to be achieved by training health providers at Aboriginal Medical Services (AMS) in a culturally competent approach, developed collaboratively with AMS...
September 15, 2017: Implementation Science: IS
https://www.readbyqxmd.com/read/28914803/achieving-congestion-mitigation-using-distributed-power-control-for-spectrum-sensor-nodes-in-sensor-network-aided-cognitive-radio-ad-hoc-networks
#11
Long Zhang, Haitao Xu, Fan Zhuo, Hucai Duan
The data sequence of spectrum sensing results injected from dedicated spectrum sensor nodes (SSNs) and the data traffic from upstream secondary users (SUs) lead to unpredictable data loads in a sensor network-aided cognitive radio ad hoc network (SN-CRN). As a result, network congestion may occur at a SU acting as fusion center when the offered data load exceeds its available capacity, which degrades network performance. In this paper, we present an effective approach to mitigate congestion of bottlenecked SUs via a proposed distributed power control framework for SSNs over a rectangular grid based SN-CRN, aiming to balance resource load and avoid excessive congestion...
September 15, 2017: Sensors
https://www.readbyqxmd.com/read/28914787/a-sparse-dictionary-learning-based-adaptive-patch-inpainting-method-for-thick-clouds-removal-from-high-spatial-resolution-remote-sensing-imagery
#12
Fan Meng, Xiaomei Yang, Chenghu Zhou, Zhi Li
Cloud cover is inevitable in optical remote sensing (RS) imagery on account of the influence of observation conditions, which limits the availability of RS data. Therefore, it is of great significance to be able to reconstruct the cloud-contaminated ground information. This paper presents a sparse dictionary learning-based image inpainting method for adaptively recovering the missing information corrupted by thick clouds patch-by-patch. A feature dictionary was learned from exemplars in the cloud-free regions, which was later utilized to infer the missing patches via sparse representation...
September 15, 2017: Sensors
https://www.readbyqxmd.com/read/28914122/improving-health-in-prisons-from-evidence-to-policy-to-implementation-experiences-from-the-uk
#13
Jane Leaman, Anna Amelia Richards, Lynn Emslie, Eamonn Joseph O'Moore
Purpose The purpose of this paper is to understand the components of a high-quality prison healthcare system and the impact, ten-years on, of the transfer of accountability in England, from a justice ministry to a health ministry. Design/methodology/approach A rapid the evidence review was undertaken, which included a review of 82 papers and qualitative interviews with key informants. The concepts and themes identified were summarised and analysed through a framework analysis, designed to improve population outcomes and address health inequalities...
September 11, 2017: International Journal of Prisoner Health
https://www.readbyqxmd.com/read/28913177/big-data-in-designing-clinical-trials-opportunities-and-challenges
#14
Charles S Mayo, Martha M Matuszak, Matthew J Schipper, Shruti Jolly, James A Hayman, Randall K Ten Haken
Emergence of big data analytics resource systems (BDARSs) as a part of routine practice in Radiation Oncology is on the horizon. Gradually, individual researchers, vendors, and professional societies are leading initiatives to create and demonstrate use of automated systems. What are the implications for design of clinical trials, as these systems emerge? Gold standard, randomized controlled trials (RCTs) have high internal validity for the patients and settings fitting constraints of the trial, but also have limitations including: reproducibility, generalizability to routine practice, infrequent external validation, selection bias, characterization of confounding factors, ethics, and use for rare events...
2017: Frontiers in Oncology
https://www.readbyqxmd.com/read/28912473/fine-scale-harbour-seal-usage-for-informed-marine-spatial-planning
#15
Esther L Jones, Carol E Sparling, Bernie J McConnell, Christopher D Morris, Sophie Smout
High-resolution distribution maps can help inform conservation measures for protected species; including where any impacts of proposed commercial developments overlap the range of focal species. Around Orkney, northern Scotland, UK, the harbour seal (Phoca vitulina) population has decreased by 78% over 20 years. Concern for the declining harbour seal population has led to constraints being placed on tidal energy generation developments. For this study area, telemetry data from 54 animals tagged between 2003 and 2015 were used to produce density estimation maps...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28910740/generation-of-low-gamma-oscillations-in-a-gabaergic-network-model-of-the-striatum
#16
Zhihua Wu, Aike Guo, Xiaodi Fu
Striatal oscillations in the low-gamma frequency range have been consistently recorded in a number of experimental studies. However, whether these rhythms are locally generated in the striatum circuit, which is mainly composed of GABAergic neurons, remains an open question. GABAergic medium spiny projection neurons represent the great majority of striatal neurons, but they fire at very low rates. GABAergic fast-spiking interneurons typically show firing rates that are approximately 10 times higher than those of principal neurons, but they are a very small minority of the total neuronal population...
September 11, 2017: Neural Networks: the Official Journal of the International Neural Network Society
https://www.readbyqxmd.com/read/28906263/governing-academic-medical-center-systems-evaluating-and-choosing-among-alternative-governance-approaches
#17
Ramya Chari, Claire O'Hanlon, Peggy Chen, Kristin Leuschner, Christopher Nelson
The ability of academic medical centers (AMCs) to fulfill their triple mission of patient care, medical education, and research is increasingly being threatened by rising financial pressures and resource constraints. Many AMCs are, therefore, looking to expand into academic medical systems, increasing their scale through consolidation or affiliation with other health care systems. As clinical operations grow, though, the need for effective governance becomes even more critical to ensure that the business of patient care does not compromise the rest of the triple mission...
September 12, 2017: Academic Medicine: Journal of the Association of American Medical Colleges
https://www.readbyqxmd.com/read/28905466/adherence-to-pi-based-2-nd-line-regimens-in-cambodia-is-not-simply-a-question-of-individual-behaviour-the-anrs-12276-2picam-study
#18
Luis Sagaon-Teyssier, Bakridine Mmadi Mrenda, Vohith Khol, Laurent Ferradini, Sovatha Mam, Sopheak Ngin, Marion Mora, Gwenaëlle Maradan, Chhi Vun Mean, Olivier Ségéral, Eric Nerrienet, Vonthanak Saphonn, Bruno Spire
OBJECTIVES: To investigate whether adherence to antiretroviral treatment (ART) can be explained not only by individual factors but also by healthcare facilities' characteristics, among a sample of people living with HIV (PLWH) treated with PI-based regimens in Cambodia. METHODS: The ANRS 12276 2PICAM cross-sectional survey was conducted between February 2013 and April 2014 among PLWH followed up in 13 healthcare facilities. The 1316 patients in this analysis corresponded to 90% of the total number of adult patients treated with 2(nd) line PI-based regimens in Cambodia in the study period...
September 14, 2017: Tropical Medicine & International Health: TM & IH
https://www.readbyqxmd.com/read/28905411/joint-arterial-input-function-and-tracker-kinetic-parameter-estimation-from-undersampled-dynamic-contrast-enhanced-mri-using-a-model-consistency-constraint
#19
Yi Guo, Sajan Goud Lingala, Yannick Bliesener, R Marc Lebel, Yinghua Zhu, Krishna S Nayak
PURPOSE: To develop and evaluate a model-based reconstruction framework for joint arterial input function (AIF) and kinetic parameter estimation from undersampled brain tumor dynamic contrast-enhanced MRI (DCE-MRI) data. METHODS: The proposed method poses the tracer-kinetic (TK) model as a model consistency constraint, enabling the flexible inclusion of different TK models and TK solvers, and the joint estimation of the AIF. The proposed method is evaluated using an anatomic realistic digital reference object (DRO), and nine retrospectively down-sampled brain tumor DCE-MRI datasets...
September 14, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28901625/systemic-challenges-in-bipolar-disorder-management-a-patient-centered-approach
#20
Anastasiya Nestsiarovich, Nathaniel G Hurwitz, Stuart J Nelson, Annette S Crisanti, Berit Kerner, Matt J Kuntz, Alicia N Smith, Emma Volesky, Quentin L Schroeter, Jason L DeShaw, S Stanley Young, Robert L Obenchain, Ronald L Krall, Kimmie Jordan, Jan Fawcett, Mauricio Tohen, Douglas J Perkins, Christophe G Lambert
OBJECTIVES: As part of a series of Patient-Centered Outcomes Research Institute-funded large-scale retrospective observational studies on bipolar disorder (BD) treatments and outcomes, we sought the input of patients with BD and their family members to develop research questions. We aimed to identify systemic root causes of patient-reported challenges with BD management in order to guide subsequent studies and initiatives. METHODS: Three focus groups were conducted where patients and their family members (total n = 34) formulated questions around the central theme, "What do you wish you had known in advance or over the course of treatment for BD?" In an affinity mapping exercise, participants clustered their questions and ranked the resulting categories by importance...
September 13, 2017: Bipolar Disorders
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