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Constraint based modeling

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https://www.readbyqxmd.com/read/27924867/constraints-and-spandrels-of-interareal-connectomes
#1
Mikail Rubinov
Interareal connectomes are whole-brain wiring diagrams of white-matter pathways. Recent studies have identified modules, hubs, module hierarchies and rich clubs as structural hallmarks of these wiring diagrams. An influential current theory postulates that connectome modules are adequately explained by evolutionary pressures for wiring economy, but that the other hallmarks are not explained by such pressures and are therefore less trivial. Here, we use constraint network models to test these postulates in current gold-standard vertebrate and invertebrate interareal-connectome reconstructions...
December 7, 2016: Nature Communications
https://www.readbyqxmd.com/read/27920377/phenological-shifts-of-native-and-invasive-species-under-climate-change-insights-from-the-boechera-lythrum-model
#2
REVIEW
Robert I Colautti, Jon Ågren, Jill T Anderson
Warmer and drier climates have shifted phenologies of many species. However, the magnitude and direction of phenological shifts vary widely among taxa, and it is often unclear when shifts are adaptive or how they affect long-term viability. Here, we model evolution of flowering phenology based on our long-term research of two species exhibiting opposite shifts in floral phenology: Lythrum salicaria, which is invasive in North America, and the sparse Rocky Mountain native Boechera stricta Genetic constraints are similar in both species, but differences in the timing of environmental conditions that favour growth lead to opposite phenological shifts under climate change...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27918483/a-fault-tolerance-mechanism-for-on-road-sensor-networks
#3
Lei Feng, Shaoyong Guo, Jialu Sun, Peng Yu, Wenjing Li
On-Road Sensor Networks (ORSNs) play an important role in capturing traffic flow data for predicting short-term traffic patterns, driving assistance and self-driving vehicles. However, this kind of network is prone to large-scale communication failure if a few sensors physically fail. In this paper, to ensure that the network works normally, an effective fault-tolerance mechanism for ORSNs which mainly consists of backup on-road sensor deployment, redundant cluster head deployment and an adaptive failure detection and recovery method is proposed...
December 3, 2016: Sensors
https://www.readbyqxmd.com/read/27916341/hospital-influenza-pandemic-stockpiling-needs-a-computer-simulation
#4
Mark N Abramovich, John C Hershey, Byron Callies, Amesh A Adalja, Pritish K Tosh, Eric S Toner
BACKGROUND: A severe influenza pandemic could overwhelm hospitals but planning guidance that accounts for the dynamic interrelationships between planning elements is lacking. We developed a methodology to calculate pandemic supply needs based on operational considerations in hospitals and then tested the methodology at Mayo Clinic in Rochester, MN. METHODS: We upgraded a previously designed computer modeling tool and input carefully researched resource data from the hospital to run 10,000 Monte Carlo simulations using various combinations of variables to determine resource needs across a spectrum of scenarios...
December 2, 2016: American Journal of Infection Control
https://www.readbyqxmd.com/read/27913364/an-intelligible-risk-stratification-model-based-on-pairwise-and-size-constrained-kmeans
#5
Longfei Han, Senlin Luo, Huaiqing Wang, Limin Pan, Xincheng Ma, Tiemei Zhang
Having a system to stratify individuals according to risk is key to clinical disease prevention, this allows individuals identified at different risk tiers benefit from further investigation and intervention. But the same risk score estimated for two different persons doesn't mean they need the same further investigation or represent the similarity health condition between two persons. Meanwhile, users still does not know a prior what most of the risk tiers are, and how many tiers should be found in risk stratification...
November 29, 2016: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/27913361/constrained-null-space-component-analysis-for-semiblind-source-separation-problem
#6
Wen-Liang Hwang, Keng-Shih Lu, Jinn Ho
The blind source separation (BSS) problem extracts unknown sources from observations of their unknown mixtures. A current trend in BSS is the semiblind approach, which incorporates prior information on sources or how the sources are mixed. The constrained independent component analysis (ICA) approach has been studied to impose constraints on the famous ICA framework. We introduced an alternative approach based on the null space component (NCA) framework and referred to the approach as the c-NCA approach. We also presented the c-NCA algorithm that uses signal-dependent semidefinite operators, which is a bilinear mapping, as signatures for operator design in the c-NCA approach...
November 29, 2016: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/27910824/accelerated-high-resolution-photoacoustic-tomography-via-compressed-sensing
#7
Simon Arridge, Paul Beard, Marta Betcke, Ben Cox, Nam Huynh, Felix Lucka, Olumide Ogunlade, Edward Zhang
Current 3D photoacoustic tomography (PAT) systems offer either high image quality or high frame rates but are not able to deliver high spatial and temporal resolution simultaneously, which limits their ability to image dynamic processes in living tissue (4D PAT). A particular example is the planar Fabry-Pérot (FP) photoacoustic scanner, which yields high-resolution 3D images but takes several minutes to sequentially map the incident photoacoustic field on the 2D sensor plane, point-by-point. However, as the spatio-temporal complexity of many absorbing tissue structures is rather low, the data recorded in such a conventional, regularly sampled fashion is often highly redundant...
December 21, 2016: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/27908678/avoidance-of-late-rectal-toxicity-after-high-dose-rate-brachytherapy-boost-treatment-for-prostate-cancer
#8
Borut Kragelj, Jernej Zlatic, Lijana Zaletel-Kragelj
PURPOSE: To elucidate potential risk factors important for the appearance of late rectal toxicity (LRT) after high-dose-rate boost treatment (HDRBT) of prostate cancer and to validate the predictive value of the minimal dose to the most exposed 2 cc of rectum received with HDRBT (D2ccrect). METHODS AND MATERIALS: The study of LRT, defined as relative deterioration of defecation problems (RDDP) (stool frequency, pain, rectal bleeding, fecal urgency, and incontinence) during follow-up period, was carried out on 88 patients, consecutively treated from October 2006 through April 2011 with HDRBT of 3 × 6-7 Gy to 50-50...
November 28, 2016: Brachytherapy
https://www.readbyqxmd.com/read/27906316/ring-modulators-with-enhanced-efficiency-based-on-standing-wave-operation-on-a-field-matched-interdigitated-p-n-junction
#9
Fabio Pavanello, Xiaoge Zeng, Mark T Wade, Miloš A Popović
We propose ring modulators based on interdigitated p-n junctions that exploit standing rather than traveling-wave resonant modes to improve modulation efficiency, insertion loss and speed. Matching the longitudinal nodes and antinodes of a standing-wave mode with high (contacts) and low (depletion regions) carrier density regions, respectively, simultaneously lowers loss and increases sensitivity significantly. This approach permits further to relax optical constraints on contacts placement and can lead to lower device capacitance...
November 28, 2016: Optics Express
https://www.readbyqxmd.com/read/27905897/cost-and-cost-effectiveness-of-tuberculosis-treatment-shortening-a-model-based-analysis
#10
G B Gomez, D W Dowdy, M L Bastos, A Zwerling, S Sweeney, N Foster, A Trajman, M A Islam, S Kapiga, E Sinanovic, G M Knight, R G White, W A Wells, F G Cobelens, A Vassall
BACKGROUND: Despite improvements in treatment success rates for tuberculosis (TB), current six-month regimen duration remains a challenge for many National TB Programmes, health systems, and patients. There is increasing investment in the development of shortened regimens with a number of candidates in phase 3 trials. METHODS: We developed an individual-based decision analytic model to assess the cost-effectiveness of a hypothetical four-month regimen for first-line treatment of TB, assuming non-inferiority to current regimens of six-month duration...
December 1, 2016: BMC Infectious Diseases
https://www.readbyqxmd.com/read/27905145/the-public-multi-coil-information-pumcin-policy
#11
Christoph Juchem, Robin A de Graaf
PURPOSE: Multi-coil (MC) magnetic field modeling has emerged as a viable alternative to conventional field generation based on spherical harmonic shapes, and an active MC community is forming. Although all MC applications share the same modeling concept, the specific MC designs can largely differ as a result of disparities in region of interest (eg, human versus rodent), intended MR application (eg, B0 shimming versus spatial encoding), or other experimental constraints (eg, available bore space or integration with radiofrequency technology)...
December 1, 2016: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/27900933/race-to-the-top-evaluation-of-a-novel-performance-based-financing-initiative-to-promote-healthcare-delivery-in-rural-rwanda
#12
Evrard Nahimana, Ryan McBain, Anatole Manzi, Hari Iyer, Alice Uwingabiye, Neil Gupta, Gerald Muzungu, Peter Drobac, Lisa R Hirschhorn
BACKGROUND: Performance-based financing (PBF) has demonstrated a range of successes and failures in improving health outcomes across low- and middle-income countries. Evidence indicates that the success of PBF depends, in large part, on the model selected, in relation to a variety of contextual factors. OBJECTIVE: Partners In Health∣Inshuti Mu Buzima aimed to evaluate health outcomes associated with a novel capacity-building model of PBF at health centers throughout Kirehe district, Rwanda...
2016: Global Health Action
https://www.readbyqxmd.com/read/27897000/identifying-cancer-specific-metabolic-signatures-using-constraint-based-models
#13
A Schultz, S Mehta, C W Hu, F W Hoff, T M Horton, S M Kornblau, A A Qutub
Cancer metabolism differs remarkably from the metabolism of healthy surrounding tissues, and it is extremely heterogeneous across cancer types. While these metabolic differences provide promising avenues for cancer treatments, much work remains to be done in understanding how metabolism is rewired in malignant tissues. To that end, constraint-based models provide a powerful computational tool for the study of metabolism at the genome scale. To generate meaningful predictions, however, these generalized human models must first be tailored for specific cell or tissue sub-types...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27889874/decision-support-provided-by-a-temporally-oriented-health-care-assistant-an-implementation-of-computer-interpretable-guidelines
#14
Tiago Oliveira, António Silva, José Neves, Paulo Novais
The automatic interpretation of clinical recommendations is a difficult task, even more so when it involves the processing of complex temporal constraints. In order to address this issue, a web-based system is presented herein. Its underlying model provides a comprehensive representation of temporal constraints in Clinical Practice Guidelines. The expressiveness and range of the model are shown through a case study featuring a Clinical Practice Guideline for the diagnosis and management of colon cancer. The proposed model was sufficient to represent the temporal constraints in the guideline, especially those that defined periodic events and placed temporal constraints on the assessment of patient states...
January 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/27889365/characterizing-and-modelling-river-channel-migration-rates-at-a-regional-scale-case-study-of-south-east-france
#15
Adrien Alber, Hervé Piégay
An increased awareness by river managers of the importance of river channel migration to sediment dynamics, habitat complexity and other ecosystem functions has led to an advance in the science and practice of identifying, protecting or restoring specific erodible corridors across which rivers are free to migrate. One current challenge is the application of these watershed-specific goals at the regional planning scales (e.g., the European Water Framework Directive). This study provides a GIS-based spatial analysis of the channel migration rates at the regional-scale...
November 23, 2016: Journal of Environmental Management
https://www.readbyqxmd.com/read/27887759/implementing-an-open-access-casa-software-for-the-assessment-of-stallion-sperm-motility-relationship-with-other-sperm-quality-parameters
#16
Elisa Giaretta, Mauro Munerato, Marc Yeste, Giovanna Galeati, Marcella Spinaci, Carlo Tamanini, Gaetano Mari, Diego Bucci
Setting an open-access computer assisted sperm analysis (CASA) may benefit the evaluation of motility in mammalian sperm, especially when economic constraints do not allow the use of a commercial system. There have been successful attempts to develop such a device in Zebra fish sperm and the system has been used in very few studies on mammalian spermatozoa. Against this background, the present study aimed at developing an open-access CASA system for mammalian sperm using the horse as a model and based upon the Image J software previously established for Zebra fish sperm...
November 13, 2016: Animal Reproduction Science
https://www.readbyqxmd.com/read/27885853/nomogram-for-radiation-induced-hypothyroidism-prediction-in-nasopharyngeal-carcinoma-after-treatment
#17
Ren Luo, Mei Li, Zhining Yang, Yizhou Zhan, Baotian Huang, Jiayang Lu, Zhenxi Xu, Zhixiong Lin
OBJECTIVE: The aim of this study was to develop a nomogram for radiation-induced hypothyroidism (RHT) prediction. METHODS: We collected data from 164 NPC patients in our previous prospective study. Biochemical hypothyroidism (HT) was defined as a serum thyroid stimulating hormone (TSH) level greater than the normal value. We collected both clinical and dose-volume factors. A univariate Cox regression analysis was performed to identify RHT risk factors. Optimal predictors were selected according to the least absolute shrinkage and selection operator (LASSO)...
November 25, 2016: British Journal of Radiology
https://www.readbyqxmd.com/read/27883344/analysis-of-non-eeg-evidence-for-preparatory-activity-in-the-human-brain-pre-contraction-impedance-changes-in-skeletal-muscles
#18
Carl Shiffman
Precontraction impedance changes (PICs) are known to occur during isometric contractions of the human forearm finger flexors. Without reliance on electroencephalogical data these are construed as evidence for the construction of a 'template of instructions' in the brain for muscle contractions to be performed once a 'go' instruction is received, as widely expected from EEG measurements A model is proposed to explain earlier impedance results, based on a PIC-associated time-dependent inhibitory constraint and a modified role for the 'go' command...
November 24, 2016: Physiological Measurement
https://www.readbyqxmd.com/read/27881075/modelling-microbial-metabolic-rewiring-during-growth-in-a-complex-medium
#19
Marco Fondi, Emanuele Bosi, Luana Presta, Diletta Natoli, Renato Fani
BACKGROUND: In their natural environment, bacteria face a wide range of environmental conditions that change over time and that impose continuous rearrangements at all the cellular levels (e.g. gene expression, metabolism). When facing a nutritionally rich environment, for example, microbes first use the preferred compound(s) and only later start metabolizing the other one(s). A systemic re-organization of the overall microbial metabolic network in response to a variation in the composition/concentration of the surrounding nutrients has been suggested, although the range and the entity of such modifications in organisms other than a few model microbes has been scarcely described up to now...
November 24, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27878852/optimal-design-of-longitudinal-data-analysis-using-generalized-estimating-equation-models
#20
Jingxia Liu, Graham A Colditz
Longitudinal studies are often applied in biomedical research and clinical trials to evaluate the treatment effect. The association pattern within the subject must be considered in both sample size calculation and the analysis. One of the most important approaches to analyze such a study is the generalized estimating equation (GEE) proposed by Liang and Zeger, in which "working correlation structure" is introduced and the association pattern within the subject depends on a vector of association parameters denoted by ρ...
November 23, 2016: Biometrical Journal. Biometrische Zeitschrift
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