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Clinical use of computational modeling for surgical planning of arteriovenous fistula for hemodialysis

BMC MEDICAL INFORMATICS AND DECISION MAKING 2017年第1期17卷 26-26页

作者： Bozzetto, Michela Rota, Stefano Vigo, Valentina Casucci, Francesco Lomonte, Carlo Morale, Walter Senatore, Massimo Tazza, Luigi Lodi, Massimo Remuzzi, Giuseppe Remuzzi, Andrea IRCCS Dept Biomed Engn Ist Ric Farmacol Mario Negri Bergamo Italy ASST Papa Giovanni XXIII Unit Nephrol & Dialysis Bergamo Italy Ente Ecclesiastico F Miulli Unit Nephrol & Dialysis Acquaviva Delle Fonti BA Italy AO Cannizzaro Unit Nephrol & Dialysis Catania Italy Osped Annunziata Unit Nephrol & Dialysis Cosenza Italy Catholic Univ Dept Urol & Nephrol Rome Italy Osped S Spirito Unit Nephrol & Dialysis Pescara Italy Univ Milan Dept Biomed & Clin Sci Milan Italy Univ Bergamo Dept Management Informat & Prod Engn Bergamo Italy

Background: Autogenous arteriovenous fistula (AVF) is the best vascular access (VA) for hemodialysis, but its creation is still a critical procedure. Physical examination, vascular mapping and doppler ultrasound (DUS) evaluation are recommended for AVF planning, but they can not provide direct indication on AVF outcome. We recently developed and validated in a clinical trial a patient-specific computational model to predict pre-operatively the blood flow volume (BFV) in AVF for different surgical configuration on the basis of demographic, clinical and DUS data. In the present investigation we tested power of prediction and usability of the computational model in routine clinical setting. Methods: We developed a web-based system (***) that integrates the computational model in a single procedure, including data collection and transfer, simulation management and data storage. A usability test on observational data was designed to compare predicted vs. measured BFV and evaluate the acceptance of the system in the clinical setting. Six Italian nephrology units were involved in the evaluation for a 6-month period that included all incident dialysis patients with indication for AVF surgery. Results: Out of the 74 patients, complete data from 60 patients were included in the final dataset. Predicted brachial BFV at 40 days after surgery showed a good correlation with measured values (in average 787 +/- 306 vs. 751 +/- 267 mL/min, R = 0.81, p < 0.001). For distal AVFs the mean difference (+/- SD) between predicted vs. measured BFV was -2.0 +/- 20.9%, with 50% of predicted values in the range of 86-121% of measured BFV. Feedbacks provided by clinicians indicate that *** is easy to use and well accepted in clinical routine, with limited additional workload. Conclusions: Clinical use of computational modeling for AVF surgical planning can help the surgeon to select the best surgical strategy, reducing AVF early failures and complications. This approach allows individua

关键词： Arteriovenous fistula computational modeling Surgical planning Hemodialysis vascular access

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Structure of Scots pine defensin 1 by spectroscopic methods and computational modeling

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INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES 2016年第0期84卷 142-152页

作者： Ermakova, Elena A. Faizullin, Dzhigangir A. Idiyatullin, Bulat Z. Khairutdinov, Bulat I. Mukhamedova, Liya N. Tarasova, Nadezhda B. Toporkova, Yana Y. Osipova, Elena V. Kovaleva, Valentina Gogolev, Yuri V. Zuev, Yuriy F. Nesmelova, Irina V. Kazan Inst Biochem & Biophys RAS POB 30 Kazan 420111 Russia Ukrainian Natl Forestry Univ Lvov Ukraine Univ N Carolina Dept Phys & Opt Sci Grigg Hall 3069201 Univ City Blvd Charlotte NC 28223 USA Univ N Carolina Ctr Biomed Engn & Sci Charlotte NC 28223 USA

Defensins are part of the innate immune system in plants with activity against a broad range of pathogens, including bacteria, fungi and viruses. Several defensins from conifers, including Scots pine defensin 1 (Pinus sylvestris defensin 1, (PsDef1)) have shown a strong antifungal activity, however structural and physico-chemical properties of the family, needed for establishing the structure-dynamics-function relationships, remain poorly characterized. We use several spectroscopic and computational methods to characterize the structure, dynamics, and oligomeric state of PsDef1. The three-dimensional structure was modeled by comparative modeling using several programs (Geno3D, SWISS-MODEL, I-TASSER, Phyre(2), and FUGUE) and verified by circular dichroism (CD) and infrared (FTIR) spectroscopy. Furthermore, FTIR data indicates that the structure of PsDef1 is highly resistant to high temperatures. NMR diffusion experiments show that defensin exists in solution in the equilibrium between monomers and dimers. Four types of dimers were constructed using the HADDOCK program and compared to the known dimer structures of other plant defensins. Gaussian network model was used to characterize the internal dynamics of PsDef1 in monomer and dimer states. PsDef1 is a typical representative of P. sylvestris defensins and hence the results of this study are applicable to other members of the family. (C) 2015 Elsevier B.V. All rights reserved.

关键词： Defensin Structure Dimer computational modeling Circular dichroism FTIR

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Current advances in molecular, biochemical, and computational modeling analysis of microalgal triacylglycerol biosynthesis

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BIOTECHNOLOGY ADVANCES 2016年第5期34卷 1046-1063页

作者： Lenka, Sangram K. Carbonaro, Nicole Park, Rudolph Miller, Stephen M. Thorpe, Ian Li, Yantao Univ Maryland Ctr Environm Sci Inst Marine & Environm Technol Baltimore MD 21202 USA Univ Maryland Baltimore Cty Baltimore MD 21202 USA Univ Maryland Dept Chem & Biochem Baltimore MD 21202 USA Univ Maryland Dept Biol Sci Baltimore MD 21202 USA

Triacylglycerols (TAGs) are highly reduced energy storage molecules ideal for biodiesel production. Microalgal TAG biosynthesis has been studied extensively in recent years, both at the molecular level and systems level through experimental studies and computational modeling. However, discussions of the strategies and products of the experimental and modeling approaches are rarely integrated and summarized together in a way that promotes collaboration among modelers and biologists in this field. In this review, we outline advances toward understanding the cellular and molecular factors regulating TAG biosynthesis in unicellular microalgae with an emphasis on recent studies on rate-limiting steps in fatty acid and TAG synthesis, while also highlighting new insights obtained from the integration of multi-omics datasets with mathematical models. computational methodologies such as kinetic modeling, metabolic flux analysis, and new variants of flux balance analysis are explained in detail. We discuss how these methods have been used to simulate algae growth and lipid metabolism in response to changing culture conditions and how they have been used in conjunction with experimental validations. Since emerging evidence indicates that TAG synthesis in microalgae operates through coordinated crosstalk between multiple pathways in diverse subcellular destinations including the endoplasmic reticulum and plastids, we discuss new experimental studies and models that incorporate these findings for discovering key regulatory checkpoints. Finally, we describe tools for genetic manipulation of microalgae and their potential for future rational algal strain design. This comprehensive review explores the potential synergistic impact of pathway analysis, computational approaches, and molecular genetic manipulation strategies on improving TAG production in microalgae. (C) 2016 Elsevier Inc. All rights reserved.

关键词： Microalgae Lipid Triacylglycerol biosynthesis Metabolic engineering computational modeling Flux balance analysis Omics Biofuels

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The promotional role of water in heterogeneous catalysis: mechanism insights from computational modeling

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WILEY INTERDISCIPLINARY REVIEWS-computational MOLECULAR SCIENCE 2016年第6期6卷 679-693页

作者： Chang, Chun-Ran Huang, Zheng-Qing Li, Jun Xi An Jiao Tong Univ Inst Ind Catalysis Sch Chem Engn & Technol Xian Peoples R China Tsinghua Univ Dept Chem & Key Lab Organ Optoelectron & Mol Engn Minist Educ Beijing Peoples R China

Water is the key to life in our planet. As one of the most abundant resources on the earth, water may play important roles in chemical reactions in addition to being a reaction medium. In this review, we highlight recent advances in experimental observations and mechanistic understanding of the promotional role of water in chemical reactions, with an emphasis on the essential effects of water in heterogeneous catalysis. As water may exist in molecular state or dissociate to hydroxyl (OH) and hydrogen (H) species on catalyst surfaces, we have outlined the roles of water from three aspects: (1) the promotional role of molecular water including the solvation-like effect and water-mediated H-transfer, (2) the promotional role of OH/OH (-) and H/H+ species, and (3) some miscellaneous effects of water, such as water-assisted carbon removal, surface reconstruction, and active sites blocking. The results discussed here provide a fundamental understanding of the promotional role of water in heterogeneous reactions and may inspire the theoretical studies of water effects on other fields of chemistry and atmospheric science as well. WIREs Comput Mol Sci 2016, 6:679-693. doi: 10.1002/wcms.1272 For further resources related to this article, please visit the .

关键词： Active Site meteorology and climatology Heterogeneous catalysis chemical reactions MOLECULAR STATES Theoretical Study computational modeling

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Optimization of experimental temperature measurement in GTAW process by means of DoE technique and computational modeling

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MEASUREMENT 2016年 88卷 297-309页

作者： Garcia-Garcia, Victor Reyes-Calderon, Francisco Cristobal Camacho-Arriaga, Juan Inst Tecnol Morelia Met Mech Engn Dept Ave Tecnol 1500 Morelia 58120 Michoacan Mexico

The prediction of temperature distribution is a critical process in the study of welding thermal field. Therefore, the accuracy in temperature measurement is quite important to provide meaningful results and to establish the coupling among thermal field results and other studies in welding as mechanical and microstructural analyses. This work deals with statistical analysis and design of experiments (DoE) in order to establish an optimal experimental design for thermal history measurements in welding processes with thermocouples independent of base material. Calculations from theoretical correlations and computational modeling of heat flow were used to accomplish the present study. The Gas Tungsten Arc Welding process (GTAW) was used in the experiments along with plates of a structural steel (ASTM A 36) and a martensitic stainless steel (AISI CrMo 12-1). Four different parameters were studied related with the disposition, separation, depth, thermocouple arrangement and application of thermal paste. An optimal design was able to measure the maximum temperatures in adjacent zones to the weld bead, which are important for the study of welding thermal behavior. (C) 2016 Elsevier Ltd. All rights reserved.

关键词： Statistical analysis Factorial design of experiments computational modeling Optimal experiment design Welding thermal field

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Optimization of the moving-bed biofilm sequencing batch reactor (MBSBR) to control aeration time by kinetic computational modeling: Simulated sugar-industry wastewater treatment

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BIORESOURCE TECHNOLOGY 2016年 208卷 149-160页

作者： Faridnasr, Maryam Ghanbari, Bastam Sassani, Ardavan Islamic Azad Univ Grad Sch Environm & Energy Sci & Res Branch Dept Environm Engn Tehran Iran Islamic Azad Univ Tehran Med Sci Branch Grad Sch Publ Hlth Dept Environm Hlth Engn Tehran Iran Islamic Azad Univ Tehran Med Sci Branch WPRC Tehran Iran Khaghani St Shariati AvePOB 19395-1495 Tehran Iran

A novel approach was applied for optimization of a moving-bed biofilm sequencing batch reactor (MBSBR) to treat sugar-industry wastewater (BOD5 = 500-2500 and COD = 750-3750 mg/L) at 2-4 h of cycle time (CT). Although the experimental data showed that MBSBR reached high BOD5 and COD removal performances, it failed to achieve the standard limits at the mentioned CTs. Thus, optimization of the reactor was rendered by kinetic computational modeling and using statistical error indicator normalized root mean square error (NRMSE). The results of NRMSE revealed that Stover-Kincannon (error = 6.40%) and Grau (error = 6.15%) models provide better fits to the experimental data and may be used for CT optimization in the reactor. The models predicted required CTs of 4.5, 6.5, 7 and 7.5 h for effluent standardization of 500, 1000, 1500 and 2500 mg/L influent BOD5 concentrations, respectively. Similar pattern of the experimental data also confirmed these findings. (C) 2016 Elsevier Ltd. All rights reserved.

关键词： Kinetic modeling Optimization Industrial wastewater Performance prediction computational modeling

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A Comprehensive computational modeling Approach for AlGaN/GaN HEMTs

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IEEE TRANSACTIONS ON NANOTECHNOLOGY 2016年第6期15卷 947-955页

作者： Joshi, Vipin Soni, Ankit Tiwari, Shree Prakash Shrivastava, Mayank Indian Inst Technol Dept Elect Engn Jodhpur 342001 Rajasthan India Indian Inst Sci Adv Nanoelect Device & Circuit Res Lab Dept Elect Syst Engn Bangalore 560012 Karnataka India

This paper for the first time presents a comprehensive computational modeling approach for AlGaN/GaN high electron mobility transistors. Impact of the polarization charge at different material interfaces on the energy band profile as well as parasitic charge across the epitaxial stack is modeled and studied. Furthermore, impact of surface and bulk traps on two-dimensional electron gas, device characteristics, and gate leakage is accounted in this paper. For the first time, surface states modeled as donor type traps were correlated with gate leakage. Moreover, a new approach to accurately model the forward gate leakage in Schottky gate devices is proposed. Finally, impact of lattice and carrier heating is studied, while highlighting the relevance of carrier heating, lattice heating, and bulk traps over the device characteristics. In addition to this, modeling strategy for other critical aspects like parasitic charges, quantum effects, S/D Schottky contacts, and high field effects is presented.

关键词： AlGaN/GaN computational modeling HEMT hot electrons surface traps 2-DEG

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Neural mechanisms of transient neocortical beta rhythms: Converging evidence from humans, computational modeling, monkeys, and mice

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2016年第33期113卷 E4885-E4894页

作者： Sherman, Maxwell A. Lee, Shane Law, Robert Haegens, Saskia Thorn, Catherine A. Hamalainen, Matti S. Moore, Christopher I. Jones, Stephanie R. Brown Univ Dept Neurosci Providence RI 02912 USA Brown Univ Dept Appl Math Providence RI 02912 USA Nathan S Kline Inst Psychiat Res Cognit Neurosci & Schizophrenia Program Orangeburg NY 10962 USA Columbia Univ Coll Phys & Surg Dept Neurol Surg New York NY 10032 USA Massachusetts Gen Hosp Athinola A Martinos Ctr Boston MA 02129 USA Aalto Univ Sch Sci Dept Neurosci & Biomed Engn Espoo 02150 Finland Harvard Med Sch Boston MA 02115 USA

Human neocortical 15-29-Hz beta oscillations are strong predictors of perceptual and motor performance. However, the mechanistic origin of beta in vivo is unknown, hindering understanding of its functional role. Combining human magnetoencephalography (MEG), computational modeling, and laminar recordings in animals, we present a new theory that accounts for the origin of spontaneous neocortical beta. In our MEG data, spontaneous beta activity from somatosensory and frontal cortex emerged as noncontinuous beta events typically lasting < 150 ms with a stereotypical waveform. computational modeling uniquely designed to infer the electrical currents underlying these signals showed that beta events could emerge from the integration of nearly synchronous bursts of excitatory synaptic drive targeting proximal and distal dendrites of pyramidal neurons, where the defining feature of a beta event was a strong distal drive that lasted one beta period (similar to 50 ms). This beta mechanism rigorously accounted for the beta event profiles;several other mechanisms did not. The spatial location of synaptic drive in the model to supragranular and infragranular layers was critical to the emergence of beta events and led to the prediction that beta events should be associated with a specific laminar current profile. Laminar recordings in somatosensory neocortex from anesthetized mice and awake monkeys supported these predictions, suggesting this beta mechanism is conserved across species and recording modalities. These findings make several predictions about optimal states for perceptual and motor performance and guide causal interventions to modulate beta for optimal function.

关键词： beta rhythm magnetoencephalography computational modeling sensorimotor processing Parkinson's disease

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Spatiotemporal dynamics of the Ebola epidemic in Guinea and implications for vaccination and disease elimination: a computational modeling analysis

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BMC MEDICINE 2016年第1期14卷 1-10页

作者： Ajelli, Marco Merler, Stefano Fumanelli, Laura Pastore y Piontti, Ana Dean, Natalie E. Longini, Ira M., Jr. Halloran, M. Elizabeth Vespignani, Alessandro Bruno Kessler Fdn Via Sommar 18 I-38123 Trento Italy Northeastern Univ Lab Modeling Biol & Sociotech Syst 360 Huntington Ave Boston MA 02115 USA Univ Florida Dept Biostat 2004 Mowry Rd Gainesville FL 32611 USA Fred Hutchinson Canc Res Ctr Vaccine & Infect Dis Div 1100 Fairview Ave N Seattle WA 98109 USA Univ Washington Sch Publ Hlth 1959 NE Pacific St Seattle WA 98195 USA Harvard Univ Inst Quantitat Social Sci 1737 Cambridge St Cambridge MA 02138 USA Inst Sci Interchange Fdn Via Alassio 11-C I-10126 Turin Italy

Background: Among the three countries most affected by the Ebola virus disease outbreak in 2014-2015, Guinea presents an unusual spatiotemporal epidemic pattern, with several waves and a long tail in the decay of the epidemic incidence. Methods: Here, we develop a stochastic agent-based model at the level of a single household that integrates detailed data on Guinean demography, hospitals, Ebola treatment units, contact tracing, and safe burial interventions. The microsimulation-based model is used to assess the effect of each control strategy and the probability of elimination of the epidemic according to different intervention scenarios, including ring vaccination with the recombinant vesicular stomatitis virus-vectored vaccine. Results: The numerical results indicate that the dynamics of the Ebola epidemic in Guinea can be quantitatively explained by the timeline of the implemented interventions. In particular, the early availability of Ebola treatment units and the associated isolation of cases and safe burials helped to limit the number of Ebola cases experienced by Guinea. We provide quantitative evidence of a strong negative correlation between the time series of cases and the number of traced contacts. This result is confirmed by the computational model that suggests that contact tracing effort is a key determinant in the control and elimination of the disease. In data-driven microsimulations, we find that tracing at least 5-10 contacts per case is crucial in preventing epidemic resurgence during the epidemic elimination phase. The computational model is used to provide an analysis of the ring vaccination trial highlighting its potential effect on disease elimination. Conclusions: We identify contact tracing as one of the key determinants of the epidemic's behavior in Guinea, and we show that the early availability of Ebola treatment unit beds helped to limit the number of Ebola cases in Guinea.

关键词： computational modeling Intervention strategies Ebola epidemiology

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Allostatic Load as a Complex Clinical Construct: A Case-Based computational modeling Approach

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COMPLEXITY 2016年第S1期21卷 291-306页

作者： Buckwalter, J. Galen Castellani, Brian McEwen, Bruce Karlamangla, Arun S. Rizzo, Albert A. John, Bruce O'Donnell, Kyle Seeman, Teresa Univ Southern Calif Inst Creat Technol Los Angeles CA 90094 USA Kent State Univ Dept Sociol Kent OH 44240 USA Rockefeller Univ Neuroendocrinol Lab New York NY 10065 USA Univ Calif Los Angeles David Geffen Sch Med Div Geriatr Los Angeles CA 90095 USA

Allostatic load (AL) is a complex clinical construct, providing a unique window into the cumulative impact of stress. However, due to its inherent complexity, AL presents two major measurement challenges to conventional statistical modeling (the field's dominant methodology): it is comprised of a complex causal network of bioallostatic systems, represented by an even larger set of dynamic biomarkers;and, it is situated within a web of antecedent socioecological systems, linking AL to differences in health outcomes and disparities. To address these challenges, we employed case-based computational modeling (CBM), which allowed us to make four advances: (1) we developed a multisystem, 7-factor (20 biomarker) model of AL's network of allostatic systems;(2) used it to create a catalog of nine different clinical AL profiles (causal pathways);(3) linked each clinical profile to a typology of 23 health outcomes;and (4) explored our results (post hoc) as a function of gender, a key socioecological factor. In terms of highlights, (a) the Healthy clinical profile had few health risks;(b) the pro-inflammatory profile linked to high blood pressure and diabetes;(c) Low Stress Hormones linked to heart disease, TIA/Stroke, diabetes, and circulation problems;and (d) high stress hormones linked to heart disease and high blood pressure. Post hoc analyses also found that males were overrepresented on the High Blood Pressure (61.2%), Metabolic Syndrome (63.2%), High Stress Hormones (66.4%), and High Blood Sugar (57.1%);while females were overrepresented on the Healthy (81.9%), Low Stress Hormones (66.3%), and Low Stress Antagonists (stress buffers) (95.4%) profiles. (C) 2015 Wiley Periodicals, Inc.

关键词： allostatic load health risk outcomes complexity theory artificial neural nets computational modeling case-based modeling

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