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A Bayesian model calibration framework for stochastic compartmental models with both time-varying and timeinvariant parameters

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Infectious Disease Modelling 2024年第4期9卷 1224-1249页

作者： brandon Robinson Philippe Bisaillon Jodi D.Edwards Tetyana Kendzerska Mohammad Khalil Dominique Poirel Abhijit Sarkar Department of Civil and Environmental Engineering Carleton UniversityOttawaON K1S 5B6Canada School of Epidemiology and Public Health University of Ottawa and University of Ottawa Heart InstituteOttawaOntarioCanada ICES OttawaOntarioCanada The Ottawa Hospital Research Institute OttawaOntarioCanada Department of Medicine Faculty of MedicineDivision of RespirologyUniversity of OttawaOttawaOntarioCanada Quantitative Modeling&Analysis Department Sandia National LaboratoriesLivermoreCAUSA Department of Mechanical and Aerospace Engineering Royal Military College of CanadaKingstonONCanada

We consider state and parameter estimation for compartmental models having both timevarying and time-invariant *** this manuscript,we first detail a general Bayesian computational framework as a continuation of our previous ***,this framework is specifically tailored to the susceptible-infectious-removed(SIR)model which describes a basic mechanism for the spread of infectious diseases through a system of coupled nonlinear differential *** SIR model consists of three states,namely,the susceptible,infectious,and removed *** coupling among these states is controlled by two parameters,the infection rate and the recovery *** simplicity of the SIR model and similar compartmental models make them applicable to many classes of infectious ***,the combined assumption of a deterministic model and time-invariance among the model parameters are two significant impediments which critically limit their use for long-term *** tendency of certain model parameters to vary in time due to seasonal trends,non-pharmaceutical interventions,and other random effects necessitates a model that structurally permits the incorporation of such time-varying *** to this,is the need for a robust mechanism for the estimation of the parameters of the resulting model from *** this end,we consider an augmented state vector,which appends the time-varying parameters to the original system states whereby the time evolution of the time-varying parameters are driven by an artificial noise process in a standard *** between time-varying and time-invariant parameters in this fashion limits the introduction of artificial dynamics into the system,and provides a robust,fully Bayesian approach for estimating the timeinvariant system parameters as well as the elements of the process noise covariance *** computational framework is implemented by leveraging the robustness of the Markov chain Mont

关键词： Time-varying parameter estimation Bayesian inference Stochastic compartmental models

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Laboratory studies of rice bran as a carbon source to stimulate indigenous microorganisms in oil reservoirs

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Petroleum Science 2016年第3期13卷 572-583页

作者： Chun-Mao Chen Jin-Ling Wang Jung Bong Kim Qing-Hong Wang Jing Wang brandon A.Yoza Qing X.Li State Key Laboratory of Heavy Oil Processing China University of Petroleum Department of Molecular Biosciences and Bioengineering University of Hawaii at Manoa Department of Agro-Food Resources National Institute of Agricultural SciencesRural Development Administration Hawaii Natural Energy Institute University of Hawaii at Manoa

There is a great interest in developing cost-efficient nutrients to stimulate microorganisms in indigenous microbial enhanced oil recovery（IMEOR） *** the present study,the potential of rice bran as a carbon source for promoting IMEOR was investigated on a laboratory *** co-applications of rice bran,K2HPO4 and urea under optimized bio-stimulation conditions significantly increased the production of gases,acids and *** structure and diversity of microbial community greatly changed during the IMEOR process,in which Clostridium sp.,Acidobacteria sp.,Bacillus sp.,and Pseudomonas *** ***,acidification and emulsification due to microbial activities and interactions markedly improved the IMEOR *** study indicated that rice bran is a potential carbon source for IMEOR.

关键词： Rice bran Bio-stimulation Petroleum Microbial diversity Indigenous microbial enhanced oil recovery

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Recent advances in the diagnostic evaluation of pancreatic cystic lesions

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World Journal of Gastroenterology 2022年第6期28卷 624-634页

作者： Devarshi R Ardeshna Troy Cao brandon Rodgers Chidiebere Onongaya Dan Jones Wei Chen Eugene J Koay Somashekar G Krishna Department of Internal Medicine Ohio State University Wexner Medical CenterColumbusOH 43210United States College of Medicine Ohio State UniversityColumbusOH 43210United States James Molecular Laboratory Ohio State University Wexner Medical CenterColumbusOH 43210United States Department of Pathology Ohio State University Wexner Medical CenterColumbusOH 43210United States Department of GI Radiation Oncology The University of Texas MD AndersonHoustonTX77030United States Division of Gastroenterology Department of Internal MedicineOhio State University Wexner Medical CenterColumbusOH 43210United States

Pancreatic cystic lesions(PCLs)are becoming more prevalent due to more frequent abdominal imaging and the increasing age of the general *** has become crucial to identify these PCLs and subsequently risk stratify them to guide *** the high morbidity associated with pancreatic surgery,only those PCLs at high risk for malignancy should undergo such ***,current diagnostic testing is suboptimal at accurately diagnosing and risk stratifying ***,research has focused on developing new techniques for differentiating mucinous from non-mucinous PCLs and identifying high risk lesions for *** sectional imaging radiomics can potentially improve the predictive accuracy of primary risk stratification of PCLs at the time of detection to guide invasive *** cyst fluid glucose has reemerged as a potential biomarker,cyst fluid molecular markers have improved accuracy for identifying specific types of *** ultrasound guided approaches such as confocal laser endomicroscopy and through the needle microforceps biopsy have shown a good correlation with histopathological findings and are evolving techniques for identifying and risk stratifying *** most of these recent diagnostics are only practiced at selective tertiary care centers,they hold a promise that management of PCLs will only get better in the future.

关键词： Pancreatic cystic lesion Intraductal papillary mucinous neoplasms Mucinous cystic neoplasm Microforceps biopsy Radiomics Confocal laser endomicroscopy

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AdsorbML: a leap in efficiency for adsorption energy calculations using generalizable machine learning potentials

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npj Computational Materials 2023年第1期9卷 565-573页

作者： Janice Lan Aini Palizhati Muhammed Shuaibi brandon M.Wood Brook Wander Abhishek Das Matt Uyttendaele C.Lawrence Zitnick Zachary W.Ulissi Fundamental AI Research(FAIR) Meta AIMetaMenlo ParkCAUSA Department of Chemical Engineering Carnegie Mellon UniversityPittsburghPAUSA Scott Institute for Energy Innovation Carnegie Mellon UniversityPittsburghPAUSA

Computational catalysis is playing an increasingly significant role in the design of catalysts across a wide range of applications.A common task for many computational methods is the need to accurately compute the adsorption energy for an adsorbate and a catalyst surface of ***,the identification of low-energy adsorbate-surface configurations relies on heuristic methods and researcher *** the desire to perform high-throughput screening increases,it becomes challenging to use heuristics and intuition *** this paper,we demonstrate machine learning potentials can be leveraged to identify low-energy adsorbate-surface configurations more accurately and *** algorithm provides a spectrum of trade-offs between accuracy and efficiency,with one balanced option finding the lowest energy configuration 87.36%of the time,while achieving a~2000×speedup in *** standardize benchmarking,we introduce the Open Catalyst Dense dataset containing nearly 1000 diverse surfaces and~100,000 unique configurations.

关键词： adsorption configuration energy

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Fluorescence and SEM correlative microscopy for nanomanipulation of subcellular structures

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Light(Science & Applications) 2014年第1期3卷 13-19页

作者： Zheng Gong brandon K Chen Jun Liu Chao Zhou Dave Anchel Xiao Li Ji Ge David P Bazett-Jones Yu Sun Advanced Micro and Nanosystems Laboratory University of TorontoTorontoON M5S 3G8Canada State Key Laboratory of Intelligent Control and Management of Complex Systems Institute of AutomationChinese Academy of SciencesBeijing 100190China The Genetics and Genome Biology Program the Hospital for Sick ChildrenTorontoON M5G 1X8Canada

Nanomanipulation under scanning electron microscopy(SEM)enables direct interactions of a tool with a *** recently developed a nanomanipulation technique for the extraction and identification of DNA contained within sub-nuclear locations of a single cell *** nanomanipulation of sub-cellular structures,a key step is to identify targets of interest through correlating fluorescence and SEM *** DNA extraction task must be conducted with low accelerating voltages resulting in low imaging *** is imposed by the necessity of preserving the biochemical integrity of the *** poor imaging conditions make the identification of nanometer-sized fiducial marks *** paper presents an affine scale-invariant feature transform(ASIFT)based method for correlating SEM images and fluorescence microscopy *** performance of the image correlation approach under different noise levels and imaging magnifications was quantitatively *** optimal mean absolute error(MAE)of correlation results is 68634 nm under standard *** with manual correlation by skilled operators,the automated correlation approach demonstrates a speed that is higher by an order of *** the SEM-fluorescence image correlation approach,targeted DNA was successfully extracted via nanomanipulation under SEM conditions.

关键词： correlative microscopy fluorescence image correlation nanomanipulation SEM subcellular structures

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Nitro-PAH exposures of occupationally-exposed traffic workers and associated urinary 1-nitropyrene metabolite concentrations

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Journal of Environmental Sciences 2016年第11期28卷 213-221页

作者： Justin P.Miller-Schulze Michael Paulsen Takayuki Kameda Akira Toriba Kazuichi Hayakawa brandon Cassidy Luke Naeher Manuel Aguilar Villalobos Christopher D.Simpson Department of Chemistry University of Washington WA 98195-1700 USA. Department of Environmental and Occupational Health Sciences University of Washington WA 98195 Seattle USA Laboratory of Hygienic Chemistry Instkute of Medical Pharmaceutical and Health Sciences Faculty of Pharmacy Kanazawa UniversityKakurna-machi Kanazawa Ishikawa 920-1192 Japan Graduate School of Natural Science and Technology Kanazawa University Kakma-machi Kanazawa Ishikawa 920-1192 Japan Department of Enuironmental Health Sciences University of Georgia Athens CA 30602-2102 USA Asociacion del Aire Ambiental Lima Peru

The assessment of occupational exposure to diesel exhaust（DE） is important from an epidemiological perspective. Urinary biomarkers of exposure have been proposed as a novel approach for measuring exposure to DE. In this study, we measured the concentrations of two urinary metabolites of 1-nitropyrene（1NP）, a nitrated polycyclic aromatic hydrocarbon that has been suggested as a molecular marker of diesel particulate matter. These two metabolites, 6-hydroxy-1-nitropyrene and 8-hydroxy-1-nitropyrene, were determined in urine samples（10 m L） from a small group of workers who were occupationally-exposed to vehicle exhaust in Trujillo, Peru, before and after their workshifts. Workshift exposures to1 NP, as well as PM_（2.5）, 2-nitropyrene and 2-nitrofluoranthene, were also *** to 1NP were similar in all studied workers, averaging 105 ± 57.9 pg/m^3（±standard deviation）. Median urinary concentrations of the average of the pre- and post-exposure samples for 6-hydroxy-1-nitropyrene and 8-hydroxy-1-nitropyrene, were found to be 3.9 and 2.3 pg metabolite/mg creatinine, respectively in the group of occupationally-exposed subjects（n = 17） studied. A direct relationship between workshift exposure to 1NP and urinary 1NP metabolites concentrations was not observed. However,the 1NP exposures and the creatinine-corrected urinary concentrations of the hydroxynitropyrene metabolites in these Peruvian traffic workers were similar to occupationally-exposed taxi drivers in Shenyang, China, and were higher than biomarker levels in office workers from Trujillo without occupational exposure to vehicle *** study provides further evidence that urinary metabolites of 1NP are associated with exposure to DE and may serve as a useful exposure biomarker.

关键词： Urinary biomarkers 1-Nitropyrene Diesel particulate matter

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Advanced breast cancer metastasized in the brain: treatment standards and innovations

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Journal of Cancer Metastasis and Treatment 2023年第1期9卷 170-184页

作者： Elizabeth Klaas Eric Sung Esaan Azizi Melanie Martinez Arnav Barpujari Jeffery Roberts brandon Lucke-Wold Department of Neurosurgery University of FloridaGainesvilleFL 32610USA

Breast cancer continues to be a difficult disease to treat due to high rates of *** to the brain presents a unique and often overlooked *** this focused review,we discuss the epidemiology of breast cancer and which types frequently metastasize to the *** treatment approaches are highlighted with supporting scientific *** role of the blood-brain barrier and how it may become altered with metastasis is *** then highlight new innovations for Her2-positive and triple-negative breast ***,recent directions for luminal breast cancer are *** review serves to enhance understanding of pathophysiology,spark continued innovation,and provide a user-friendly resource through tables and easy-to-process figures.

关键词： Breast cancer innovation blood-brain barrier luminal metastasis new directions

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The Time Horizon in the Evaluation of Sustainable Development

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Journal of Civil Engineering and Architecture 2012年第3期6卷 334-343页

作者： Manila De Iuliis Peter brandon Building and Planning Office Town Hall Lungomare D 'Albertis 4 Santo Stefano al Mare Imperia Italy School of the Built Environment University of Salford UK

Current methods of evaluating long term Sustainable Development seldom take into account the time period over which an evaluation is made except through simplistic economic models which heavily discount the future. If sustainable development is to be a serious issue then the impact on the future of decisions made today must be properly assessed and evaluated. This requires a new understanding of time as a key feature of the Sustainability debate and new models of how this new understanding can be brought into the evaluation process. This was at the heart of the Torino declaration signed by the University organisations of the G8, G20 and developing nations in April 2009. Time is a critical part of the sustainability debate and is seldom addressed directly. This paper will provide a possible solution based on a strong theoretical and philosophical framework of how this difficult subject can be approached and applied to sustainable urban planning. The work presented is based on a philosophical model of the cosmos which has both internal and external credibility. It forms the basis ofa PhD study and has been applied to small case studies in Italy and elsewhere. These will be presented to encourage further study into this important area within the evaluation and assessment of sustainable development.

关键词： Time sustainable development sustainable urban planning temporal analysis.

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Natural exosome-like nanovesicles from edible tea flowers suppress metastatic breast cancer via ROS generation and microbiota modulation

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Acta Pharmaceutica Sinica B 2022年第2期12卷 907-923页

作者： Qiubing Chen Qian Li Yuqi Liang Menghang Zu Nanxi Chen brandon S.B.Canup Liyong Luo Chenhui Wang Liang Zeng Bo Xiao State Key Laboratory of Silkworm Genome Biology College of SericultureTextileand Biomass SciencesSouthwest UniversityChongqing 400715China Chongqing Key Laboratory of Soft-Matter Material Chemistry and Function Manufacturing School of Materials and EnergySouthwest UniversityChongqing 400715China Department of Chemistry Center for Diagnostics and TherapeuticsGeorgia State UniversityAtlantaGA 30303USA College of Food Science Southwest UniversityChongqing 400715China Chongqing Key Laboratory of Natural Product Synthesis and Drug Research School of Pharmaceutical SciencesChongqing UniversityChongqing 401331China

Although several artificial nanotherapeutics have been approved for practical treatment of metastatic breast cancer,their inefficient therapeutic outcomes,serious adverse effects,and high cost of mass production remain crucial ***,we developed an alternative strategy to specifically trigger apoptosis of breast tumors and inhibit their lung metastasis by using natural nanovehicles from tea flowers(TFENs).These nanovehicles had desirable particle sizes(131 nm),exosome-like morphology,and negative zeta ***,TFENs were found to contain large amounts of polyphenols,flavonoids,functional proteins,and *** experiments revealed that TFENs showed strong cytotoxicities against cancer cells due to the stimulation of reactive oxygen species(ROS)*** increased intracellular ROS amounts could not only trigger mitochondrial damage,but also arrest cell cycle,resulting in the in vitro anti-proliferation,anti-migration,and anti-invasion activities against breast cancer *** mice investigations demonstrated that TFENs after intravenous(i.v.)injection or oral administration could accumulate in breast tumors and lung metastatic sites,inhibit the growth and metastasis of breast cancer,and modulate gut *** study brings new insights to the green production of natural exosome-like nanoplatform for the inhibition of breast cancer and its lung metastasis via *** oral routes.

关键词： Tea flower Exosome-like nanoparticle Breast cancer Metastasis ROS generation Microbiota modulation Intravenous injection Oral administration

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Pylephlebitis-induced acute liver failure: A case report and review of literature

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World Journal of Hepatology 2024年第1期16卷 103-108页

作者： Vera Hapshy Steven Imburgio Harshavardhan Sanekommu brandon Nightingale Sobaan Taj Mohammad A Hossain Swapnil Patel Department of Internal Medicine Jersey Shore University Medical CenterNeptuneNJ 07753United States

BACKGROUND Pylephlebitis is an extremely rare form of septic thrombophlebitis involving the portal vein,carrying high rates of morbidity and *** SUMMARY We present a case of a 42-year-old male with no past medical history who presented with acute onset of abdominal pain and altered mental status with laboratory tests demonstrating new-onset acute liver *** was determined to be the underlying etiology due to subsequent workup revealing polymicrobial gram-negative anaerobic bacteremia and complete thrombosis of the main and left portal *** our knowledge,this is the first documented case of acute liver failure as a potential life-threatening complication of *** Our case highlights the importance of considering pylephlebitis in the broad differential for abdominal pain,especially if there are co-existing risk factors for *** also demonstrate that fulminant hepatic failure in these patients can potentially be reversible with the immediate initiation of antibiotics and anticoagulation.

关键词： Portal vein thrombosis Septic thrombophlebitis Gram negative anaerobic bacteremia Pylephlebitis Acute liver failure Case report

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