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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

IoT-Enabled Autonomous System Collaboration for Disaster-Area Management

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IEEE/CAA Journal of Automatica Sinica 2020年第5期7卷 1249-1262页

作者： Abenezer Girma Niloofar Bahadori Mrinmoy sarkar Tadewos G.Tadewos mohammad R.Behnia M.Nabil Mahmoud Ali Karimoddini Abdollah Homaifar IEEE Department of Electrical and Computer Engineering North Carolina A&T State UniversityGreensboroNC 27411 USA

Timely investigating post-disaster situations to locate survivors and secure hazardous sources is critical,but also very challenging and *** first responders putting their lives at risk in saving others,human-physical limits cause delays in response time,resulting in fatality and property *** this paper,we proposed and implemented a framework intended for creating collaboration between heterogeneous unmanned vehicles and first responders to make search and rescue operations safer and *** framework consists of unmanned aerial vehicles(UAVs),unmanned ground vehicles(UGVs),a cloud-based remote control station(RCS).A light-weight message queuing telemetry transport(MQTT)based communication is adopted for facilitating collaboration between autonomous *** effectively work under unfavorable disaster conditions,antenna tracker is developed as a tool to extend network coverage to distant areas,and mobile charging points for the UAVs are also *** proposed framework’s performance is evaluated in terms of end-to-end delay and analyzed using architectural analysis and design language(AADL).Experimental measurements and simulation results show that the adopted communication protocol performs more efficiently than other conventional communication protocols,and the implemented UAV control mechanisms are functioning *** scenarios are implemented to validate the overall effectiveness of the proposed framework and demonstrate possible use cases.

关键词： Architectural analysis and design language(AADL)and cloud computing disaster area management internet of things(IoT) message queuing telemetry transport(MQTT) unmanned aerial vehicle(UAV) unmanned ground vehicle(UGV)

In Silico Screening of Natural Products as Potential Inhibitors of SARS-CoV-2 Using Molecular Docking Simulation

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Chinese Journal of Integrative Medicine 2022年第3期28卷 249-256页

作者： Rajib Hossain Chandan sarkar Shardar mohammad Hafiz Hassan Rasel Ahmed Khan mohammad Arman Pranta Ray Muhammad Torequl Islam Sevgi Durna Dastan Javad Sharifi-Rad Zainab M. Almarhoon Miquel Martorell William N. Setzer Daniela Calina Department of Pharmacy Life Science FacultyBangabandhu Sheikh Mujibur Rahman Science and Technology UniversityGopalganj(8100)Bangladesh Harmacy Discipline Life Science SchoolKhulna UniversityKhulna-9280Bangladesh Departme nt of Pharmacy In ternational Islamic UniversityChittagongBangladesh Department of Biomedical Engin eeri ng Huazho ng Un iversity of Science and Tech no logyWuhan(430074)China Department of Biology Faculty of ScienceSivas Cumhuriyet UniversitySivas(58140)Turkey Beekeeping Development Application and Research Center Sivas Cumhuriyet UniversitySivas(58140)Turkey School of Medicine University of AzuayCuencaEcuador Department of Chemistry College of ScienceKing Saud UniversityRiyadh(11451)Saudi Arabia Department of Nutrition and Dietetics Faculty of Pharmacyand Centre for Healthy LivingUniversity of ConcepcionConcepcion(4070386)Chile Department of Chemistry University of Alabama in HuntsvilleHuntsvilleAL(35899)USA Aromatic Plant Research Center 230 N 1200 ESuite 100LehiUT(84043)USA Department of Clinical Pharmacy University of Medicine and Pharmacy of CraiovaCraiova(200349)Romania

Objective:To explore potential natural products against severe acute respiratory syndrome coronavirus(SARS-CoV-2)via the study of structural and non-structural proteins of human ***:In this study,we performed an in-silico survey of 25 potential natural compounds acting against *** docking studies were carried out using compounds against 3-chymotrypsin-like protease(3 CL^(PHO)),papain-like protease(PL^(PRO)),RNA-dependent RNA polymerase(RdRp),non-structural protein(nsp),human angiotensin converting enzyme 2 receptor(hACE2 R),sapike glycoprotein(S protein),abelson murine leukemia viral oncogene homolog 1(ABL1),calcineurin-nuclear factor of activated T-cells(NFAT)and transmembrane protease serine ***:Among the screened compounds,amentoflavone showed the best binding affinity with the 3 CL^(PRO),RdRp,nsp13,nsp15,hACE2 R,ABL1 and calcineurin-NFAT;berbamine with hACE2 R and ABL1;cepharanthine with nsp10,nsp14,nsp16,S protein and ABL1;glucogallin with nsp15;and papyriflavonol A with PL^(PRO)*** good interacting compounds were juglanin,betulinic acid,betulonic acid,broussooflavan A,tomentin A,B and E,7-methoxycryptopleurine,aloe emodin,quercetin,tanshinone I,tylophorine and furruginol,which also showed excellent binding affinity towards a number of target *** of these compounds showed better binding affinities towards the target proteins than the standard drugs used in this ***:Natural products or their derivatives may be one of the potential targets to fight against SARS-CoV-2.

关键词： SARS-CoV-2 natural products-derived anti-SARS-CoV-2 candidates structural proteins nonstructural proteins molecular docking

Security in Multicast Over α-μ Fading Channels with Orthogonal Frequency Division Multiplexing

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Journal of Computer and Communications 2022年第11期10卷 72-90页

作者： mohammad Mahmud Hasan Md. Zahurul Islam sarkar Department of Electrical and Electronic Engineering Rajshahi University of Engineering and Technology Rajshahi Bangladesh

The orthogonal space-frequency block coding (OSFBC) with orthogonal frequency division multiplexing (OFDM) system reduces complexity in the receiver which improves the system performance significantly. Motivated by these advantages of OSFBC-OFDM system, this paper considers a secure wireless multicasting scenario through multiple-input multiple-output (MIMO) OFDM system employing OSFBC over frequency selective α-μ fading channels. The authors are interested to protect the desired signals from eavesdropping considering the impact of the number of multicast users and eavesdroppers, and the fading parameters α and μ. A mathematical model has been developed based on the closed-form analytical expressions of the probability of non-zero secrecy multicast capacity (PNSMC) and the secure outage probability for multi-casting (SOPM) to ensure the security in the presence of multiple eaves-droppers. The results show that the security in MIMO OSFBC OFDM system over α-μ fading is more sensitive to the magnitude of α and μ and this effect increases in the high signal-to-noise ratio (SNR) region of the main channel.

关键词： Orthogonal Space-Frequency Block Coding Orthogonal Frequency Division Multiplexing Probability of Non-Zero Secrecy Multicast Capacity Secure Outage Probability for Multicasting

Long-Term Suboxone Maintenance Therapy for Opioid Use Disorder: 2 Case Reports

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Open Journal of Psychiatry 2016年第2期6卷 191-194页

作者： Akikur mohammad Joshua Busse Rebecca Ninah Shub Alexandria sarkar Department of Psychiatry LAC-USC Los Angeles CA USA

The medical profession is divided in its approach to treating patients with addiction issues, particularly in regards to the treatment of opioid use disorder with Suboxone (buprenorphine/naloxone). Here we present two cases of patients who have achieved over 11 years of sobriety with long-term Suboxone maintenance therapy. Their stories help to demonstrate that Suboxone is a viable long-term treatment option for severe opioid addiction. While life-long Suboxone use can lead to physical dependence on the drug, this is far from simply replacing one addiction with another. Some providers may feel that physical dependence on a medication does not represent appropriate or adequate treatment of opioid use disorder;however, when compared with the grave potential consequences of severe opioid use disorder, the potential benefits of achieving sobriety with Suboxone maintenance far outweigh the risks.

关键词： Suboxone Buprenorphine Naloxone Opioid Use Disorder Long-Term

Addiction Treatment Aftercare Outcome Study

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Open Journal of Psychiatry 2017年第1期7卷 51-60页

作者： Akikur mohammad Kristopher J. Irizarry Rebecca Ninah Shub Alexandria sarkar Department of Psychiatry LAC-USC Los Angeles CA USA

Aftercare is crucial once an individual has completed drug or alcohol treatment and is in recovery. There is a continuity of care that should be followed once initial treatment is completed. This usually involves a lower level of treatment such as outpatient care and a sober living environment. In order to assess the efficacy and benefit of our addiction treatment program, we investigate a set of patients in which addiction treatment outcome and rehabilitation is determined for patients who have completed treatment and followed up. We determine abstinence rates and identify predictors of treatment outcome.

关键词： Addiction Treatment Dual Diagnosis Dependence Abstinence Naltrexone Vivitrol Antabuse Acamprosate

Secure Wireless Multicasting through Nakagami-m Fading Channels with Multi-Hop Relaying

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Journal of Computer and Communications 2023年第5期11卷 177-193页

作者： Md. Mizanur Rahman Md. Zahurul Islam sarkar mohammad Mahmud Hasan Department of Electrical and Electronic Engineering RUET Rajshahi Bangladesh

The additional diversity gain provided by the relays improves the secrecy capacity of communications system significantly. The multiple hops in the relaying system is an important technique to improve this diversity gain. The development of an analytical mathematical model of ensuring security in multicasting through fading channels incorporating this benefit of multi-hop relaying is still an open problem. Motivated by this issue, this paper considers a secure wireless multicasting scenario employing multi-hop relaying technique over frequency selective Nakagami-m fading channel and develops an analytical mathematical model to ensure the security against multiple eavesdroppers. This mathematical model has been developed based on the closed-form analytical expressions of the probability of non-zero secrecy multicast capacity (PNSMC) and the secure outage probability for multicasting (SOPM) to ensure the security in the presence of multiple eavesdroppers. Moreover, the effects of the fading parameter of multicast channel, the number of hops and eavesdropper are investigated. The results show that the security in multicasting through Nakagami-m fading channel with multi-hop relaying system is more sensitive to the number of hops and eavesdroppers. The fading of multicast channel helps to improve the secrecy multicast capacity and is not the enemy of security in multicasting.

关键词： Frequency Selective Fading Multi-Hop Relaying Probability of Non-Zero Secrecy Multicast Capacity Secure Outage Probability for Multicasting

Evaluation of Physicochemical Properties and Antioxidant Activity of Wheat-Red Kidney Bean Biscuits

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World Journal of Engineering and Technology 2020年第4期8卷 689-699页

作者： Mukta Roy Sheikh mohammad Nasirul Haque Rana Das Manobendro Sarker Md. Azmain Al Faik Shagor sarkar Department of Food Engineering and Tea Technology Shahjalal University of Science and Technology Sylhet Bangladesh Department of Food Engineering and Technology State University of Bangladesh Dhaka Bangladesh Department of Biomass Energy Engineering Shanghai Jiao Tong University Shanghai China Department of Biosystems Engineering Gyeongsang National University Jinju Republic of Korea

This research was aimed to study the physicochemical properties and antioxidant activity of biscuits fortified with red kidney bean (Phaseolus vulgaris) powder. Proximate compositions, total phenol content, antioxidant activity, and functional properties of red kidney bean (RKB) powder were studied before and after the incorporation of red kidney bean in the biscuits. The bean powder was mixed with wheat flour at a level of 0% as control, 10%, 20%, and 30% during dough preparation. Results revealed that RKB powder is a rich source of protein (26.25%) together with carbohydrate (59.7%), fat (2.4%), and ash (3.27%). The total phenolic content of bean powder was 14.15 mg GAE/g. Kidney bean powder showed good functional properties including water absorption capacity (149.7%), oil holding capacity (99.54%), swelling capacity (4.6%), and bulk density of 0.74 g/ml. After increasing the percentage of RKB with control, there were significant increases (p < 0.05) in the levels of protein, moisture, ash, fat, while carbohydrate content and total gross energy decreased significantly. Investigation of total phenolic content showed the increasing trend with the higher RKB fortification, which amounted to 10.31 mg GAE/g for control and 12.50 mg GAE/g for 30% RKB. DPPH radical scavenging activity was investigated for all the samples at five different concentrations. As there was an increase in the percentage of RKB and concentration of the samples, the antioxidant activity also increased significantly (p < 0.05), where IC50 value decreased from 0.0228 mg/ml for control to 0.0289 mg/ml for 10% RKB, followed by 20% and 30% RKB, respectively. In sensory test, the control cake secured the highest score in color, f

关键词： Red Kidney Bean Biscuit Physicochemical Phenol Antioxidant Activity

DFT-Based Chemical Reactivity Descriptors, Pharmacokinetics and Molecular Docking Studies of Thymidine Derivatives

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Computational Chemistry 2023年第4期11卷 81-103页

作者： mohammad Ahad Hossain Shahin Sultana mohammad Mazherul Islam Sonia Akhter Faria Nur Fatima Majabin Kantom Islam Kazi Jawad Hossain Yasuhiro Ozeki sarkar M. A. Kawsar Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC) Department of Chemistry Faculty of Science University of Chittagong Bangladesh Graduate School of NanoBio Sciences Yokohama City University Yokohama Japan

Thymidine-containing derivatives are considered to be among the most significant derivatives in medicinal chemistry. In this study, we employed a combined computational approach involving density-functional theory (DFT) calculations, molecular docking simulations, and absorption, distribution, metabolism, excretion, and toxicity (ADMET) property predictions. Prediction of activity spectra for substances (PASS) revealed promising antiviral, antimicrobial and anti-carcinogenic activities of these thymidine derivatives. Using Gaussian 09, we optimized the molecular structures of the thymidine derivatives to obtain their stable conformations and calculate their electronic properties. Subsequently, molecular docking simulations were performed to explore the binding interactions between the thymidine derivatives and the active site of the Candida albicans (PDB: 1IYL and 2Y7L) proteins. The docking results were evaluated based on docking scores, hydrogen bonding, and hydrophobic interactions and revealed favorable binding interactions between the thymidine derivatives and the proteins, suggesting their potential as antifungal agents. The thermodynamic properties, including binding free energy, enthalpy, and entropy changes were determined to assess the stability and strength of the ligands-protein complexes. The calculated pharmacokinetic parameters, such as ADMET properties, provided insights into the drug-likeness and potential bioavailability of the thymidine derivatives. These results offer a foundation for further experimental investigations and the design of novel antifungal agents targeting Candida albicans infections.

关键词： Thymidine DFT Molecular Docking Pharmacokinetics Candida albicans