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Machine Learning Modeling of Protein-intrinsic Features Predicts Tractability of Targeted Protein Degradation

Genomics, Proteomics & Bioinformatics 2022年第5期20卷 882-898页

作者： Wubing Zhang shourya s.roy burman Jiaye Chen Katherine A.Donovan Yang Cao Chelsea shu Boning Zhang Zexian Zeng shengqing Gu Yi Zhang Dian Li Eric s.Fischer Collin Tokheim X.shirley Liu Department of Data science Dana-Farber Cancer InstituteBostonMA 02215USA Department of Biostatistics Harvard T.H.Chan School of Public HealthBostonMA 02115USA Department of Cancer Biology Dana-Farber Cancer InstituteBostonMA 02215USA Department of Biological Chemistry and Molecular Pharmacology Harvard Medical SchoolBostonMA 02115USA Department of Biomedical Informatics Harvard Medical SchoolBostonMA 02115USA Center of Growth Metabolismand AgingKey Laboratory of Bio-resource and Eco-environmentMinistry of EducationCollege of Life SciencesSichuan UniversityChengdu 610064China Research scholar Initiative Graduate School of Arts and SciencesHarvard UniversityCambridgeMA 02138USA

Targeted protein degradation(TPD)has rapidly emerged as a therapeutic modality to eliminate previously undruggable proteins by repurposing the cell’s endogenous protein degradation ***,the susceptibility of proteins for targeting by TPD approaches,termed“degradability”,is largely ***,we developed a machine learning model,model-free analysis of protein degradability(MAPD),to predict degradability from features intrinsic to protein *** shows accurate performance in predicting kinases that are degradable by TPD compounds[with an area under the precision–recall curve(AUPRC)of 0.759 and an area under the receiver operating characteristic curve(AUROC)of 0.775]and is likely generalizable to independent non-kinase *** found five features with statistical significance to achieve optimal prediction,with ubiquitination potential being the most *** structural modeling,we found that E2-accessible ubiquitination sites,but not lysine residues in general,are particularly associated with kinase ***,we extended MAPD predictions to the entire proteome to find964 disease-causing proteins(including proteins encoded by 278 cancer genes)that may be tractable to TPD drug development.

关键词： Targeted protein degradation Degradability Protein-intrinsic feature Ubiquitination Machine learning

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Biological analysis of an innovative biodegradable antibiotic eluting bioactive glass/gypsum composite bone cement for treating experimental chronic MRsA osteomyelitis

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Journal of Pharmaceutical Analysis 2022年第1期12卷 164-177页

作者： surajit Mistry subhasish burman subhasis.roy Nilendu Jyoti Maitra Rajiv roy Abhijit Chanda Department of Periodontics Burdwan Dental College&HospitalBurdwan713101India Department of Oral&Maxillofacial surgery Burdwan Dental College&HospitalBurdwan713101India Department of Veterinary Clinical Complex(surgery&Radiology) West Bengal University of Animal&Fishery SciencesKolkata700037India Directorate of Research Extension&Farms West Bengal University of Animal&Fishery SciencesKolkata700037India Department of Orthopaedics Calcutta National Medical College&HospitalKolkata700014India school of Bio-science&Engineering Jadavpur UniversityKolkata734432India

A multi-barrier antibiotics loaded biodegradable composite bone cement for resolving chronic osteomyelitis has been studied to understand the physico-mechanical properties,drug loading/eluting efficiency,and different merits and demerits prior to clinical *** successful induction of bone infection in 28 rabbits using methicillin-resistant staphylococcus aureus(MRsA)strains,calcium sulfate/bioactive glass based composite cement was implanted in 12 defects to assess its performance over parenteral therapy with microscopic and radiological examination for 90 *** composite cement revealed acceptable physico-mechanical properties and controlled drug elution ***,the antibiotics concentrations in bone up to 42 days were sufficient to kill MRsA without eliciting adverse drug *** striking feature of platelets aggregation by composite cement could assist bone *** controlled degradation with simultaneous entrapment of composite cement within the osteoid tissues and complete repair of infected cortical defects(holes)in rabbit tibia at 6 weeks indicated the excellent anti-infective and osteoconductive properties of composite ***,the animal study demonstrated the superiority of composite over injectable antibiotic therapy based on infection resolution and bone *** thereby conclude that the composite cement can be effectively applied in the treatment of resistant cases of chronic osteomyelitis.

关键词： Antibiotics Biodegradable composite Osteomyelitis MRsA strains Osteoconduction

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Hybrid High‑Order Methods for the Acoustic Wave Equation in the Time Domain

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Communications on Applied Mathematics and Computation 2022年第2期4卷 597-633页

作者： Erik burman Omar Duran Alexandre Ern Department of Mathematics University College LondonLondon WC1E 6BTUK CERMICs Ecole des Ponts77455 Marne la Vallée Cedex 2France INRIA Paris 75589 ParisFrance

We devise hybrid high-order(HHO)methods for the acoustic wave equation in the time *** frst consider the second-order formulation in *** the Newmark scheme for the temporal discretization,we show that the resulting HHO-Newmark scheme is energy-conservative,and this scheme is also amenable to static condensation at each time *** then consider the formulation of the acoustic wave equation as a frst-order system together with singly-diagonally implicit and explicit Runge-Kutta(sDIRK and ERK)***-sDIRK schemes are amenable to static condensation at each time *** HHO-ERK schemes,the use of the mixed-order formulation,where the polynomial degree of the cell unknowns is one order higher than that of the face unknowns,is key to beneft from the explicit structure of the *** results on test cases with analytical solutions show that the methods can deliver optimal convergence rates for smooth solutions of order O(hk+1)in the H1-norm and of order O(h^(k+2))in the L^(2)-***,test cases on wave propagation in heterogeneous media indicate the benefts of using high-order methods.

关键词： Hybrid high-order methods Wave equation Newmark scheme Runge-Kutta scheme

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Local Discontinuous Galerkin Method with Reduced stabilization for Diffusion Equations

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Communications in Computational Physics 2009年第2期5卷 498-514页

作者： E.burman B.stamm Department of Mathematics Mantell BuildingUniversity of SussexFalmerBrightonBN19RFUK Institute of Analysis and scientific Computing Swiss Institute of TechnologyLausanneCH-1015Switzerland

We extend the results on minimal stabilization of burman and stamm[***.,33(2007),pp.183-208]to the case of the local discontinuous Galerkin methods on mixed *** penalization term on the faces is relaxed to act only on a part of the polynomial *** in the form of a discrete inf-sup condition is proved and optimal convergence *** numerical examples using high order approximation spaces illustrate the theory.

关键词： Local discontinuous Galerkin h-FEM interior penalty diffusion equation

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Advanced glycation end products:Key mediator and therapeutic target of cardiovascular complications in diabetes

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World Journal of Diabetes 2023年第8期14卷 1146-1162页

作者： savita Bansal Archana burman Asok Kumar Tripathi Department of Biochemistry Institute of Home SciencesUniversity of DelhiNew Delhi 110016India Department of Biochemistry Institute of Home EconomicsUniversity of DelhiNew Delhi 110016India Department of Biochemistry University College of Medical SciencesUniversity of DelhiNew Delhi 110095India

The incidence of type 2 diabetes mellitus is growing in epidemic proportions and has become one of the most critical public health *** complications associated with diabetes are the leading cause of morbidity and *** cardiovascular diseases that accompany diabetes include angina,myocardial infarction,stroke,peripheral artery disease,and congestive heart *** the various risk factors generated secondary to hyperglycemic situations,advanced glycation end products(AGEs)are one of the important targets for future diagnosis and prevention of *** the last decade,AGEs have drawn a lot of attention due to their involvement in diabetic *** can be derived exogenously and endogenously through various *** are a nonhomogeneous,chemically diverse group of compounds formed nonenzymatically by condensation between carbonyl groups of reducing sugars and free amino groups of protein,lipids,and nucleic *** mediate their pathological effects at the cellular and extracellular levels by multiple *** the cellular level,they activate signaling cascades via the receptor for AGEs and initiate a complex series of intracellular signaling resulting in reactive oxygen species generation,inflammation,cellular proliferation,and fibrosis that may possibly exacerbate the damaging effects on cardiac functions in *** also cause covalent modifications and cross-linking of serum and extracellular matrix proteins;altering their structure,stability,and *** diagnosis of diabetes may prevent its progression to complications and decrease its associated *** the present review,we recapitulate the role of AGEs as a crucial mediator of hyperglycemia-mediated detrimental effects in diabetes-associated ***,this review presents an overview of future perspectives for new therapeutic interventions to ameliorate cardiovascular complications in diabetes.

关键词： Type 2 diabetes mellitus Cardiovascular complications Hyperglycemia Advanced glycation end products Reactive oxygen species Oxidative stress Endothelial cells Receptor of advanced glycation end products Anti-advanced glycation end products strategies

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Hybrid ensemble soft computing approach for predicting penetration rate of tunnel boring machine in a rock environment

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Journal of Rock Mechanics and Geotechnical Engineering 2021年第6期13卷 1398-1412页

作者： Abidhan Bardhan Navid Kardani Anasua GuhaRay Avijit burman Pijush samui Yanmei Zhang National Institute of Technology Patna PatnaBiharIndia Civil and Infrastructure Engineering Discipline School of EngineeringRoyal Melbourne Institute of Technology(RMIT)Victoria3001Australia Department of Civil Engineering BITS-Pilani Hyderabad CampusHyderabadTelanganaIndia College of Aerospace Engineering Chongqing UniversityChongqing400044China

This study implements a hybrid ensemble machine learning method for forecasting the rate of penetration(ROP) of tunnel boring machine(TBM),which is becoming a prerequisite for reliable cost assessment and project scheduling in tunnelling and underground projects in a rock *** this purpose,a sum of 185 datasets was collected from the literature and used to predict the ROP of ***,the main dataset was utilised to construct and validate four conventional soft computing(CsC)models,*** probability machine regression,relevance vector machine,extreme learning machine,and functional ***,the estimated outputs of CsC models were united and trained using an artificial neural network(ANN) to construct a hybrid ensemble model(HENsM).The outcomes of the proposed HENsM are superior to other CsC models employed in this *** on the experimental results(training RMsE=0.0283 and testing RMsE=0.0418),the newly proposed HENsM is potential to assist engineers in predicting ROP of TBM in the design phase of tunnelling and underground projects.

关键词： Tunnel boring machine(TBM) Rate of penetration(ROP) Artificial intelligence Artificial neural network(ANN) Ensemble modelling

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Reliability Analysis of Piled Raft Foundation Using a Novel Hybrid Approach of ANN and Equilibrium Optimizer

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Computer Modeling in Engineering & sciences 2021年第9期128卷 1033-1067页

作者： Abidhan Bardhan Priyadip Manna Vinay Kumar Avijit burman Bojan Zlender Pijush samui Department of Civil Engineering National Institute of TechnologyPatnaBiharIndia Faculty of Civil Engineering Transportation Engineering and ArchitectureUniversity of MariborMariborSlovenia

In many civil engineering projects,Piled Raft Foundations(PRFs)are usually preferred where the incoming load fromthe superstructures is very *** geotechnical engineering practice,the settlement of soil layers is a critical issue for the serviceability of the ***,assessment of risk associated with the structures corresponding to the maximum allowable settlement of soils needs to be carried out in the design *** this study,reliability analysis of PRF based on settlement criteria is performed using a high-performance hybrid soft computing *** new approach is an integration of the artificial neural network(ANN)and a recently developed meta-heuristic algorithm called equilibrium optimizer(EO).The concept of reliability index was used to explore the feasibility of a newly constructed hybrid model of ANN and EO(i.e.,ANN-EO)against the conventional approach of calculating the probability of failure of *** results show that the proposed ANN-EO attained the most accurate prediction with R^(2)=0.9914 and RMsE=0.0518 in the testing phase,which are significantly better than those obtained from conventional ANN,multivariate adaptive regression splines,and genetic programming,including the ANNoptimized with particle swarmoptimization developed in this *** on the experimental results of different settlement values,the newly constructedANN-EOis very potential to analyze the risk associatedwith civil engineering ***,the present study would significantly contribute to the knowledge pool of reliability studies related to piled raft systems because the works of literature on reliability analysis of piled raft systems are relatively scarce.

关键词： Risk analysis soil meta-heuristic optimization particle swarm optimization

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Endoscopic fasciotomy for chronic exertional compartment syndrome of the forearm:systematic review of outcomes and complications

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World Journal of Orthopedics 2021年第5期12卷 320-328页

作者： Yousef Marwan Abdullah Addar Nizar Algarni Nabil Algarni Mark burman Paul A Martineau Division of Orthopaedic surgery McGill University Health CentreMontreal H3G-1A4QuebecCanada Department of Orthopaedic surgery King Fahad Medical CityRiyadh 00966Saudi Arabia

BACKGROUND Endoscopic fasciotomy of the forearm for chronic exertional compartment syndrome(CECs)has gained popularity *** To systematically review the literature of endoscopic fasciotomy for CECs of the forearm,aiming to assess the outcomes and complications of the different endoscopic fasciotomy techniques described in the *** On January 18,2021,PubMed and EMBAsE were searched by 3 reviewers independently,and all relevant studies published up to that date were considered based on predetermined inclusion/exclusion *** subject headings“endoscopic fasciotomy”and“compartment syndrome”and their related key terms were *** Preferred Reporting Item for systematic Reviews and Meta-Analyses statement was used to screen the *** A total of seven studies including 183 patients(355 forearms)were *** mean age of the patients was 31.2 years(range:15-42 years).The postoperative follow-up duration ranged from 6 wk to 4.9 *** patients were able to return to sport activities between postoperative weeks 1 to *** of the compartment syndrome occurred in three patients,giving a rate of 1.6%per patient and 0.8%per *** overall complication rate was 8.7%per patient,and 4.5%per *** most common reported complication was hematoma(7 forearms;2.0%).CONCLUsION Endoscopic fasciotomy for CECs of the forearm has favorable short-and midterm outcomes with very low recurrence and complication ***,however,needs to be confirmed in larger,long-term follow-up,prospective,comparative studies between open,mini-open and endoscopic fasciotomy techniques.

关键词： Exertional compartment syndrome Compartment syndrome Fasciotomy Forearm Endoscopy

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stabilized Finite Element schemes for Incompressible Flow Using Velocity/Pressure spaces satisfying the Inf-sup Condition

Stabilized Finite Element Schemes for Incompressible Flow Us...

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The sixth World Congress on Computational Mechanics in Conjunction with the second Asian-Pacific Congress on Computational MechanicsⅠ

作者： Erik burman Institute of Analysis and scientific Computing Ecole Polytechnique Federale de Lausanne CH1015 Ecublens switzerland

Recently a new stabilized method for flow problems was proposed. The idea is to obtain stability by adding a least squares term penalizing the jump in the gradient or the streamline derivative over element boundaries to the standard Galerkin formulation. The method was successfully applied to the convection-diffusion-reaction equation in [1] and to the generalized stokes problem in [2]. Using the interior penalty approach we may circumvent several of the shortcomings suffered by the GLs/sUPG formulation. For instance we have no artificial boundary conditions on the pressure for the stokes equation, we have no artificial velocity/pressure couplings for the Navier-stokes equations, and we may use masslumping for efficient treatment of source terms and timestepping. Moreover the use of finite element spaces for the velocit ies and the pressures satisfying the LBB-condition for Navier-stokes equations in combination with stabilization only of the inertial terms and the incompressibility condition is transparent, a fact first exploited in [3]. In this paper we will focus on this last point and show how the method permits stabilization of convective instabilities without artificial coupling of velocities and pressures. The theoretical background of the method will be outlined showing in a general framework how to prove an inf-sup condition yielding stability both for the pressure and the convective term for conforming approximations. The Fortin criterion is applied to control the pressure and the interior penalty term is used to control instabilities due to the incompressibility constraint and the convective terms. Then We will discuss how some classical inf-sup stable finite element space pairs for the velocities and the Pressures fit the general framework. We exemplify the theory with some numerical examples.

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Three Dimensional Expansion of Margins for single-fraction Treatments: stereotactic Radiosurgery Brain Cases

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International Journal of Medical Physics, Clinical Engineering and Radiation Oncology 2012年第2期1卷 15-22页

作者： Qinghui Zhang Maria Chan Yulin song Chandra burman Department of Medical Physics Memorial Sloan Kettering Cancer Center New York NY 10065

Purpose: To derive a clinically-practical margin formula between clinical target volume (CTV) and planning target volume (PTV) for single-fraction stereotactic radiosurgery (sRs). Methods: In previous publications on the margin between the CTV and the PTV, a Gaussian function with zero mean was assumed for the systematic error and the machine systematic error was completely ignored. In this work we adopted a Dirac delta function for the machine systematic error for a given machine with nonzero mean systematic error. Mathematical formulas for calculating the CTV-PTV margin for single-fraction sRs treatments were proposed. Results: Margins for single fraction treatments were derived such that the CTVs received the prescribed dose in 95% of the sRs patients. The margin defined in this study was machine specific and accounted for nonzero mean systematic error. The differences between our formulas and a previously published formula were discussed. Conclusion: Clinical margin formulas were proposed for determining the margin between the CTV and the PTV in sRs treatments. Previous margin’s recipes, being derived specifically for conventional treatments, may be inappropriate for single-fraction sRs and could result in geometric miss of the target and even treatment failure for machines possessing of large systematic errors.

关键词： Margin Cone-beam CT Image-guided Radiation Treatment Radiosurgery Brain tumor

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