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Getting physical with medical education:Exercise based virtual anatomy review classes for medical students

World Journal of Methodology 2025年第1期15卷 20-25页

作者： nadeesha r samarasinghe Taniya S Nagpal Michele L Barbeau Charys M Martin Division of General Surgery Faculty of MedicineUniversity of British ColumbiaVancouver V6T 1Z3BCCanada Faculty of Kinesiology Sport and RecreationUniversity of AlbertaEdmonton T6G 2R3ABCanada Anatomy and Cell Biology University of Western OntarioLondon N6A 3K7ONCanada Department of Anatomy and Cell Biology Schulich School of Medicine and DentistryThe University of Western OntarioLondon N6A 3K7ONCanada

The benefits of regular physical activity are well ***,few studies have examined the effectiveness of integrating physical activity(PA)into curricula within a post-secondary *** investigate the incorporation of PA into medical curriculum,we developed a series of optional exercise-based review sessions designed to reinforce musculoskeletal(MSK)anatomy course *** synchronous sessions were co-taught by a group fitness instructor and an anatomy *** fitness instructor would lead students through both strength and yoga style exercises,while the anatomy instructor asked questions about relevant anatomical structures related to course material previously *** the sessions,participants were asked to evaluate the classes on their self-reported exam preparedness in improving MSK anatomy knowledge,PA levels,and mental *** participants completed surveys;a majority agreed that the classes increased understanding of MSK concepts(90.0%)and activity levels(97.7%).Many(70.0%)felt that the classes helped reduce *** majority of respondents(90.0%)agreed that the classes contributed to increased feelings of social ***,medical students saw benefit in PA based interventions to supplement MSK course *** with increasing activity levels and promoting health behaviours,integrating PA into medical curriculum may improve comprehension of learning material,alleviate stress and foster social connectivity among medical students.

关键词： Medical education Musculoskeletal Anatomy Exercise Online learning

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Modeling protein-protein interactions in axon initial segment to understand their potential impact on action potential initiation

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Neural regeneration research 2021年第4期16卷 700-706页

作者： Piyush Bhardwaj Don Kulasiri Sandhya samarasinghe Centre of Advanced Computational Solutions(C-fACS) Lincoln UniversityChristchurchNew Zealand Department of Molecular Biosciences Lincoln UniversityChristchurchNew Zealand

The axon initial segment(AIS)region is crucial for action potential initiation due to the presence of high-density AIS protein voltage-gated sodium channels(Nav).Nav channels comprise several serine residues responsible for the recruitment of Nav channels into the structure of AIS through interactions with ankyrin-G(AnkG).In this study,a series of computational experiments are performed to understand the role of AIS proteins casein kinase 2 and AnkG on Nav channel recruitment into the *** computational simulation results using Virtual cell software indicate that Nav channels with all serine sites available for phosphorylation bind to AnkG with strong *** the low initial concentration of AnkG and casein kinase 2,the concentration of Nav channels reduces significantly,suggesting the importance of casein kinase 2 and AnkG in the recruitment of Nav channels.

关键词： Alzheimer’s disease ankyrin-G axon initial segment casein kinase-2 microtubules voltage-gated potassium channel voltage-gated sodium channel

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Functional repertoire of protein kinases and phosphatases in synaptic plasticity and associated neurological disorders

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Neural regeneration research 2021年第6期16卷 1150-1157页

作者： raheel Khan Don Kulasiri Sandhya samarasinghe Centre for Advanced Computational Solutions(C-fACS) Lincoln UniversityChristchurchNew Zealand Department of Molecular Biosciences Lincoln UniversityChristchurchNew Zealand

Protein phosphorylation and dephosphorylation are two essential and vital cellular mechanisms that regulate many receptors and enzymes through kinases and ***^2+- dependent kinases and phosphatases are responsible for controlling neuronal processing;balance is achieved through *** molecular mechanisms of learning and memory,kinases generally modulate positively while phosphatases modulate *** review outlines some of the critical physiological and structural aspects of kinases and phosphatases involved in maintaining postsynaptic structural *** also explores the link between neuronal disorders and the deregulation of phosphatases and kinases.

关键词： Alzheimer’s disease autism spectrum disorder CaMKII calcineurin longterm depression long-term potentiation protein kinase A protein phosphatase 1 protein dephosphorylation protein phosphorylation

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Detection of Alzheimer’s disease onset using MrI and PET neuroimaging:longitudinal data analysis and machine learning

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Neural regeneration research 2023年第10期18卷 2134-2140页

作者： Iroshan Aberathne Don Kulasiri Sandhya samarasinghe Centre for Advanced Computational Solutions(C-fACS) Lincoln UniversityChristchurchNew Zealand

The scientists are dedicated to studying the detection of Alzheimer’s disease onset to find a cure, or at the very least, medication that can slow the progression of the disease. This article explores the effectiveness of longitudinal data analysis, artificial intelligence, and machine learning approaches based on magnetic resonance imaging and positron emission tomography neuroimaging modalities for progression estimation and the detection of Alzheimer’s disease onset. The significance of feature extraction in highly complex neuroimaging data, identification of vulnerable brain regions, and the determination of the threshold values for plaques, tangles, and neurodegeneration of these regions will extensively be evaluated. Developing automated methods to improve the aforementioned research areas would enable specialists to determine the progression of the disease and find the link between the biomarkers and more accurate detection of Alzheimer’s disease onset.

关键词： deep learning image processing linear mixed effect model neuroimaging neuroimaging data sources onset of Alzheimer’s disease detection pattern recognition

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Alleviating the unwanted effects of oxidative stress on Aβclearance:a review of related concepts and strategies for the development of computational modelling

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Translational Neurodegeneration 2023年第1期12卷 702-721页

作者： Sarawoot Somin Don Kulasiri Sandhya samarasinghe Centre for Advanced Computational Solutions(C-fACS) Lincoln UniversityChristchurch 7647New Zealand Department of Wine Food and Molecular BiosciencesLincoln UniversityChristchurch 7647New Zealand

Treatment for Alzheimer’s disease(AD)can be more effective in the early *** we do not completely understand the aetiology of the early stages of AD,potential pathological factors(amyloid beta[Aβ]and tau)and other co-factors have been identified as causes of AD,which may indicate some of the mechanism at work in the early stages of ***,one of the primary techniques used to help delay or prevent AD in the early stages involves alleviating the unwanted effects of oxidative stress on Aβclearance.4-Hydroxynonenal(HNE),a product of lipid peroxidation caused by oxidative stress,plays a key role in the adduction of the degrading *** HNE employs a mechanism which decreases catalytic *** process ultimately impairs Aβ*** degradation of HNE-modified proteins helps to alleviate the unwanted effects of oxidative *** a clear understanding of the mechanisms associated with the degradation of the HNE-modified proteins is essential for the development of strategies and for alleviating the unwanted effects of oxidative *** strategies which could be employed to decrease the effects of oxidative stress include enhancing antioxidant activity,as well as the use of nanozymes and/or specific *** area which shows promise in reducing oxidative stress is protein ***,more research is needed to improve the effectiveness and accuracy of this *** paper discusses the interplay of potential pathological factors and *** particular,it focuses on the effect of oxidative stress on the expression of the Aβ-degrading proteases through adduction of the degrading proteases caused by *** paper also elucidates other strategies that can be used to alleviate the unwanted effects of oxidative stress on Aβ*** improve the effectiveness and accuracy of protein design,we explain the application of quantum mechanical/molecular mechanical approach.

关键词： Alzheimer’s disease Oxidative stress Amyloid beta clearance Protein design

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On electrostatic interactions of adenosine triphosphate-insulin-degrading enzyme revealed by quantum mechanics/molecular mechanics and molecular dynamics

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Quantitative Biology 2024年第4期12卷 414-432页

作者： Sarawoot Somin Don Kulasiri Sandhya samarasinghe Centre for Advanced Computational Solutions(C‐fACS) Lincoln UniversityChristchurchNew Zealand Department of Molecular Biosciences Lincoln UniversityChristchurchNew Zealand

The insulin-degrading enzyme(IDE)plays a significant role in the degradation of the amyloid beta(Aβ),a peptide found in the brain regions of the patients with early Alzheimer’s *** triphosphate(ATP)allosterically regulates the Aβ-degrading activity of *** present study investigates the electrostatic interactions between ATP-IDE at the allosteric site of IDE,including thermostabilities/flexibilities of IDE residues,which have not yet been explored *** study applies the quantum mechanics/molecular mechanics(QM/MM)to the proposed computational model for exploring electrostatic interactions between ATP and *** dynamic(MD)simulations are performed at different temperatures for identifying flexible and thermostable residues of *** proposed computational model predicts QM/MM energy-minimised structures providing the IDE residues(Lys530 and Asp385)with high binding *** root mean square fluctuation values during the MD simulations at 300.00 K including heat-shock temperatures(321.15 K and 315.15 K)indicates that Lys530 and Asp385 are also the thermostable residues of IDE,whereas Ser576 and Lys858 have high flexibilities with compromised *** present study sheds light on the phenomenon of biological recognition and interactions at the ATP-binding domain,which may have important implications for pharmacological drug *** proposed computational model may facilitate the development of allosteric IDE activators/inhibitors,which mimic ATP interactions.

关键词： electrostatic interactions molecular dynamic simulation QM/MM calculation method thermostability/flexibility

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Fundamental Boolean network modelling for childhood acute lymphoblastic leukaemia pathways

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Quantitative Biology 2022年第1期10卷 94-121页

作者： Leshi Chen Don Kulasiri Sandhya samarasinghe Computational Systems Biology Laboratory Centre for Advanced Computational Solutions(C-fACS)Lincoln UniversityLincolnCanterbury 7647New Zealand Integrated Systems Modelling Group Centre for Advanced Computational Solutions(C-fACS)Lincoln UniversityLincolnCanterbury 7647New Zealand

Background:A novel data-driven Boolean model,namely,the fundamental Boolean model(FBM),has been proposed to draw genetic regulatory insights into gene activation,inhibition,and protein decay,published in *** novel Boolean model facilitates the analysis of the activation and inhibition ***,the novel model does not handle the situation well,where genetic regulation might require more time steps to ***:Here,we propose extending the fundamental Boolean modelling to address the issue that some gene regulations might require more time steps to complete than *** denoted this extension model as the temporal fundamental Boolean model(TFBM)and related networks as the temporal fundamental Boolean networks(TFBNs).The leukaemia microarray datasets downloaded from the National Centre for Biotechnology Information have been adopted to demonstrate the utility of the proposed TFBM and ***:We developed the TFBNs that contain 285 components and 2775 Boolean rules based on TFBM on the leukaemia microarray datasets,which are in the form of short-time *** data contain gene expression measurements for 13 GC-sensitive children under therapy for acute lymphoblastic leukaemia,and each sample has three time points:0 hour(before GC treatment),6/8 hours(after GC treatment)and 24 hours(after GC treatment).Conclusion:We conclude that the proposed TFBM unlocks their predecessor’s limitation,Le.,FBM,that could help pharmaceutical agents identify any side effects on clinic-related *** hypotheses could be identified by analysing the extracted fundamental Boolean networks and analysing their up-regulatory and down-regulatory pathways.

关键词： Boolean modelling Boolean network time series data network inference data-driven boolean modelling fundamental boolean model fundamental boolean networks orchard cube

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神经网络在应用科学和工程中的应用

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作者： (美)Sandhya samarasinghe

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Estimating Out-Crossing rate of Bg 379-2 Using Morphological Markers and Confirmation by Molecular Markers

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rice science 2012年第2期19卷 166-168页

作者： L.H.M.Y.K.SOMArATNE A.S.M.T.ABAYAWICKrAMA I.P.WICKrAMASINGHE W.L.G.samarasinghe Department of Agricultural Biology Faculty of AgricultureUniversity of PeradeniyaSri Lanka rice research and Development Institute BatalagodaIbbagamuwaSri Lanka

rice is largely self-fertilized and accordingly a field population of rice is completely composed of near homozygotes. Due to the emergence of off-types, homozygosity will be affected. With the time, this will cause the reduction of genetic purity in some rice varieties. One of the reasons has been suspected to be the high out-crossing frequencies of such varieties. Studies were conducted at the rice research and Development Institute, Batalagoda, Sri Lanka to estimate the out-crossing rate of Bg 379-2, a variety having the problem of maintaining genetic purity. Bg 379-2 was allowed to out-cross with Bg 450 and the number of out- crossed plants were counted using dominant morphological markers such as short-round grain and purple culm of pollen donor. A molecular confirmation of out-crossing was also performed using sequence tagged site （STS） molecular marker pTA248. The variety Bg 379-2 showed a potential out-crossing rate of 3.41% and an average out-crossing rate of 1.29% using dominant morphological markers. Polymorphism was cleady detected between parents and out-crossed plants as well as selfed plants of Bg 379-2 using their banding patterns. A similar study can be performed to determine the out-crossing rates of other varieties which show high percentage of off-types in the population for the better understanding of the breeding behavior of the varieties.

关键词： rice genetic purity out-crossing marker polymorphism

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Characterization and Selection of Phosphorus Deficiency Tolerant rice Genotypes in Sri Lanka

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rice science 2016年第4期23卷 184-195页

作者： Y. C. ALUWIHArE M. ISHAN M. D. M. CHAMIKArA C. K. WEEBADDE D. N. SIrISENA W. L. G. samarasinghe S. D. S. S. SOOrIYAPATHIrANA Department of Molecular Biology and Biotechnology Faculty of Science University of Peradeniya Peradeniya 20400 Sri Postgraduate Institute of Science University of Peradeniya Peradeniya 20400 Sri Lanka Departments of Plant Soil and Microbial Sciences and Horticulture College of Agriculture and Natural Resources Michigan State University East LansingMichigan 48824 USA rice research and Development Institute Bathalagoda Ibbagamuwa 60500 Sri Lanka

Phosphorus(P) deficiency in soil is a major constrain for rice production. An important set of rice genotypes(landraces, old improved and new improved varieties) were screened for P deficiency tolerance in two major cropping seasons of Sri Lanka, in 2012. The Ultisol soil, which was collected from a plot cultivated with rice without fertilizer application for past 40 years(P_0) at the rice research and Development Institute(rrDI), Bathalagoda, Sri Lanka, was used as the potting medium for greenhouse trials. Two field trials were conducted in the same plots at rrDI. Both P_0 and P_(30)(30 mg/kg P_2O_5) conditions were used in the two greenhouse trials. At the early vegetative(three weeks after transplanting), late vegetative(six weeks after transplanting) and flowering stages, plant height and number of tillers per plant were recorded. At the flowering stage, shoots were harvested and shoot dry weight, shoot P concentration, shoot P uptake and P utilization efficiency were measured. All data were statistically analyzed using analysis of variance, regression and cluster procedures. The measured parameters were significantly different between P_0 and P_(30) conditions(P r shoot dry weight was reported by the rice genotypes H4 and Marss under P_0 conditions. The regression analysis between shoot dry weight and P utilization efficiency revealed that the studied rice genotypes could be categorized to three P deficiency tolerance classes. A total of 13 genotypes could be considered as highly tolerant and 4 genotypes as sensitive for P deficiency. These results could be used to select parental genotypes for breeding and genetic studies and also to select interesting varieties or landraces for organic rice production.

关键词： phosphorus tolerance rice genotype phosphorus utilization efficiency landrace

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