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single-cell trajectories of melanoma cell resistance to targeted treatment

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Cancer Biology & Medicine 2022年第1期19卷 56-73页

作者： Maria schmidt Lena sünke Mortensen henry Loeffler-Wirth Corinna Kosnopfel Knut Krohn Hans Binder Manfred Kunz Interdisciplinary Centre for Bioinformatics University of LeipzigLeipzig 04107Germany Department of Dermatology Venereology and AllergologyUniversity of WürzburgWürzburg 97074Germany Core Unit DNA Technologies Medical FacultyUniversity of LeipzigLeipzig 04103Germany Department of Dermatology Venereology and AllergologyUniversity of Leipzig Medical CenterLeipzig 04103Germany

Objective:Cellular heterogeneity is regarded as a major factor affecting treatment response and resistance in malignant *** developments in single-cell sequencing technology have provided deeper insights into these ***:Here,we analyzed a BRAFV600 E-mutant melanoma cell line by single-cell RNA-seq under various conditions:cells sensitive to BRAF inhibition with BRAF inhibitor vemurafenib and cells resistant to BRAF inhibition with vemurafenib alone or vemurafenib in combination with the MEK1/2 inhibitors cobimetinib or *** reduction by t-distributed stochastic neighbor embedding and self-organizing maps identified distinct trajectories of resistance development clearly separating the 4 treatment conditions in cell and gene state ***:Trajectories associated with resistance to single-agent treatment involved cell cycle,extracellular matrix,and de-differentiation *** contrast,shifts detected in double-resistant cells primarily affected translation and mitogen-activated protein kinase pathway reactivation,with a small subpopulation showing markers of *** findings were validated in pseudotime analyses and RNA velocity ***:The single-cell transcriptomic analyses reported here employed a spectrum of bioinformatics methods to identify mechanisms of melanoma resistance to single-and double-agent *** study deepens our understanding of treatmentinduced cellular reprogramming and plasticity in melanoma cells and identifies targets of potential relevance to the management of treatment resistance.

关键词： Melanoma single-cell transcriptome sequencing treatment response

Machine learning enabled autonomous microstructural characterization in 3D samples

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npj Computational Materials 2020年第1期6卷 1654-1662页

作者： henry Chan Mathew Cherukara Troy D.Loeffler Badri Narayanan subramanian K.R.s.sankaranarayanan Center for Nanoscale Materials Argonne National LaboratoryArgonneILUSA Department of Mechanical Engineering University of LouisvilleLouisvilleKYUSA Department of Mechanical and Industrial Engineering University of Illinois at ChicagoChicagoILUSA

We introduce an unsupervised machine learning(ML)based technique for the identification and characterization of microstructures in three-dimensional(3D)samples obtained from molecular dynamics simulations,particle tracking data,or *** technique combines topology classification,image processing,and clustering algorithms,and can handle a wide range of microstructure types including grains in polycrystalline materials,voids in porous systems,and structures from self/directed assembly in soft-matter complex *** technique does not require a priori microstructure description of the target system and is insensitive to disorder such as extended defects in polycrystals arising from line and plane *** demonstrate quantitively that our technique provides unbiased microstructural information such as precise quantification of grains and their size distributions in 3D polycrystalline samples,characterizes features such as voids and porosity in 3D polymeric samples and micellar size distribution in 3D complex *** demonstrate the efficacy of our ML approach,we benchmark it against a diverse set of synthetic data samples representing nanocrystalline metals,polymers and complex fluids as well as experimentally published characterization *** technique is computationally efficient and provides a way to quickly identify,track,and quantify complex microstructural features that impact the observed material behavior.

关键词： microstructure polycrystalline porosity

The Irony of Flood Risks in African Dryland Environments: Human security in North Cameroon

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World Journal of Engineering and Technology 2017年第3期5卷 109-121页

作者： henry Bang Lee Miles richard Gordon Disaster Management Centre Faculty of Management Bournemouth University Bournemouth United Kingdom

North Cameroon, though located in an arid environment, ironically also suffers from the serious threat of flooding in the region. This article examines contemporary challenges resulting from frequent flooding in North Cameroon. Using Cutter’s “Hazard of Place Model” of vulnerability as the conceptual basis, the article triangulates data from a variety of sources to analyze environmental risks, social and biophysical vulnerability and flood impact, including flood risk management in North Cameroon. The findings reveal that North Cameroon is vulnerable to frequent flooding due to a combination of environmental, socio-economic, and geographic factors further compounded by low organizational resilience to flooding with dire consequences for livelihoods. We argue that, if not handled appropriately, the impact of flooding in North Cameroon risks trapping the population in a permanent and vicious cycle of destitution and poverty. The government urgently needs to review its disaster management policies to be more proactive and strategic in flood management in order to enhance human security and prevent permanent damage to the livelihoods and the micro-economy of the region. Lessons learned from this research, when applied, can help to reduce the vulnerabilities of the poverty-stricken population and enhance resilience to flood risks.

关键词： Frequent Flooding North Cameroon Vulnerability Flood Management

sequence assembly using next generation sequencing data —challenges and solutions

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science China(Life sciences) 2014年第11期57卷 1140-1148页

作者： CHIN Francis Y.L. LEUNG henry C.M. YIU s.M. Department of Computer science The University of Hong Kong

sequence assembling is an important step for bioinformatics *** the help of next generation sequencing(NGs)technology,high throughput DNA fragment(reads)can be randomly sampled from DNA or RNA molecular ***,as the positions of reads being sampled are unknown,assembling process is required for combining overlapped reads to reconstruct the original DNA or RNA *** with traditional sanger sequencing methods,although the throughput of NGs reads increases,the read length is shorter and the error rate is *** introduces several problems in ***,paired-end reads instead of single-end reads can be sampled which contain more *** existing assemblers cannot fully utilize this information and fails to assemble longer *** this article,we will revisit the major problems of assembling NGs reads on genomic,transcriptomic,metagenomic and metatranscriptomic *** will also describe our IDBA package for solving these *** package has adopted several novel ideas in assembling,including using multiple k,local assembling and progressive depth *** with existence assemblers,IDBA has better performance on many simulated and real sequencing datasets.

关键词： genomic assembling de Bruijn graph paired-end reads next generation sequencing

Gym-ANM: Reinforcement learning environments for active network management tasks in electricity distribution systems

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Energy and AI 2021年第3期5卷 171-193页

作者： Robin henry Damien Ernst school of Engineering Sanderson BuildingThe University of EdinburghEdinburgh EH93FBUK Department of Electrical Engineering and Computer science Montefiore InstituteUniversity of LiegeLiege B-4000Belgium

Active network management(ANM)of electricity distribution networks include many complex stochastic sequential optimization *** problems need to be solved for integrating renewable energies and distributed storage into future electrical *** this work,we introduce Gym-ANM,a framework for designing reinforcement learning(RL)environments that model ANM tasks in electricity distribution *** environments provide new playgrounds for RL research in the management of electricity networks that do not require an extensive knowledge of the underlying dynamics of such *** with this work,we are releasing an implementation of an introductory toy-environment,ANM6-Easy,designed to emphasize common challenges in *** also show that state-of-the-art RL algorithms can already achieve good performance on ANM6-Easy when compared against a model predictive control(MPC)***,we provide guidelines to create new Gym-ANM environments differing in terms of(a)the distribution network topology and param-eters,(b)the observation space,(c)the modeling of the stochastic processes present in the system,and(d)a set of hyperparameters influencing the reward ***-ANM can be downloaded at https://***/robinhenr y/gym-anm.

关键词： Gym-ANM Reinforcement learning Active network management Distribution networks Renewable energy

Unsupervised spectral feature selection algorithms for high dimensional data

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Frontiers of Computer science 2023年第5期17卷 27-40页

作者： Mingzhao WANG henry HAN Zhao HUANG Juanying XIE school of Computer science Shaanxi Normal UniversityXi’an 710119China Department of Computer science School of Engineering&Computer ScienceBaylor UniversityWacoTX 76798USA

It is a significant and challenging task to detect the informative features to carry out explainable analysis for high dimensional data,especially for those with very small number of *** selection especially the unsupervised ones are the right way to deal with this challenge and realize the ***,two unsupervised spectral feature selection algorithms are proposed in this *** group features using advanced self-Tuning spectral clustering algorithm based on local standard deviation,so as to detect the global optimal feature clusters as far as *** two feature ranking techniques,including cosine-similarity-based feature ranking and entropy-based feature ranking,are proposed,so that the representative feature of each cluster can be detected to comprise the feature subset on which the explainable classification system will be *** effectiveness of the proposed algorithms is tested on high dimensional benchmark omics datasets and compared to peer methods,and the statistical test are conducted to determine whether or not the proposed spectral feature selection algorithms are significantly different from those of the peer *** extensive experiments demonstrate the proposed unsupervised spectral feature selection algorithms outperform the peer ones in comparison,especially the one based on cosine similarity feature ranking *** statistical test results show that the entropy feature ranking based spectral feature selection algorithm performs *** detected features demonstrate strong discriminative capabilities in downstream classifiers for omics data,such that the AI system built on them would be reliable and *** is especially significant in building transparent and trustworthy medical diagnostic systems from an interpretable AI perspective.

关键词： feature selection spectral clustering feature ranking techniques entropy cosine similarity

synergy between thermal and nonthermal effects in plasmonic photocatalysis

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Nano Research 2020年第5期13卷 1268-1280页

作者： Xueqian Li henry O.Everitt Jie Liu Department of Chemistry Duke UniversityDurhamNC 27708USA 2 U.S.Army Combat Capabilities Development CommandAviation&Missile CenterRedstone ArsenalAL 35898USA Department of Physics Duke UniversityDurhamNC 27708USA Present address:Department of Applied Physics and Materials science California Institute of TechnologyPasadenaCA 91125USA

Plasmonic photocatalysis represents the synergetic union of two active fields of research:plasmonic effects in illuminated metallic nanoparticles and catalytic effects in tailored metallic ***,metallic nanoparticles that excel for one application are limited for the other,but recent developments have shown that desirable catalytic behaviors,such as reduced activation barriers and improved product selectivity,derive from nonthermal behaviors uniquely produced by this *** examining such findings,this review will address a specific debate that has recently surfaced:what is the relative degree of contributions of thermal and nonthermal effects in plasmonic photocatalysis?We demonstrate the importance of correctly accounting for thermal effects before characterizing nonthermal *** show that another synergy occurs:these desirable nonthermal behaviors have a temperature dependence,and the resulting temperature-dependent reaction rates far exceed what can be explained from purely thermal effects ***,the synergy of plasmonic photocatalysis offers an exciting new contribution to the quest for efficient,selective,sustainable methods for chemical synthesis and energy conversion.

关键词： plasmonic catalysis hot carriers photothermal catalysis localized surface plasmon

Implementing physically active learning:Future directions for research,policy,and practice

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Journal of sport and Health science 2020年第1期9卷 41-49,F0003页

作者： Andy Daly-smith Thomas Quarmby Victoria s.J.Archbold Ash C.Routen Jade L.Morris Catherine Gammon John B.Bartholomew Geir Kare Resaland Bryn Llewellyn richard Allman henry Dorling school of sport Leeds Beckett UniversityLeedsLS63QSUK school of sport Exercise and Health SciencesLoughborough UniversityE152GZUK school of Health Promotion and Human Performance Eastern Michigan UniversityYpsilantiMI 48197USA Centre for Diet and Activity Research MRC Epidemiology UnitUniversity of CambridgeCambridgeCB21TNUK Department of Kinesiology and Health Education The University of Texas at AustinAustinTX 78705USA Center for Physically Active Learning Faculty of EducationArts and SportsWestern Norway University of Applied SciencesSogndal5020 BergenNorway Tagtiv8 Ltd and Move&Learn LeedsWF27BSUK school of sport Health and Social ScienceSolent UniversitySouthamptonSO 14 ORTUK

Purpose:To identify co-produced multi-stakeholder perspectives important for successful widespread physically active learning(PAL) adoption and ***:A total of 35 stakeholders(policymakers n=9;commercial education sector,n=8;teachers,n=3;researchers,n=15) attended a design thinking PAL *** formed 5 multi-disciplinary groups with at least 1 representative from each stakeholder *** group,facilitated by a researcher,undertook 2 tasks:(1) using Post-it Notes,the following question was answered:within the school day,what are the opportunities for learning combined with movement?and(2) structured as a washing-line task,the following question was answered:how can we establish PAL as the norm?All discussions were audio-recorded and *** analyses were conducted by 4 *** the analyses were complete,the main themes and subthemes were assigned to 4 predetermined categories:(1) PAL design and implementation,(2) priorities for practice,(3) priorities for policy,and(4) priorities for ***:The following were the main themes for PAL implementation:opportunities for PAL within the school day,delivery environments,learning approaches,and the intensity of *** main themes for the priorities for practice included teacher confidence and competence,resources to support delivery,and community of *** main themes for the policy for priorities included self-governance,the Office for standards in Education,Children’s services,and skill,policy investment in initial teacher training,and curriculum *** main themes for the research priorities included establishing a strong evidence base,school-based PAL implementation,and a whole-systems ***:The present study is the first to identify PAL implementation factors using a combined multi-stakeholder *** achieve wider PAL adoption and implementation,future interventions should be evidence based and address implementation factors

关键词： Children Physical activity Physically active learning Policy school

Branding"Literary Genius"in Jin shengtan's 70-Chapter Edition of the Water Margin

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Frontiers of Literary studies in China-selected Publications from Chinese Universities 2020年第3期14卷 480-513页

作者： henry Lem Asian school I Department of ChineseDefense Language InstituteMontereysCA 93944USA

Jin shengtan wrote his commentaries to the novel Water Margin(shuihuzhuan)between 1641 and 1644,during the final years before the fall of the Ming *** commentaries are exceptional at least in part because they reflect Jin's frustrations that came from trying to understand this period of *** they are also a good example of how fiction commentary helped to shape the trajectory that the development of Chinese fiction would take,in the form of commentaries and *** article offers a reading of Jin's commentaries to his 70-chapter edition of the Water Margin,to investigate how Jin radically reshaped the Water Margin as the masterpiece of a commentator of great literary *** analyses Jin's rhetoric of controlling interpretation and concludes that Jin's ultimate goal was to stabilize and prevent tampering of his"original"70-chapter edition,in an attempt to close off future possibilities of"sequeling"the Water Margin.

关键词： Jin shengtan Water Margin literary genius fiction commentaries sequels rhetoric