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Substance graphs are optimal simple-graph representations of metabolism

Chinese Science Bulletin 2010年第27期55卷 3161-3168页

作者： holme petter HUSS Mikael Department of Physics Ume University Department of Energy Science Sungkyunkwan University Science for Life Laboratory Stockholm Box 1031 171 21 SolnaSweden Computational and Systems Biology Genome Institute of Singapore

One approach to study the system-wide organization of biochemistry is to use statistical graph theory.In such heavily simplified methods,which disregard most of the dynamic aspects of biochemistry,one is faced with fundamental questions.One such question is how the chemical reaction systems should be reduced to a graph retaining as much functional information as possible from the original reaction system.In these graph representations,should the edges go between substrates and products,or substrates and substrates,or both?Should vertices represent substances or reactions?Different representations encode different information about the reaction system and affect network measures in different ways.This paper investigates which representation reflects the functional organization of the metabolic system in the best way,according to the defined criteria.Four different graph representations of metabolism(three where the vertices are metabolites,one where the vertices are reactions)are evaluated using data from different organisms and databases.The graph representations are evaluated by comparing the overlap between clusters(network modules)and annotated functions,and also by comparing the set of identified currency metabolites with those that other authors have identified using qualitative biological arguments.It is found that a"substance network",where all metabolites participating in a reaction are connected,is better than others,evaluated with respect to both the functional overlap between modules and functions and to the number and identity of the identified currency metabolites.

关键词：图形表示代谢物物质生物数据库反应体系化学反应系统顶点表示代谢产物

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Epidemic Surveillance of Influenza Infections:A Network-Free Strategy—Hong Kong Special Administrative Region,China,2008–2011

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China CDC weekly 2022年第46期4卷 1025-1031,I0002-I0005页

作者： Zhanwei Du Qi Tan Yuan Bai Lin Wang Benjamin J.Cowling petter holme WHO Collaborating Centre for Infectious Disease Epidemiology and Control School of Public HealthLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina Laboratory of Data Discovery for Health Limited(D24H) Hong Kong Science and Technology ParkHong Kong SARChina Department of Genetics University of CambridgeCambridgeUK Department of Computer Science Aalto UniversityEspooFinland

Introduction:The ease of coronavirus disease 2019(COVID-19)non-pharmacological interventions and the increased susceptibility during the past COVID-19 pandemic could be a precursor for the resurgence of influenza,potentially leading to a severe outbreak in the winter of 2022 and future seasons.The recent increased availability of data on Electronic Health Records(EHR)in public health systems,offers new opportunities to monitor individuals to mitigate outbreaks.Methods:We introduced a new methodology to rank individuals for surveillance in temporal networks,which was more practical than the static networks.By targeting previously infected nodes,this method used readily available EHR data instead of the contactnetwork structure.Results:We validated this method qualitatively in a real-world cohort study and evaluated our approach quantitatively by comparing it to other surveillance methods on three temporal and empirical networks.We found that,despite not explicitly exploiting the contacts’network structure,it remained the best or close to the best strategy.We related the performance of the method to the public health goals,the reproduction number of the disease,and the underlying temporal-network structure(e.g.,burstiness).Discussion:The proposed strategy of using historical records for sentinel surveillance selection can be taken as a practical and robust alternative without the knowledge of individual contact behaviors for public health policymakers.

关键词： network policy networks

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Understanding and Exploiting Information Spreading and Integrating Technologies

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Journal of Computer Science & Technology 2011年第5期26卷 829-836页

作者： petter holme Mikael Huss IceLab Department of PhysicsUme a University901 87 Ume aSweden Department of Energy Science Sungkyunkwan University Science of Life Laboratory Stockholm Karolinska Institute Science ParkBox 1031171 21 SolnaSweden Department of Biochemistry and Biophysics The Arrhenius Laboratories for Natural SciencesStockholm University 106 91 StockholmSweden

Our daily life leaves an increasing amount of digital traces,footprints that are improving our lives.Data-mining tools,like recommender systems,convert these traces to information for aiding decisions in an ever-increasing number of areas in our lives.The feedback loop from what we do,to the information this produces,to decisions what to do next,will likely be an increasingly important factor in human behavior on all levels from individuals to societies.In this essay,we review some effects of this feedback and discuss how to understand and exploit them beyond mapping them on more well-understood phenomena.We take examples from models of spreading phenomena in social media to argue that analogies can be deceptive,instead we need to fresh approaches to the new types of data,something we exemplify with promising applications in medicine.

关键词： modeling and prediction computer-supported collaborative work health care

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China CDC weekly 2022年第40期4卷 885-889,I0002-I0005页

作者： Yuan Bai Mingda Xu Caifen Liu Mingwang Shen Lin Wang Linwei Tian Suoyi Tan Lei Zhang petter holme Xin Lu Eric H.Y.Lau Benjamin J.Cowling Zhanwei Du WHO Collaborating Centre for Infectious Disease Epidemiology and Control School of Public HealthLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong Special Administrative RegionChina Laboratory of Data Discovery for Health Limited(D24H) Hong Kong Science ParkHong Kong Special Administrative RegionChina China-Australia Joint Research Center for Infectious Diseases School of Public HealthXi’an Jiaotong University Health Science CenterXi’an CityShaanxi ProvinceChina Department of Genetics University of CambridgeCambridge CB23EHUK College of Systems Engineering National University of Defense TechnologyChangsha CityHunan ProvinceChina Department of Computer Science Aalto UniversityEspooFinland Center for Computational Social Science Kobe UniversityKobeJapan

Introduction:Minimizing the importation and exportation risks of coronavirus disease 2019(COVID-19)is a primary concern for sustaining the“Dynamic COVID-zero”strategy in China.Risk estimation is essential for cities to conduct before relaxing border control measures.Methods:Informed by the daily number of passengers traveling between 367 prefectures(cities)in China,this study used a stochastic metapopulation model parameterized with COVID-19 epidemic characteristics to estimate the importation and exportation risks.Results:Under the transmission scenario(R0=5.49),this study estimated the cumulative case incidence of Changchun City,Jilin Province as 3,233(95%confidence interval:1,480,4,986)before a lockdown on March 14,2022,which is close to the 3,168 cases reported in real life by March 16,2022.In a total of 367 prefectures(cities),127(35%)had high exportation risks according to the simulation and could transmit the disease to 50%of all other regions within a period from 17 to 94 days.The average time until a new infection arrives in a location in 1 of the 367 prefectures(cities)ranged from 26 to 101 days.Conclusions:Estimating COVID-19 importation and exportation risks is necessary for preparedness,prevention,and control measures of COVID-19—especially when new variants emerge.

关键词： Export Changchun prevention

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Model Versions and Fast Algorithms for Network Epidemiology

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后勤工程学院学报 2014年第3期30卷 1-7页

作者： petter holme Dept.of Energy Science Sungkyunkwan University Dept.of Physics IceLab Ume University Dept.of Sociology Stockholm University

Network epidemiology has become a core framework for investigating the role of human contact patterns in the spreadingof infectious diseases.In network epidemiology,one represents the contact structure as a network of nodes(individuals)connected bylinks(sometimes as a temporal network where the links are not continuously active)and the disease as a compartmental model(whereindividuals are assigned states with respect to the disease and follow certain transition rules between the states).In this paper,we discussfast algorithms for such simulations and also compare two commonly used versions,one where there is a constant recovery rate(the numberof individuals that stop being infectious per time is proportional to the number of such people);the other where the duration of the diseaseis constant.The results show that,for most practical purposes,these versions are qualitatively the same.

关键词： network theory algorithm stochastic simulation infectious disease

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基于Swarm卫星数据及CHAOS-6模型的中国地区岩石圈磁场研究

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Applied Geophysics 2023年第4期20卷 422-431,669,670页

作者：姜乙 Richard holme 蒋勇南京信息工程大学空间天气研究所中国南京210044 利物浦大学环境科学学院英国利物浦L693GP 澳门科技大学月球与行星科学国家重点实验室中国澳门999078 无锡太湖学院苏格兰学院中国无锡214064

本研究主要关注Swarm卫星数据及CHAOS-6模型对岩石圈磁场的应用。重点考察该模型能否较好地模拟中国地区岩石圈磁场,同时检验高质量的卫星数据中是否还包含模型模拟部分以外的其他信息,特别是岩石圈磁场中的一些小尺度特征,这些信息有... 详细信息

本研究主要关注Swarm卫星数据及CHAOS-6模型对岩石圈磁场的应用。重点考察该模型能否较好地模拟中国地区岩石圈磁场,同时检验高质量的卫星数据中是否还包含模型模拟部分以外的其他信息,特别是岩石圈磁场中的一些小尺度特征,这些信息有助于研究岩石圈磁场并提高模型的精度。基于Swarm卫星数据和CHAOS-6模型,将卫星数据沿轨道按纬度1^°为间隔网格化后,计算相邻网格的差值,即差分计算。对比不同轨道,不同时间段之间的轨道差分,同时还考虑模型中15-20阶磁场的长期变化,以研究岩石圈磁场中所包含的小尺度成分。结果显示CHAOS-6模型可以很好地模拟Swarm卫星数据,均方偏差在3nT左右,模型基本反映了地磁场的长期变化。此外,从数据上还发现了一个未被模拟的磁异常,该异常位于磁赤道附近,有可能是外源场影响的结果。对于岩石圈磁场的研究应更侧重于所建立的模型而非卫星数据本身。

关键词：地磁场 Swarm卫星任务岩石圈磁场 CHAOS-6模型

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Vapour retarders in wood frame walls and their effect on the drying capability

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Frontiers of Architectural Research 2013年第1期2卷 42-49页

作者： Stig Geving Jonas holme Norwegian University of Science and Technology Trondheim NO-7491 Norway SINTEF Building and Infrastructure Trondheim NO-7465 Norwoy

Wood frame wails typically need a vapour barrier at the warm side to avoid interstitial condensation due to vapour diffusion and air leakages from the interior. A more vapour open material than the traditional vapour barriers, here calted vapour retarder, could allow condensed moisture, buiLt-in-moisture or moisture from minor leakages to dry to the interior in addition to the outward drying. The application of permeable vapour retarders in wood frame wails have been investigated in this study by the use of a hygrothermat simulation tool. A traditional wood frame wail usually has good drying possibilities to the exterior. If a vapour retarder should have an effect on the total drying, it must not be too vapour tight. The purpose of this study was to find some threshold value for the maximum vapour resistance of a vapour retarder--when a requirement is that it should have a relatively large effect of the total drying of the wail. The increased risk for condensation as the vapour resistance decreases has however not been investigated in this study. In general it was found that permeable vapour barriers have retatively littte effect on the total drying of ordinary wood frame waits in a Nordic ctimate.

关键词： Vapour barrier Vapour retarder Wood frame watt Drying Moisture

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Integrating big data and blockchain to manage energy smart grids—TOTEM framework

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Blockchain(Research and Applications) 2022年第3期3卷 36-45页

作者： Dhanya Therese Jose Jørgen holme Antorweep Chakravorty Chunming Rong Department of Computer Science Electrical Engineering University of Stavanger4036StavangerNorway

The demand for electricity is increasing exponentially day by day,especially with the arrival of electric vehicles.In the smart community neighborhood project,electricity should be produced at the household or community level and sold or bought according to the demands.Since the actors can produce,sell,and buy according to the demands,thus the name prosumers.ICT solutions can contribute to this in several ways,such as machine learning for analyzing the household data for customer demand and peak hours for the usage of electricity,blockchain as a trustworthy platform for selling or buying,data hub,and ensuring data security and privacy of prosumers.TOTEM:Token for controlled computation is a framework that allows users to analyze the data without moving the data from the data owner's environment.It also ensures the data security and privacy of the data.Here,in this article,we will show the importance of the TOTEM architecture in the EnergiX project and how the extended version of TOTEM can be efficiently merged with the demands of the current and similar projects.

关键词： Blockchain Big data analytic Hyperledger fabric Hadoop Map Reduce Docker PIVT

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SURFACE TREATMENT OF POLY (ETHYLENE TEREPHTHALATE) FABRIC WITH POLYETHYLENEIMINE

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Chinese Journal of Polymer Science 1997年第4期15卷 311-318页

作者： O.J.ATEIZA I.holme J.E.McINTYRE Department of Textile Industries The University of Leeds Leeds LS2 9JT UKDepartment of Textile Industries The University of Leeds Leeds LS2 9JT UKDepartment of Textile Industries The University of Leeds Leeds LS2 9JT UK

A branched polyethyleneimine (BPEI) was applied to poly(ethylene terephthalate)(PET) fabric to improve its surface moisture absorption so that the fabric becomes lessliable to retention of electrostatic charg. The durability of this treatment was assessed bywashing and followed by measurement of charge development on the fabric. The treatedsamples showed improved surface wetting compared to the untreated. The results areconsistent with attachment of the BPEI to the PET surface by a cross-linking mechanism.

关键词： Surface modification Polyester Antistatic Polyethyleneimine treatment

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Mobility in China, 2020: a tale of four phases

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National Science Review 2021年第11期8卷 110-120页

作者： Suoyi Tan Shengjie Lai Fan Fang Ziqiang Cao Bin Sai Bing Song Bitao Dai Shuhui Guo Chuchu Liu Mengsi Cai Tong Wang Mengning Wang Jiaxu Li Saran Chen Shuo Qin Jessica R.Floyd Zhidong Cao Jing Tan Xin Sun Tao Zhou Wei Zhang Andrew J.Tatem petter holme Xiaohong Chen Xin Lu School of Business Central South University Institute of Big Data and Internet Innovations Hunan University of Technology and Business College of Systems Engineering National University of Defense Technology WorldPop School of Geography and Environmental ScienceUniversity of Southampton School of Mathematics and Big Data Foshan University State Key Laboratory on Blind Signal Processing State Key Laboratory of Management and Control for Complex Systems Institute of AutomationChinese Academy of Sciences Chinese Evidence-Based Medicine Center National Clinical Research Center for Geriatrics West China Hospital Sichuan University Big Data Research Center University of Electronic Science and Technology of China West China Biomedical Big Data Center West China Hospital Sichuan University Tokyo Tech World Hub Research Initiative Institute of Innovative Research Tokyo Institute of Technology

2020 was an unprecedented year,with rapid and drastic changes in human mobility due to the COVID-19 pandemic.To understand the variation in commuting patterns among the Chinese population across stable and unstable periods,we used nationwide mobility data from 318 million mobile phone users in China to examine the extreme fluctuations of population movements in 2020,ranging from the Lunar New Year travel season(chunyun), to the exceptional calm of COVID-19 lockdown,and then to the recovery period.We observed that cross-city movements,which increased substantially in chunyun and then dropped sharply during the lockdown,are primarily dependent on travel distance and the socio-economic development of cities.Following the Lunar New Year holiday,national mobility remained low until mid-February,and COVID-19 interventions delayed more than 72.89 million people returning to large cities.Mobility network analysis revealed clusters of highly connected cities,conforming to the social-economic division of urban agglomerations in China.While the mass migration back to large cities was delayed,smaller cities connected more densely to form new clusters.During the recovery period after travel restrictions were lifted,the netflows of over 55% city pairs reversed in direction compared to before the lockdown.These findings offer the most comprehensive picture of Chinese mobility at fine resolution across various scenarios in China and are of critical importance for decision making regarding future public-health-emergency response,transportation planning and regional economic development,among others.

关键词： human mobility travel restrictions COVID-19 mobile phone data behavioral response

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