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Modeling the early transmission of COVID-19 in New York and San Francisco using a pairwise network model

Infectious Disease Modelling 2022年第1期7卷 212-230页

作者： Shanshan Feng Xiao-Feng luo Xin Pei Zhen Jin mark lewis Hao Wang Department of Mathematics North University of ChinaTaiyuanShanxi030051China College of Mathematics Taiyuan University of TechnologyShanxiTaiyuan030024China Complex System Research Center Shanxi UniversityTaiyuan030006ShanxiChina Shanxi Key laboratory of Mathematical Techniques and Big Data Analysis on Disease Control and Prevention Shanxi UniversityTaiyuan030006ShanxiChina Department of Mathematics and Statistics Sciences University of AlbertaEdmontonAlbertaT6G 2G1Canada Department of Biological Sciences University of AlbertaEdmontonAlbertaT6G 2E9Canada

Classical epidemiological models assume mass ***,this assumption is violated when interactions are not *** the recent COVID-19 pandemic,and resulting shelter in place social distancing directives,mass action models must be modified to account for limited social *** this paper we apply a pairwise network model with moment closure to study the early transmission of COVID-19 in New York and San Francisco and to investigate the factors determining the severity and duration of outbreak in these two *** particular,we consider the role of population density,transmission rates and social distancing on the disease dynamics and *** analysis shows that there is a strongly negative correlation between the clustering coefficient in the pairwise model and the basic reproduction number and the effective reproduction *** shelter in place policy makes the clustering coefficient increase thereby reducing the basic reproduction number and the effective reproduction *** switching population densities in New York and San Francisco we demonstrate how the outbreak would progress if New York had the same density as San Francisco and *** results underscore the crucial role that population density has in the epidemic *** also show that under the assumption of no further changes in policy or transmission dynamics not lifting the shelter in place policy would have little effect on final outbreak size in New York,but would reduce the final size in San Francisco by 97%.

关键词： COVID-19 Social network Quarantine Social distance Clustering coefficient

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Efficacy of equine-assisted psychotherapy in veterans with posttraumatic stress disorder

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Journal of Integrative Medicine 2019年第1期17卷 14-19页

作者： l.Elisabeth Burton Fares Qeadan mark R.Burge College of Nursing University of New Mexico Health Sciences Center Department of Internal Medicine/Epidemiology Biostatistics & Preventive Medicine University of New Mexico Health Sciences Center Department of Internal Medicine/Endocrinology University of New Mexico Health Sciences Center

Background: Posttraumatic stress disorder(PTSD) is a common and debilitating disorder among war veterans. Although complementary and alternative therapies are gaining acceptance in the treatment of PTSD, the efficacy of animal-based therapies in this disorder is unknown. The goal of equine-assisted psychotherapy(EAP) is to improve the social, emotional, and/or cognitive functions of individuals with ***: This study aims to explore the effects of EAP on PTSD symptoms. We hypothesized that veterans with PTSD who participate in a standardized EAP program for 1 h per week for 6 weeks would experience decreased PTSD symptoms and would demonstrate increased resilience as compared with individuals who do not receive EAP ***, setting, participants and interventions: We conducted a sequentially assigned, two-arm parallel group trial comparing 6 weeks of EAP with standard, previously established, ongoing PTSD *** was conducted at a community EAP facility in conjunction with an academic University Hospital. Twenty adult veterans with symptomatic PTSD completed the study. Ten adult veterans with previously diagnosed PTSD were assigned to EAP and received directed interaction with trained horses for one hour a week in groups of 3 or 4 individuals, while also continuing their previously established therapies. A certified therapist supervised the sessions, and a professional horse handler was also *** were compared with those from 10 adult veterans who only received their standard previously established PTSD care as prescribed by their *** outcome measures: Changes in salivary cortisol, scores for the PTSD Check list-Military Version(PCl-M) and the Connor-Davidson Resilience Scale(CD-RISC) after 6 weeks of study were ***: Of the 20 enrolled patients, 10 served in Afghanistan, 5 served in Iraq, and 3 served in Vietnam. Subjects were(47 ± 14) years old, were predominantly male, and had a body mass index of(29

关键词： Posttraumatic stress disorder Military veterans Alternative therapy Equine-assisted psychotherapy Clinical trial

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Differential effects of short term winter thermal stress on diapausing tiger swallowtail butterflies （Papilio spp.）

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Insect Science 2012年第3期19卷 277-285页

作者： J. mark Scriber Emily Maher Matthew l. Aardema Department of Entomology Michigan State University East Lansing MI McGuire Center for lepidoptera and Biodiversity Florida Museum of Natural History University of Florida Gainesville FL Department of Ecology and Evolutionary Biology Princeton University Princeton N J USA

It is generally thought that insects inhabiting lower latitudes are more severely impacted by changes in their thermal environment than are high latitude species. This is attributed to the wider range of temperatures to which high-latitude species are exposed. By contrast, low-latitude species have typically evolved in more thermally stable environments with a narrower range of temperature variation. However, deviation from this pattern can occur and here we report that under variable winter conditions a higher latitude species may be more sensitive to thermal variation than its lower latitude sister species. Using split broods, we examined the survival and adult emergence success of diapausing pupae of Papilio canadensis and P. glaucus, as well as a unique, recombinant hybrid population （＂late-flight＂） to short periods of mid-winter cold and heat stress. Our results indicate that the higher latitude, univoltine populations （P. canadensis and late-flights） exhibit lower pupal survival than the lower latitude, facultative diapauser （P. glaucus） for all mid-winter thermal stress treatments, both high and low. Size differences alone do not appear to account for the observed differences in survival or metabolic costs in these three pheno- types, as late-flight individuals are similar in size to R glaucus. We attribute the observed differences in survival and weight loss to potential metabolic differences and variation in the intensity of diapause, in addition to divergent adaptation to winter precipitation levels （e.g. snow cover） and the influences this may have on microhabitat temperature moderation.

关键词： climate change developmental threshold incipient hybrid species metabolic cost Papilionidae post-diapause delays thermal stress

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The structure of Rap1 in complex with RIAM reveals specificity determinants and recruitment mechanism

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Journal of Molecular Cell Biology 2014年第2期8卷 128-139页

作者： Hao Zhang Yu-Chung Chang mark l. Brennan Jinhua Wu Developmental Therapeutics Program Fox Chase Cancer Center 333 Cottman Avenue Philadelphia PA 19111 USA

The small GTPase Rap1 induces integrin activation via an inside-out signaling pathway mediated by the Rapl-interacting adaptor mol- ecule （RIAM）. Blocking this pathway may suppress tumor metastasis and other diseases that are related to hyperactive integrins. However, the molecular basis for the specific recognition of RIAM by Rap1 remains largely unknown. Herein we present the crystal structure of an active, GTP-bound GTPase domain of Rap1 in complex with the Ras association （RA）-pleckstrin homology （PH） structural module of RIAM at 1.65 A. The structure reveals that the recognition of RIAM by Rap1 is governed by side-chain interactions. Several side chains are critical in determining specificity of this recognition, particularly the lys31 residue in Rap1 that is oppositely charged compared with the Glu31/Asp31 residue in other Ras GTPases. lys31 forms a salt bridge with RIAM residue Glu212, making it the key specificity determinant of the interaction. We also show that disruption of these interactions results in reduction of Rapl：RIAM association, leadingto a loss of co-clustering and cell adhesion. Our findings elucidate the molecular mechanism by which RIAM med- iates Rapl-induced integrin activation. The crystal structure also offers new insight into the structural basis for the specific recruitment of RA-PH module-containing effector proteins by their smaU GTPase partners.

关键词： RIAM Rap1 integrin signaling inside-out signaling crystal structure RA-PH

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Alternatives for large-scale production of cultured beef: A review

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Journal of Integrative Agriculture 2015年第2期14卷 208-216页

作者： Matilda S M Moritz Sanne E l Verbruggen mark J Post Department of Physiology Maastricht UniversityMaastricht 6229 ER The Netherlands Department of Physics Chemistry and Biology Linkping UniversityLinkping SE-581 83 Sweden

Cultured beef is a method where stem cells from skeletal muscle of cows are cultured in vitro to gain edible muscle tissue. For large-scale production of cultured beef, the culture technique needs to become more efficient than today＇s 2-dimensional（2D） standard technique that was used to make the first cultured hamburger. Options for efficient large-scale production of stem cells are to culture cells on microcarriers, either in suspension or in a packed bed bioreactor, or to culture aggregated cells in suspension. We discuss the pros and cons of these systems as well as the possibilities to use the systems for tissue culture. Either of the production systems needs to be optimized to achieve an efficient production of cultured beef. It is anticipated that the optimization of large-scale cell culture as performed for other stem cells can be translated into successful protocols for bovine satellite cells resulting in resource and cost efficient cultured beef.

关键词： cultured beef microcarriers aggregated cells packed bed bioreactor cell culture

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Multi-length scale bioprinting towards simulating microenvironmental cues

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Bio-Design and Manufacturing 2018年第2期1卷 77-88页

作者： Elisabeth l Gill Xia li mark A. Birch Yan Yan Shery Huang Department of Engineering University of CambridgeTrumpington Street Cambridge CB2 1PZ UK Division of Trauma and Orthopaedic Surgery Department of Surgery University of Cambridge Cambridge UK

It is envisaged that the creation of cellular environments at multiple length scales, that recapitulate in vivo bioactive and structural roles, may hold the key to creating functional, complex tissues in the laboratory. This review considers recent advances in biofabrication and bioprinting techniques across different length scales. Particular focus is placed on 3D printing of hydrogels and fabrication of biomaterial fibres that could extend the feature resolution and material functionality of soft tissue constructs. The outlook from this review discusses how one might create and simulate microenvironmental cues in vitro. A fabrication platform that integrates the competencies of different biofabrication technologies is proposed. Such a multi-process, multiscale fabrication strategy may ultimately translate engineering capability into an accessible life sciences toolkit, fulfilling its potential to deliver in vitro disease models and engineered tissue implants.

关键词： 3D bioprinting Electrospinning Additive manufacturing Microenvironment Disease modelling Tissueengineering

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Antibiotic prophylaxis in variceal hemorrhage:Timing,effectiveness and Clostridium difficile rates

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World Journal of Gastroenterology 2010年第42期16卷 5317-5323页

作者： Matthew Rl Brown Graeme Jones Kathryn l Nash mark Wright Indra Neil Guha National Institute for Health Research Nottingham Digestive Diseases Centre Biomedical Research Unit Nottingham University Hospitals NHS TrustE Level West BlockQueens Medical Centre CampusDerby RoadNottinghamNG7 2UHUnited kingdom Department of Microbiology Southampton University Hospital TrustLevel BSouthampton General HospitalSouthamptonS016 6YDUnited Kingdom liver Unit Southampton University Hospital TrustLevel FSouthampton General HospitalSouthamptonSO16 6YDUnited Kingdom

AIM:To investigate if antibiotics administered within 8 h of endoscopy reduce mortality or increase the incidence of Clostridium difficile infection(CDI).METHODS:A 2-year retrospective analysis of all patients who presented with first variceal hemorrhage was *** primary outcome measure was 28-d *** outcome measures were 28-d rebleeding rates and 28-d incidence of *** patients were admitted to a tertiary liver unit with a consultantled,24-h endoscopy *** received standard care including terlipressin *** collection included:primary and secondary outcome measures,timing of first administration of intravenous antibiotics,eti-ology of liver disease,demographics,endoscopy details and complications.A prospective study was undertaken to determine the incidence of CDI in the study population and general medical inpatients admitted for antibiotic therapy of at least 5 d *** analysis was undertaken using univariate,non-parametric tests and multivariate logistic regression ***:There were 70 first presentations of variceal hemorrhage during the study *** percent of cases were male and 65.7% were due to chronic alcoholic liver *** total,64/70(91.4%) patients received antibiotics as prophylaxis during their ***,53/70(75.7%) received antibiotics either before endoscopy or within 8 h of endoscopy [peri-endoscopy(8 h) group],whereas 17/70(24.3%) received antibiotics at > 8 h after endoscopy or not at all(non peri-endoscopy group).Overall mortality and rebleeding rates were 13/70(18.6%) and 14/70(20%),*** periendoscopy(8 h) group was significantly less likely to die compared with the non peri-endoscopy group [13.2% vs 35.3%,P = 0.04,odds ratio(OR) = 0.28(0.078-0.997)] and showed a trend towards reduced rebleeding [17.0% vs 29.4%,P = 0.27,OR = 0.49(0.14-1.74)].On univariate analysis,the non peri-endoscopy group [P = 0.02,OR = 3.58(1.00-12.81)],higher mode

关键词： Variceal hemorrhage Mortality Antibiotics Prophylaxis Clostridium difficile

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Tropical cyclone activities in the Western North Paci fi c in 2022

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TROPICAl CYClONE RESEARCH AND REVIEW 2024年第2期13卷 125-135页

作者： Huang, Xin Bai, lina Yu, Zifeng Chan, Johnny C. l. Yu, Hui Tang, Jie Guo, Rong Wan, Rijin China Meteorol Adm Shanghai Typhoon Inst Shanghai 200030 Peoples R China Asia Pacific Typhoon Collaborat Res Ctr Shanghai Peoples R China City Univ Hong Kong Sch Energy & Environm Hong Kong Peoples R China

Based on the best-track dataset from the Shanghai Typhoon Institute/China Meteorological Administration, the paper provides a comprehensive summary and analysis of tropical cyclone (TC) activities in the Western North Pacific (WNP) and the South China Sea (SCS) for 2022. Using the historical climatology from 1951 to 2020, the anomalous conditions during 2022 in TC frequency, origin locations, tracks, intensity, and duration for the entire ocean basin as well as landfall events in China are examined. Results show that the overall TC frequency is slightly lower than normal, but the multiple TC events have a very high frequency of occurrence. Origin locations of TCs, which mark the starting points of their paths, show a large westward and northward deviation from climatology. Around 40% of the named TCs exhibit a shift in their direction of movement from westerly to easterly. Additionally, comparisons of the means, medians, upper and lower quartiles all indicate that the intensity of TCs in 2022 is generally lower than the climatology, with the duration of TCs at tropical storm intensity or above being shorter than usual. A notable observation is the fewer incidence of TC landfalls in China, but with a geographical concentration in Guangdong Province. These anomalous annual TC activities are influenced by related atmospheric and oceanic environmental conditions modulated by multi-scale climate variability. The findings provide useful information for enhancing disaster mitigation strategies in the Asia-Pacific region. (c) 2024 The Shanghai Typhoon Institute of China Meteorological Administration. Publishing services by Elsevier B.V. on behalf of KeAi Communication Co. ltd. This is an open access article under the CC BY-NC-ND license (http://***/licenses/by-nc-nd/4.0/).

关键词： Tropical cyclone Western North Paci fi c Anomalous characteristics Annual report TYPHOON COMMITTEE REGION El-NINO INTERANNUAl VARIABIlITY INTERDECADAl VARIATIONS GENESIS FREQUENCY 3RD ASSESSMENT ClIMATE-CHANGE ENSO OSCIllATION INTENSITY

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Building Expertise on FAIR Through Evolving Bring Your Own Data(BYOD) Workshops: Describing the Data, Software, and Management-focused Approaches and Their Evolution

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Data Intelligence 2024年第2期6卷 429-456页

作者： César H.Bernabé lieze Thielemans Rajaram Kaliyaperumal Claudio Carta Shuxin Zhang Celia W.G.van Gelder Nirupama Benis luiz Olavo Bonino da Silva Santos Ronald Cornet Bruna dos Santos Vieira Nawel lalout Ines Henriques Alberto Camara Ballesteros Kees Burger Martijn G.Kersloot Friederike Ehrhart Esther van Enckevort Chris T.Evelo Alasdair J.G.Gray Marc Hanauer Kristina Hettne Joep de ligt Arnaldo Pereira Nuria Queralt-Rosinach Erik Schultes Domenica Taruscio Andra Waagmeester mark D.Wilkinson Egon l.Willighagen Mascha Jansen Barend Mons Marco Roos Annika Jacobsen Biosemantics Group Department of Human GeneticsLeiden University Medical CentreLeidenThe Netherlands NIHR Academic Fellow in General Practice University College London and The Royal Free NHS Foundation Trust National Centre for Rare Diseases Istituto Superiore di SanitaRomeItaly Department of Medical Informatics Amsterdam UMC location University of AmsterdamMeibergdreef 9AmsterdamThe Netherlands Amsterdam Public Health Methodology&Digital HealthAmsterdamThe Netherlands Health-Rl UtrechtThe Netherlands Semantics Services and Cybersecurity groupUniversity of TwenteEnschedeThe Netherlands Department of Medical Imaging Radboud Institute for Health SciencesRadboud University Medical CenterNijmegenThe Netherlands Department of Medical BioSciences Radboud University Medical CenterNijmegenThe Netherlands The Duchenne Parent Project VeneendaalThe Netherlands Departamento de Biotecnologia-Biologia Vegetal Escuela Tecnica Superior de Ingenieria AgronomicaAlimentaria y de BiosistemasCentro de Biotecnologia y Genomica de PlantasUniversidad Politecnica de Madrid(UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria-CSIC(INIA-CSIC).Campus MontegancedoPozuelo de Alarcon(Madrid)Spain Castor AmsterdamThe Netherlands Department of Bioinformatics-BiGCaT Maastricht UniversityMaastrichtThe Netherlands University Medical Center Groningen University of GroningenGroningenThe Netherlands Maastricht Centre for Systems Biology(MaCSBio) Maastricht UniversityMaastrichtThe Netherlands Department of Computer Science Heriot-Watt UniversityEdinburghUK INSERM US14-OrphanetPlateforme Maladies RaresParisFrance Centre for Digital Scholarship Leiden University LibrariesThe Netherlands Center for Molecular Medicine Cancer Genomics NetherlandsDepartment of GeneticsUniversity Medical Center UtrechtUniversity UtrechtThe Netherlands University of Aveiro DETI/IEETAAveiroPortugal GO FAIR Foundation LeidenThe Netherlands The leiden Academic Center for Drug Research LeidenThe Netherlands Micel

Since 2014,"Bring Your Own Data"workshops(BYODs)have been organised to inform people about the process and benefits of making resources Findable,Accessible,Interoperable,and Reusable(FAIR,and the FAIRification process).The BYOD workshops'content and format differ depending on their goal,context,and the background and needs of ***-focused BYODs educate domain experts on how to make their data FAIR to find new answers to research ***-focused BYODs promote the benefits of making data FAIR and instruct project managers and policy-makers on the characteristics of FAIRification ***-focused BYODs gather software developers and experts on FAIR to implement or improve software resources that are used to support ***,these BYODs intend to foster collaboration between different types of stakeholders involved in data management,curation,and reuse(*** experts,trainers,developers,data owners,data analysts,FAIR experts).The BYODs also serve as an opportunity to learn what kind of support for FAIRification is needed from different communities and to develop teaching materials based on practical examples and *** this paper,we detail the three different structures of the BYODs and describe examples of early BYODs related to plant breeding data,and rare disease registries and biobanks,which have shaped the structure of the *** discuss the latest insights into making BYODs more productive by leveraging our almost ten years of training experience in these workshops,including successes and encountered ***,we examine how the participants'feedback has motivated the research on FAIR,including the development of workflows and software.

关键词： FAIR FAIRification FAIR expertise Bring Your Own Data Workshop BYOD

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length–mass allometries in amphibians

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Integrative Zoology 2018年第1期13卷 36-45页

作者： luca SANTINI Ana BENÍTEZ-lÓPEZ Gentile Francesco FICETOlA mark A.J.HUIJBREGTS Department of Environmental Science Institute for Wetland and Water ResearchFaculty of ScienceRadboud UniversityNijmegenthe Netherlands Department of Bioscience University of MilanMilanItaly Alpine Ecology laboratory Grenoble Alpes UniversityGrenobleFrance PBl Netherlands Environmental Assessment Agency The Haguethe Netherlands

Body mass is rarely recorded in amphibians,and other body measurements(*** to vent length,SVl)are generally collected ***,length measurements,when used as proxies of body mass in comparative analyses,are problematic if different taxa and morphotypes are *** developed allometric relationships to derive body mass from SVl *** fitted phylogenetic generalized least square models for frogs(Anura)and salamanders(Caudata)and for several families *** tested whether allometric relationships differed between species with different habitat preferences and between morphs in *** were fitted with SVl-mass measurements for 88 frog and 42 salamander *** assessed the predictive performance of the models by ***,the models showed high explained variance and low forecasting *** differed among semi-aquatic,terrestrial and arboreal frogs,and between paedomorphic and non-paedomorphic *** mass estimates derived from our models allow for comparability of studies on multiple taxa and can be used for testing theories built upon evolutionary and ecological processes which are directly related to body mass.

关键词： Anura body size body weight Caudata SVl

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