# pos

id: cord-303165-ikepr2p2
pos: UH
token:
  https://www.gov.uk/government/uploads/system/uploads/attach-ment_data/file/127106/121109-NHS-Outcomes-Framework-2013-14.pdf

lemma:
  https://www.gov.uk/government/uploads/system/uploads/attach-ment_data/file/127106/121109-nhs-outcomes-framework-2013-14.pdf


# ent

id: cord-010334-7ce0xhjo
type: WORK_OF_ART
entity:
  The Relationship Exploration between Public Migration Attention and Population Migration from a Perspective of Search Query date 2020 04 01


id: cord-018116-99z6ykb2
type: ORG
entity:
  Epidemiology Medicins Sans Frontieres Refugee Health An Approach to Emergency Situations Geneva International Committee


id: cord-002774-tpqsjjet
type: GGP
entity:
  Ii 0 11 p 0 01 and symptoms of pain Ii 0 14 p 0 01 fatigue ji 0 34 p 0 001 and cognitive difficulties p 0 30 P 0 001 For the three dimensions of the IIRS multiple regression results revealed 1


id: cord-002774-tpqsjjet
type: LAW
entity:
  The Collaborative Process to Achieve Access to Primary Health Care for Black Women and Women of Colour Project


id: cord-002774-tpqsjjet
type: EVENT
entity:
  Black Women and Women of Colour Women s Health in Women s Hands Community Health Centre Sistering Parkdale Community Health Centre Rexdale Community Health Centre


id: cord-002774-tpqsjjet
type: LAW
entity:
  P5 77 C Health and Livelihood Implications of Marginalization of Slum Dwellers in Provision of Water and Sanitation Services


id: cord-002774-tpqsjjet
type: DISEASE
entity:
  HIV Criminal justice system involvement was measured by arrest incarceration drug felony and loss denial of social services


id: cord-020941-1qwbkg9o
type: DISEASE
entity:
  human disturbance of the environment Red deer and feral cats for example inhabit much of New Zealand s pristine


id: cord-022506-fkddo12n
type: PROTEIN
entity:
  Cat DOI 10 1016 b978 1 4377 0660 4 00046 6 sha 2008ee1efb1933782788fb8ab79c97d58ca35028 doc_id 22506 cord_uid fkddo12n nan O U T L I N E


id: cord-022506-fkddo12n
type: ORG
entity:
  European Convention for the Protection of Vertebrate Animals Used for Experimental and Other Scientific Purposes


id: cord-265357-3f0xph0y
type: DNA
entity:
  G31 Mluc 34 D15 H19 H23 H29 35 Mnatt 1 Mnatt 2 36 Mschreib3 37 Mnatt 8 Mnatt 11 38 FV5AP 39 and GZBYR 5 TCCTTGTCACTATAAGCTCAGTGG 3 forward 5 CCAGGCAATAGTCTCCTAGCAC 3


id: cord-265357-3f0xph0y
type: DNA
entity:
  Schreibers long fingered bat Miniopterus schreibersii Chiroptera Vespertilionidae Isolation and characterization of eight polymorphic microsatellite loci


id: cord-299261-ew99nraq
type: CELL_LINE
entity:
  COVID 19 Imperial College London COVID 19 Response Team Baseline Characteristics and Outcomes of 1591 Patients Infected With SARS


id: cord-299261-ew99nraq
type: ORG
entity:
  US Centers for Disease Control and Prevention Considerations for Institutions of Higher Education Extensive


id: cord-299261-ew99nraq
type: WORK_OF_ART
entity:
  The Effect of Individual Movements and Interventions on the Spread of Influenza in Long Term Care Facilities Individual


id: cord-299261-ew99nraq
type: ORG
entity:
  The Guardian Outbreak Investigation of COVID 19 Among Residents and Staff of an Independent and Assisted Living Community for Older Adults in Infections in Residents of a Long Term Care Skilled Nursing Facility Asymptomatic SARS CoV


id: cord-176540-48mapwlq
type: GGP
entity:
  p i 1 0 1 p i 1 0 end end Iteration for i 1 n if i round k 1 dT Sder i alpha I i S i 1 p i N gamma theta S i Rder i beta I i Ider i alpha I i S i 1 p i N beta I i R i 1 R i Rder i dT I i 1 I i Ider i


id: cord-176540-48mapwlq
type: GGP
entity:
  Sder i alpha I i S i 1 p i 0 3 N gamma theta S i Rder i beta I i i S i 1 p i 0 3 N beta I i R i 1 R i Rder i dT I i 1 I i Ider i dT S i 1 S i Sder i


id: cord-176540-48mapwlq
type: GGP
entity:
  Sder i alpha I i S i 1 p i 0 4 N gamma theta S i Rder i beta I i i S i 1 p i 0 4 N beta I i R i 1 R i Rder i dT I i 1 I i Ider i dT S i 1 S i Sder i dT i 1 p i 0 45 N gamma theta S i Rder i beta I i i S i 1 p i 0 45 N beta I i R i 1 R i Rder i dT I i 1 I i Ider i dT S i 1 S i Sder i dT I 1 for i 2 Tf I_per_day i I i 1


id: cord-176540-48mapwlq
type: CHEMICAL
entity:
  N gamma theta S i Rder i beta I i Ider i alpha I i S i 1 p i N beta I i R i 1 R i Rder i dT I i 1 I i Ider i dT ylabel Recovered people n o of people Sobre


id: cord-176540-48mapwlq
type: CHEMICAL
entity:
  N gamma theta S i Rder i beta I i i S i 1 p i 0 2 N beta I i R i 1 R i Rder i dT I i 1 I i Ider i dT S i 1 S i Sder i dT


id: cord-176540-48mapwlq
type: CHEMICAL
entity:
  N gamma theta S i Rder i beta I i i S i 1 p i 0 25 N beta I i R i 1 R i Rder i dT I i 1 I i Ider i dT S i 1 S i Sder i dT


id: cord-176540-48mapwlq
type: CHEMICAL
entity:
  N gamma theta S i Rder i beta I i i S i 1 p i 0 3 N beta I i R i 1 R i Rder i dT I i 1 I i Ider i dT S i 1 S i Sder i dT


id: cord-176540-48mapwlq
type: CHEMICAL
entity:
  N gamma theta S i Rder i beta I i i S i 1 p i 0 4 N beta I i R i 1 R i Rder i dT I i 1 I i Ider i dT S i 1 S i Sder i dT i 1 p i 0 45 N gamma theta S i Rder i beta I i i S i 1 p i 0 45 N beta I i R i 1 R i Rder i dT I i 1 I i Ider i dT S i 1 S i Sder i dT I 1 for i 2 Tf I_per_day i I i 1 dT


id: cord-298009-0iv9fdof
type: ORG
entity:
  Ministry of Agriculture Forestry and Fisheries Promotion of Smart Agriculture Information and Communications


id: cord-299828-fb84rtmx
type: ORG
entity:
  National Wildlife Health Center Wildpro National Biological Information Infrastructure Wildlife Disease Information


id: cord-302056-wvf6cpib
type: WORK_OF_ART
entity:
  Cases Evaluating the Accuracy of Different Respiratory Specimens in the Laboratory Diagnosis and Monitoring the Viral Shedding


id: cord-287133-2mldz987
type: ORG
entity:
  Adaptive Environmental Assessment and Management Adaptive Management of Natural Resources Theory Concepts and Management Institutions Testing


id: cord-151532-mpv2wegm
type: PERSON
entity:
  Burkhardt Amanda M Bustamante Carlos Cao Lormeau Van Mai Corcoran Martin M Duffy Darragh Guajardo Macarena Fuentes Fujita


id: cord-304399-7t2mu13s
type: CELL_LINE
entity:
  Red Cross Integrating palliative care and symptom relief into the response to humanitarian emergencies and crises COVID 19 Operational guidance for maintaining essential health services during an outbreak United Nations Office for the Coordination of Humanitarian Affairs OCHA Population Level


id: cord-331608-ezf9r8l4
type: CHEMICAL
entity:
  certains d entre eux ont estimé que la distanciation sociale n avait pas eu d effet significatif Dans notre étude une nouvelle vision de l importance de la distanciation sociale pour prévenir la propagation du coronavirus


id: cord-312885-d4ku8dyz
type: WORK_OF_ART
entity:
  OpenSAFELY Prevalence of Underlying Medical Conditions Among Selected Essential Critical Infrastructure Workers Behavioral Risk Factor Surveillance System


id: cord-314325-nquov2i0
type: ORG
entity:
  Virus Dynamics Mathematical Principles of Immunology and Virology Emerging Microbial Threats to Health


id: cord-313869-3x2qf3yu
type: WORK_OF_ART
entity:
  Spread of Infectious Disease Modeling and Analysis of Different Factors on Spread of Infectious Disease


id: cord-313869-3x2qf3yu
type: WORK_OF_ART
entity:
  The Mathematical Theory of Infectious Diseases and Its Applications The Mathematics of Infectious Diseases Modelling


id: cord-328865-ekgqdjlk
type: ORG
entity:
  Bethesda MD National Institutes of Health National Institute of Diabetes and Digestive and Kidney Diseases Serology


id: cord-257969-2tax8ajw
type: WORK_OF_ART
entity:
  The Lancet Effect of Dexamethasone in Hospitalized Patients with COVID 19 Preliminary Report COVID 19 and Cardiovascular Disease Global


id: cord-345811-f0yt2a32
type: ORG
entity:
  CDC Public Health Program Public Health Practice Program Ofice Training and Education in Public Health Law


id: cord-345811-f0yt2a32
type: ORG
entity:
  the Ideological Impact of Legal Education on the Profession Thinking Beyond My Own Interpretation Reflections on Collaborative and Cooperative Learning Theory


id: cord-345811-f0yt2a32
type: ORG
entity:
  The Relationship Between Student Illicit Drug Use and School Drug Testing Policies Medicine and Public Health Ethics and Human Rights


id: cord-274019-dao10kx9
type: WORK_OF_ART
entity:
  The Confounding Effect of Population Structure on Bayesian Skyline Plot Inferences of Demographic History Bayesian


id: cord-274019-dao10kx9
type: ORG
entity:
  Posterior Distributions for a Star Tree IQ TREE A Fast and Effective Stochastic Algorithm for Estimating Maximum Likelihood Phylogenies


id: cord-280048-b4dz1lnn
type: WORK_OF_ART
entity:
  Thinking Outside the Triangle Replication Fidelity of the Largest RNA Viruses Theoretical Models of Generalized Quasispecies Alterations


id: cord-280048-b4dz1lnn
type: ORG
entity:
  Differential Shape of Geminivirus Mutant Spectra Across Cultivated and Wild Hosts With Invariant Viral Consensus Sequences Genetic


id: cord-345843-yz0buegp
type: ORG
entity:
  The World Health Organization International Organization for Migration International Labour Organization


id: cord-345843-yz0buegp
type: ORG
entity:
  Globalization People Perspectives and Progress Modernity at Large Cultural Dimensions of Globalization Globalization


id: cord-345843-yz0buegp
type: ORG
entity:
  Population Division World Population Prospects The United Nations Department of Economic and Social Affairs Report


id: cord-345843-yz0buegp
type: ORG
entity:
  Migration Medicine Health Principles Practice Institute of Medicine Committee on Emerging Microbial Threats to Health Emerging Infections Microbial Threats to Health


id: cord-345843-yz0buegp
type: ORG
entity:
  Uprooted People and Long Term Travellers World Health Organization International Health Regulations Delivery of health


id: cord-345843-yz0buegp
type: EVENT
entity:
  the Millennium Cohort Study International Migration and Development Perspectives and Experiences of IOM The Organization Delivery of medical


id: cord-345843-yz0buegp
type: ORG
entity:
  The Organization Department of Economic and Social Affairs Population Division International Migration Vision 2020


id: cord-329244-z28twpb1
type: ORG
entity:
  the Saguenay Fjord World Health Organization International Agency for Research on Cancer IARC Monographs


id: cord-351880-iqr419fp
type: DISEASE
entity:
  coronavirus 2019 nCoV has spread internationally since the initial report of cases by Wuhan Municipal Health Commission China


id: cord-303187-ny4qr2a2
type: ORG
entity:
  CEPEA Commission of Ethics in Research Involving Animals of the Federal University of São João del Rey


id: cord-303187-ny4qr2a2
type: WORK_OF_ART
entity:
  Revisiting the Effect of Capture Heterogeneity on Survival Estimates in Capture Mark Recapture Studies


id: cord-352664-heoj8ji8
type: CL
entity:
  red circles Y Y open circles H 2 0 negative control grey circles not determined Where shown background color reflects grouping of field samples within particular population clusters cluster 1 pink cluster 2 green cluster 3 blue cluster 4 red Numbers reflect population clusters within each genotype


id: cord-346500-uwi3ezd7
type: DISEASE
entity:
  infectious individuals P k I k j t P k N k j t Finally c j is the coupling coefficient of location j This


id: cord-349581-o320ogmg
type: WORK_OF_ART
entity:
  The Knowledge How to Rebuild Civilization in the Aftermath of a Cataclysm Black Code Censorship Surveillance


id: cord-349581-o320ogmg
type: WORK_OF_ART
entity:
  STEP Existential Risks Exploring a Robust Risk Reduction Strategy Automatic Fault Protection in the Voyager Spacecraft Disaster Prepper Health Identity


# url

id: cord-303165-ikepr2p2
domain: www.gov.uk
url:
  http://www.gov.uk/government/uploads/system/uploads/attach-ment_data/file/127106/121109-NHS-Outcomes-Framework-2013-14.pdf


# bib

id: cord-001714-jfawhnsq
title: Bridge hosts, a missing link for disease ecology in multi-host systems
author: Caron, Alexandre
date: 2015-07-21
txt: ./txt/cord-001714-jfawhnsq.txt
cache: ./cache/cord-001714-jfawhnsq.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4509689/
doi: 10.1186/s13567-015-0217-9
summary:
  We illustrate this framework using the example of the transmission of Avian Influenza Viruses across wild bird/poultry interfaces in Africa and discuss a range of other examples that demonstrate the usefulness of our definition for other multi-host systems. Lastly, we present an operational framework to identify potential bridge host populations, using as a case study the ecology of avian influenza viruses at the wild/domestic bird interface in Africa and also giving other multi-host systems examples. As a consequence, the information available on most wild bird species is scarce and has been obtained mostly from by-catch (i.e. captured non-targeted species) of studies investigating AIV in maintenance waterfowl, resulting in small sample sizes that are inadequate to provide epidemiological understanding of the host roles in AIV ecology in Africa [26] . The range of methods available to characterize host competence for AIV and contact patterns between maintenance, potential bridge and target host populations is drawn from the fields of epidemiology and avian ecology ( Table 2) .

abstract:
  In ecology, the grouping of species into functional groups has played a valuable role in simplifying ecological complexity. In epidemiology, further clarifications of epidemiological functions are needed: while host roles may be defined, they are often used loosely, partly because of a lack of clarity on the relationships between a host’s function and its epidemiological role. Here we focus on the definition of bridge hosts and their epidemiological consequences. Bridge hosts provide a link through which pathogens can be transmitted from maintenance host populations or communities to receptive populations that people want to protect (i.e., target hosts). A bridge host should (1) be competent for the pathogen or able to mechanically transmit it; and (2) come into direct contact or share habitat with both maintenance and target populations. Demonstration of bridging requires an operational framework that integrates ecological and epidemiological approaches. We illustrate this framework using the example of the transmission of Avian Influenza Viruses across wild bird/poultry interfaces in Africa and discuss a range of other examples that demonstrate the usefulness of our definition for other multi-host systems. Bridge hosts can be particularly important for understanding and managing infectious disease dynamics in multi-host systems at wildlife/domestic/human interfaces, including emerging infections. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13567-015-0217-9) contains supplementary material, which is available to authorized users.


id: cord-002774-tpqsjjet
title: Section II: Poster Sessions
author: nan
date: 2017-12-01
txt: ./txt/cord-002774-tpqsjjet.txt
cache: ./cache/cord-002774-tpqsjjet.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5711696/
doi: 10.1093/jurban/jti137
abstract: nan
summary:
  Results: The CHIP Framework The CHIP framework aims to improve the health and wellness of the urban communities served by St. Josephs Health Centre through four intersecting pillars: • Raising Community Voices provides an infrastructure and process that supports community stakeholder input into health care service planning, decision-making, and delivery by the hospital and across the continuum of care; • Sharing Reciprocal Capacity promotes healthy communities through the sharing of our intellectual and physical capacity with our community partners; • Cultivating Integration Initiatives facilitates vertical, horizontal, and intersectoral integration initiatives in support of community-identified needs and gaps; and • Facilitating Healthy Exchange develops best practices in community integration through community-based research, and facilitates community voice in informing public policy.


id: cord-005189-z92vwovw
title: Are Megacities Sustainable?
author: Saier, Milton H.
date: 2006-07-28
txt: ./txt/cord-005189-z92vwovw.txt
cache: ./cache/cord-005189-z92vwovw.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088849/
doi: 10.1007/s11270-006-9211-1
abstract: nan
summary:
  Increasing numbers of people are moving to cities, causing urban populations to expand. Moreover, the primary product produced by a particular urban population may result from the presence of a single company, and its presence in that city reflects the decisions of just a few executives. This tremendous rise results both from astronomical global birth over death rates and from the migration of rural populations to the cities. Moreover, about 1% of the world_s rural population moves from the country to the cities every two years. The sudden loss of a city_s infrastructure due to a natural or man-created disaster would be expected to promote human suffering of a magnitude that far surpasses anything that could have occurred in the past with a less centralized population living in a rural setting. Past examples of urban disasters abound: The great San Francisco earthquake and fire of 1906 caused thousands of deaths and tremendous loss of property.


id: cord-007749-lt9is0is
title: The Human Environment Interface: Applying Ecosystem Concepts to Health
author: Preston, Nicholas D.
date: 2013-05-01
txt: ./txt/cord-007749-lt9is0is.txt
cache: ./cache/cord-007749-lt9is0is.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121839/
doi: 10.1007/82_2013_317
summary:
  Despite the fact that most EIDs originate in wildlife, few studies account for the population, community, or ecosystem ecology of the host, reservoir, or vector. The dimensions of ecological approaches to public health that we propose in this chapter are, in essence, networks of population dynamics, community structure, and ecosystem matrices incorporating concepts of complexity, resilience, and biogeochemical processes. Over the past few decades, ecologists have analyzed data from field observations, laboratory studies, and large-scale field experiments to describe the structure and dynamics of populations, their interactions within communities, and the complexity of ecosystems. Availability of resources, notably nutrients, is related to population dynamics, e.g., the life cycle of organisms, and community structure, such as food webs. In conclusion, the dimensions of ecological approaches to public health that we propose in this chapter are, in essence, networks of population dynamics, community structure, and ecosystem matrices incorporating concepts of complexity, resilience, and biogeochemical processes.

abstract:
  One Health approaches have tended to focus on closer collaboration among veterinarians and medical professionals, but remain unclear about how ecological approaches could be applied or how they might benefit public health and disease control. In this chapter, we review ecological concepts, and discuss their relevance to health, with an emphasis on emerging infectious diseases (EIDs). Despite the fact that most EIDs originate in wildlife, few studies account for the population, community, or ecosystem ecology of the host, reservoir, or vector. The dimensions of ecological approaches to public health that we propose in this chapter are, in essence, networks of population dynamics, community structure, and ecosystem matrices incorporating concepts of complexity, resilience, and biogeochemical processes.


id: cord-010334-7ce0xhjo
author: Li, Chun
date: 2020-04-01
txt: ./txt/cord-010334-7ce0xhjo.txt
cache: ./cache/cord-010334-7ce0xhjo.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7177813/
doi: 10.3390/ijerph17072388
summary:
  (3) To verify the relationship between search query data in cyber space and population migration in geographical space, we select three urban agglomerations in China as case study: Beijing-Tianjin-Hebei metropolitan region (BTH), the Yangtze River Delta (YRD), and the Pearl River Delta (PRD). (3) To verify the relationship between search query data in cyber space and population migration in geographical space, we select three urban agglomerations in China as case study: Beijing-Tianjin-Hebei metropolitan region (BTH), the Yangtze River Delta (YRD), and the Pearl River Delta (PRD). Based on the different original location of migration search, we construct three MAIs as local-MAI, external-MAI, and intercity-MAI to delineate the public attention generated from local city, attention from external areas, and attention flow among urban areas; then, the correlation analysis is conducted between MAIs in cyber space and urban migrants in geographical space to further verify the aforementioned hypothesis.

title:
  The Relationship Exploration between Public Migration Attention and Population Migration from a Perspective of Search Query

abstract:
  Rapid population migration has been viewed as a critical factor impacting urban network construction and regional sustainable development. The supervision and analysis of population migration are necessary for guiding the optimal allocation of urban resources and for attaining the high efficiency development of region. Currently, the explorations of population migration are often restricted by the limitation of data. In the information era, search engines widely collect public attention, implying potential individual actions, and freely provide open, timelier, and large-scope search query data for helping explore regional phenomena and problems. In this paper, we endeavor to explore the possibility of adopting such data to depict population migration. Based on the search query from Baidu search engine, three migration attention indexes (MAIs) are constructed to capture public migration attention in cyber space. Taking three major urban agglomerations in China as case study, we conduct the correlation analysis among the cyber MAIs and population migration in geographical space. Results have shown that external-MAI and local-MAI can positively reflect the population migration inner regions and across regions from a holistic lens and that intercity-MAI can be a helpful supplement for the delineation of specific population flow. Along with the accumulation of cyber search query data, its potential in exploring population migration can be further reinforced.


id: cord-010903-kuwy7pbo
title: Development of Population and Bayesian Models for Applied Use in Patients Receiving Cefepime
author: Liu, Jiajun
date: 2020-03-05
txt: ./txt/cord-010903-kuwy7pbo.txt
cache: ./cache/cord-010903-kuwy7pbo.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7222999/
doi: 10.1007/s40262-020-00873-3
summary:
  This study sought to develop and evaluate a unified population pharmacokinetic model in both pediatric and adult patients receiving cefepime treatment. The purpose of this study was to: (1) develop and evaluate a unified cefepime population PK model for adult and pediatric patients, and (2) construct an individualized model that can be utilized to deliver precision cefepime dosing. A unified cefepime population pharmacokinetic model has been developed from adult and pediatric patients and evaluates well in independent populations. The base one-and two-compartment models (without covariate adjustment) produced reasonable fits for observed and Bayesian posterior-predicted cefepime concentrations (R 2 = 84.7% and 85.2%, respectively), but population estimates were unsatisfactory (R 2 = 22.7% and 27.8%, respectively) ( Table 1) . This study created a population and individual PK model for adult and pediatric patients and can serve as a Bayesian prior for precision dosing.

abstract:
  BACKGROUND AND OBJECTIVE: Understanding pharmacokinetic disposition of cefepime, a β-lactam antibiotic, is crucial for developing regimens to achieve optimal exposure and improved clinical outcomes. This study sought to develop and evaluate a unified population pharmacokinetic model in both pediatric and adult patients receiving cefepime treatment. METHODS: Multiple physiologically relevant models were fit to pediatric and adult subject data. To evaluate the final model performance, a withheld group of 12 pediatric patients and two separate adult populations were assessed. RESULTS: Seventy subjects with a total of 604 cefepime concentrations were included in this study. All adults (n = 34) on average weighed 82.7 kg and displayed a mean creatinine clearance of 106.7 mL/min. All pediatric subjects (n = 36) had mean weight and creatinine clearance of 16.0 kg and 195.6 mL/min, respectively. A covariate-adjusted two-compartment model described the observed concentrations well (population model R(2), 87.0%; Bayesian model R(2), 96.5%). In the evaluation subsets, the model performed similarly well (population R(2), 84.0%; Bayesian R(2), 90.2%). CONCLUSION: The identified model serves well for population dosing and as a Bayesian prior for precision dosing. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s40262-020-00873-3) contains supplementary material, which is available to authorized users.


id: cord-012356-lmnccks8
title: Ancestry inference of 96 population samples using microhaplotypes
author: Bulbul, Ozlem
date: 2017-12-16
txt: ./txt/cord-012356-lmnccks8.txt
cache: ./cache/cord-012356-lmnccks8.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5920014/
doi: 10.1007/s00414-017-1748-6
summary:
  Microhaplotypes have become a new type of forensic marker with a great ability to identify and deconvolute mixtures because massively parallel sequencing (MPS) allows the alleles (haplotypes) of the multi-SNP loci to be determined directly for an individual. As part of the discovery phase of our studies, data on 130 microhaplotype loci with estimates of haplotype frequency data on 83 populations have been published. Microhaplotypes have great ability to identify and deconvolute mixtures because massively parallel sequencing (MPS) allows the alleles (haplotypes) of the multi-SNP loci to be determined directly for an individual [1] . Thus, MPS provides phase-known data, in contrast to conventional Sanger sequencing, at any locus with two or more heterozygous SNPs. Microhaplotype loci have several desirable characteristics including, by definition, multiple alleles. Sets of microhaplotype loci can be optimized to be useful for individual identification, determining biological relationships, providing information on particular phenotypes, providing information on biogeographic ancestry, or, as noted above, deconvolution of a mixture.

abstract:
  Microhaplotypes have become a new type of forensic marker with a great ability to identify and deconvolute mixtures because massively parallel sequencing (MPS) allows the alleles (haplotypes) of the multi-SNP loci to be determined directly for an individual. As originally defined, a microhaplotype locus is a short segment of DNA with two or more SNPs defining three or more haplotypes. The length is short enough, less than about 300 bp, that the read length of current MPS technology can produce a phase-known sequence of each chromosome of an individual. As part of the discovery phase of our studies, data on 130 microhaplotype loci with estimates of haplotype frequency data on 83 populations have been published. To provide a better picture of global allele frequency variation, we have now tested 13 more populations for 65 of the microhaplotype loci from among those with higher levels of inter-population gene frequency variation, including 8 loci not previously published. These loci provide clear distinctions among 6 biogeographic regions and provide some information distinguishing up to 10 clusters of populations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00414-017-1748-6) contains supplementary material, which is available to authorized users.


id: cord-014922-pqy8bikp
title: Book reviews
author: Hayes, Adrian C.
date: 2003
txt: ./txt/cord-014922-pqy8bikp.txt
cache: ./cache/cord-014922-pqy8bikp.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7090915/
doi: 10.1007/bf03031854
abstract: nan
summary:
  In this book McMichael argues that the way to make sense of this paradox is to use a broad human ecological perspective on population health. Most of the well-known infectious ''crowd'' diseases appear to have developed during this transition; although the ''leap'' from animal species to humans can still occur today, of course, as HIV and SARS attest: writing before the recent SARS outbreak McMichael notes: ''in southern China, the intimate pig/duck farming culture creates a particularly efficient environment in which multiple strains of avian viruses infect pigs. The persuasive force of this book comes more from the weight of its examples of social-ecological processes influencing patterns of health and disease in populations than from any systematic theory describing these relationships. Australian National University This volume offers anthropological accounts of the evolution, production, and consumption of various social policies in contemporary Japan.


id: cord-016310-7655ggxz
title: Explaining the Neolithic Demographic Transition
author: Bocquet-Appel, Jean-Pierre
date: 2008
txt: ./txt/cord-016310-7655ggxz.txt
cache: ./cache/cord-016310-7655ggxz.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120555/
doi: 10.1007/978-1-4020-8539-0_3
summary:
  The demographically identifiable part of the signal indicates a sharp increase in the birth rate, and beyond, a transition towards higher fertility values than those characterising the preceding forager period. The same applies to archaeological data representing the cemeteries of forager and farming populations, whose putative gradient of mobility from nomadic to sedentary (see below) closely coincides with the expected birth rate estimates. This is the message contained Fig. 4 3D representation of demographic density (proxy for fertility), accounted for by energy expenditure (mobility, from 0 = nomadic to 7 = sedentary) and energy intake (diet from (a) hunting, (b) aquatic animals, (c) agricultural produce) with the relative metabolic load model applied to Jorgensen''s sample (1979 Jorgensen''s sample ( , 1999 of western North American Indians on first European contact.

abstract:
  Three main questions are raised in this chapter. 1. The part of the signal of the NDT which is demographically identifiable, based on the proportion of the immature skeletons in cemeteries, shows that a baby-boom occurred and, beyond that, with the onset of the change in the economic system, a fertility transition towards high values also occurred. What was the biodemographic cause of this fertility explosion, beyond the proxy variable represented by sedentarism? The cause is a major shift in the maternal energetics of farming communities relative to mobile foragers. In the energy balance there was (i) on the intake side, an underlying trend towards a reduction in low-calorie food from hunting and fishing, and a correlative increase in high-calorie food from agriculture, (ii) on the expenditure side, a reduction in the physical energy devoted to mobility and the maternal stress of child transportation. 2. The NDT is detectable from a signal representing a fertility transition, but the transition relating to mortality is missing and must be inferred. If, during the fertility transition, mortality had remained the same as in the preceding forager period, then the population would have grown infinitely. The assumption of unchanged mortality during the entire fertility transition is therefore not realistic. Mortality, in its turn, must have begun to rise well before the end of the fertility transition. But when? Why? One of the answers consists of a model where, except at the start of the process, birth and mortality rates rise more or less simultaneously, bringing about a typical rate of increase for pre-industrial populations of slightly above zero. 3. According to the level and speed of the population growth, what should we expect in terms of population structure? What are the expected effects of this growth, not only on the population in numbers but also on age distribution, the distribution and structure of families, the distribution of households and on family systems?


id: cord-018116-99z6ykb2
title: Surveillance and Control of Communicable Disease in Conflicts and Disasters
author: Healing, Tim
date: 2009
txt: ./txt/cord-018116-99z6ykb2.txt
cache: ./cache/cord-018116-99z6ykb2.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122909/
doi: 10.1007/978-1-84800-352-1_13
abstract: nan
summary:
  They must be able to • assess the health status of the population affected and identify the main health priorities • monitor the development and determine the severity of any health emergency that develops (including monitoring the incidence of and case fatality rates from diseases, receiving early warning of epidemics and monitoring responses) At first sight, undertaking public health activities in emergencies, especially in conflicts, may seem to be difficult or impossible. In other types of disaster public health activities may be expected to be less affected by the security situation than in a war (although aid workers may be at risk if populations are severely deprived of resources such as food, shelter, water, or cash), and with limited access and damage to communication systems and other parts of the infrastructure assessment, surveillance and control activities can be severely restricted.


id: cord-020941-1qwbkg9o
title: Biological Control of Vertebrate Pests
author: HODDLE, MARK S.
date: 2007-09-02
txt: ./txt/cord-020941-1qwbkg9o.txt
cache: ./cache/cord-020941-1qwbkg9o.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7148587/
doi: 10.1016/b978-012257305-7/50085-0
abstract: nan
summary:
  Historical records indicate that the majority of attempts at vertebrate biological control have been ad hoc efforts and not the product of careful studies designed to elucidate factors and conditions likely to affect the impact of natural enemy introductions on pest populations. Biological control should be fostered internationally because many countries experience similar problems (e.g., rabbits are agricultural pests in Argentina, Australia, Chile, Europe, and New Zealand; rats, cats, and dogs attack endangered faunas on many oceanic islands; feral pigs and goats in New Zealand, Australia, and the United States degrade habitat and threaten endangered flora). Rabbit populations in Australia and New Zealand are maintained at low levels by introduced predators, but regulation only occurs after pest numbers have been reduced by other means.


id: cord-022141-yxttl3gh
title: Progressive Adaptation: The Key to Sustaining a Growing Global Population
author: Siegel, Frederic R.
date: 2014-08-23
txt: ./txt/cord-022141-yxttl3gh.txt
cache: ./cache/cord-022141-yxttl3gh.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153416/
doi: 10.1007/978-3-319-09686-5_9
summary:
  Adaptation by the global community as a unit is vital to cope with the effects of increasing populations, global warming/climate change, the chemical, biological, and physical impacts on life-sustaining ecosystems, and competition for life sustaining and economically important natural resources. The chronic malnutrition that about 1 billion people suffered from in 2013 is likely to grow in number in some regions due to global warming/climate change because humans cannot adapt to less food if they are already at subsistence rations. As the global population increases and more people in developing and less developed nations have more disposable income, there will be a growing draw on natural resources other than water and food to service their industrial, agricultural, and manufacturing needs and wants. The effects of higher temperatures from global warming and climate change included what has been discussed in previous chapters of this book: heat, drought, sea level rise, coastal zones, typhoons, flooding, river runoff, water availability, ecosystem shifts, crop yields, fishing, aquaculture, livestock, health and poverty, and tourism.

abstract:
  Adaptation is an evolving long-term process during which a population of life forms adjusts to changes in its habitat and surrounding environments. Adaptation by the global community as a unit is vital to cope with the effects of increasing populations, global warming/climate change, the chemical, biological, and physical impacts on life-sustaining ecosystems, and competition for life sustaining and economically important natural resources. The latter include water, food, energy, metal ores, industrial minerals, and wood. Within this framework, it is necessary to adapt as well to changes in local and regional physical conditions brought on by natural and anthropogenic hazards, by health threats of epidemic or pandemic reach, by social conditions such as conflicts driven by religious and ethnic fanaticism, and by tribalism and clan ties.


id: cord-022506-fkddo12n
title: Population Wellness: Keeping Cats Physically and Behaviorally Healthy
author: Griffin, Brenda
date: 2011-12-05
txt: ./txt/cord-022506-fkddo12n.txt
cache: ./cache/cord-022506-fkddo12n.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7158173/
doi: 10.1016/b978-1-4377-0660-4.00046-6
abstract: nan
summary:
  Aside from informally "getting to know" cats during their initial acclimation period in a facility, a systematic â�¢ The ability to create different functional areas in the living environments for elimination, resting, and eating â�¢ The ability to hide in a secure place â�¢ The ability to rest/sleep without being disturbed â�¢ The ability to change locations within the environment, including using vertical space for perching â�¢ The ability to regulate body temperature by moving to warmer or cooler surfaces in the environment â�¢ The ability to scratch (which is necessary for claw health and stretching, as well as visual and scent marking) â�¢ The ability to play and exercise at will â�¢ The ability to acquire mental stimulation Because these needs will vary depending upon such factors as life stage, personality, and prior socialization and experience, facilities should maintain a variety of housing styles in order to meet the individual needs of different cats in the population (Figure 46-11) .


id: cord-030681-4brd2efp
title: Dynamic causal modelling of COVID-19
author: Friston, Karl J.
date: 2020-08-07
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7431977/
doi: 10.12688/wellcomeopenres.15881.2
abstract:
  This technical report describes a dynamic causal model of the spread of coronavirus through a population. The model is based upon ensemble or population dynamics that generate outcomes, like new cases and deaths over time. The purpose of this model is to quantify the uncertainty that attends predictions of relevant outcomes. By assuming suitable conditional dependencies, one can model the effects of interventions (e.g., social distancing) and differences among populations (e.g., herd immunity) to predict what might happen in different circumstances. Technically, this model leverages state-of-the-art variational (Bayesian) model inversion and comparison procedures, originally developed to characterise the responses of neuronal ensembles to perturbations. Here, this modelling is applied to epidemiological populations—to illustrate the kind of inferences that are supported and how the model per se can be optimised given timeseries data. Although the purpose of this paper is to describe a modelling protocol, the results illustrate some interesting perspectives on the current pandemic; for example, the nonlinear effects of herd immunity that speak to a self-organised mitigation process.


id: cord-033412-acjskz00
author: Ruan, Yongsen
date: 2020-09-24
txt: ./txt/cord-033412-acjskz00.txt
cache: ./cache/cord-033412-acjskz00.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7543514/
doi: 10.1093/nsr/nwaa246
summary:
  How many incoming travelers [I(0) at time 0, equivalent to the "founders" in evolutionary genetics] infected with SARS-CoV-2 who visit or return to a region could have started the epidemic of that region? To obtain I(0), we analyze the genetic divergence among viral populations of different regions. By applying the "individual-output" model of genetic drift to the SARS-CoV-2 diversities, we obtain I(0) < 10, which could have been achieved by one infected traveler in a long-distance flight. Since the epidemic in any bordered region could have been started by one single infected traveler, or by 1,000 of them, we take the population genetic approach to analyzing the divergence among viral populations in relation to the "founder effect" [4] . For studying population differentiation, the source population infecting the travelers needs to harbor genetic variants in non-trivial frequencies to yield informative data [10] .

title:
  On the founder effect in COVID-19 outbreaks – How many infected travelers may have started them all?

abstract:
  How many incoming travelers [I(0) at time 0, equivalent to the “founders” in evolutionary genetics] infected with SARS-CoV-2 who visit or return to a region could have started the epidemic of that region? I(0) would be informative about the initiation and progression of the epidemics. To obtain I(0), we analyze the genetic divergence among viral populations of different regions. By applying the “individual-output” model of genetic drift to the SARS-CoV-2 diversities, we obtain I(0) < 10, which could have been achieved by one infected traveler in a long-distance flight. The conclusion is robust regardless of the source population, the continuation of inputs (I(t) for t > 0) or the fitness of the variants. With such a tiny trickle of human movement igniting many outbreaks, the crucial stage of repressing an epidemic in any region should, therefore, be the very first sign of local contagion when positive cases first become identifiable. The implications of the highly “portable” epidemics, including their early evolution prior to any outbreak, are explored in the companion study (Ruan et al. 2020).


id: cord-034950-7gwb0o3l
author: Silva, Monalisa R.
date: 2020-11-07
txt: ./txt/cord-034950-7gwb0o3l.txt
cache: ./cache/cord-034950-7gwb0o3l.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7648403/
doi: 10.1186/s13071-020-04426-2
summary:
  title: Modeling and simulation of the spatial population dynamics of the Aedes aegypti mosquito with an insecticide application This work presents a model describing the spatial population dynamics of Aedes aegypti mosquitoes using partial differential equations (PDEs) relying on a few parameters. METHODS: We show how to estimate model parameter values from the experimental data found in the literature using concepts from dynamical systems, genetic algorithm optimization and partial differential equations. Heterogeneous scenario It considers that diffusion coefficient value inside house blocks is equal to half of that obtained in "Parameter estimation" section, since streets are more favorable place for mosquitoes movement. • Considering the limitations in data (all parameters are fitted or obtained from the literature) and modeling, our results suggest that the weekly insecticide application results in a local minimum of the average mosquitoes'' population.

title:
  Modeling and simulation of the spatial population dynamics of the Aedes aegypti mosquito with an insecticide application

abstract:
  BACKGROUND: The Aedes aegypti mosquito is the primary vector for several diseases. Its control requires a better understanding of the mosquitoes’ live cycle, including the spatial dynamics. Several models address this issue. However, they rely on many hard to measure parameters. This work presents a model describing the spatial population dynamics of Aedes aegypti mosquitoes using partial differential equations (PDEs) relying on a few parameters. METHODS: We show how to estimate model parameter values from the experimental data found in the literature using concepts from dynamical systems, genetic algorithm optimization and partial differential equations. We show that our model reproduces some analytical formulas relating the carrying capacity coefficient to experimentally measurable quantities as the maximum number of mobile female mosquitoes, the maximum number of eggs, or the maximum number of larvae. As an application of the presented methodology, we replicate one field experiment numerically and investigate the effect of different frequencies in the insecticide application in the urban environment. RESULTS: The numerical results suggest that the insecticide application has a limited impact on the mosquitoes population and that the optimal application frequency is close to one week. CONCLUSIONS: Models based on partial differential equations provide an efficient tool for simulating mosquitoes’ spatial population dynamics. The reduced model can reproduce such dynamics on a sufficiently large scale. [Image: see text]


id: cord-103990-qvuv289g
author: Amster, Guy
date: 2019-09-09
txt: ./txt/cord-103990-qvuv289g.txt
cache: ./cache/cord-103990-qvuv289g.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/763524
doi: 10.1101/763524
summary:
  We revisit this question in light of our new theory about the effects of life history and given pedigree-based estimates of the dependence of human mutation rates on sex and age. We demonstrate that life history effects, particularly higher generation times in males than females, likely had multiple effects on human X-to-autosomes (X:A) polymorphism ratios, through the extent of male mutation bias, the equilibrium X:A ratios of effective population sizes, and differential responses to changes in population size. Our results suggest that ancestral human populations were highly polygynous; that non-African populations experienced a substantial reduction in polygyny and/or increase in male-biased generation times around the out of Africa bottleneck; and that extant diversity levels were affected by fairly recent changes in sex-specific life history. Indeed, we show that the ratios observed across human populations can be explained by demographic history, assuming plausible, sex-specific mutation rates, generation times and reproductive variances.

title:
  Changes in life history and population size can explain relative neutral diversity levels on X and autosomes in extant human populations

abstract:
  In human populations, relative levels of neutral polymorphism on the X and autosomes differ markedly from each other and from the naive theoretical expectation of ¾. These differences have attracted considerable attention, with studies highlighting several potential causes, including male biased mutation and reproductive variance, historical changes in population size, and selection at linked loci. We revisit this question in light of our new theory about the effects of life history and given pedigree-based estimates of the dependence of human mutation rates on sex and age. We demonstrate that life history effects, particularly higher generation times in males than females, likely had multiple effects on human X-to-autosomes (X:A) polymorphism ratios, through the extent of male mutation bias, the equilibrium X:A ratios of effective population sizes, and differential responses to changes in population size. We also show that the standard approach of using divergence between species to correct for the male bias in mutation results in biased estimates of X:A effective population size ratios. We obtain alternative estimates using pedigree-based estimates of the male mutation bias, which reveal X:A ratios of effective population sizes to be considerably greater than previously appreciated. We then show that the joint effects of historical changes in life history and population size can explain X:A polymorphism ratios in extant human populations. Our results suggest that ancestral human populations were highly polygynous; that non-African populations experienced a substantial reduction in polygyny and/or increase in male-biased generation times around the out of Africa bottleneck; and that extant diversity levels were affected by fairly recent changes in sex-specific life history. Significance Statement All else being equal, the ratio of diversity levels on X and autosomes at selectively neutral sites should mirror the ratio of their numbers in the population and thus equal ¾. In reality, the ratios observed across human populations differ markedly from ¾ and from each other. Because from a population perspective, autosomes spend an equal number of generations in both sexes while the X spends twice as many generations in females, these departures from the naïve expectations likely reflect differences between male and female life histories and their effects on mutation processes. Indeed, we show that the ratios observed across human populations can be explained by demographic history, assuming plausible, sex-specific mutation rates, generation times and reproductive variances.


id: cord-151532-mpv2wegm
title: Diversity in immunogenomics: the value and the challenge
author: Peng, Kerui
date: 2020-10-20
txt: ./txt/cord-151532-mpv2wegm.txt
cache: ./cache/cord-151532-mpv2wegm.txt
extension: .txt
mime: text/plain
url: https://arxiv.org/pdf/2010.10402v3.pdf
doi: nan
summary:
  With the recent advent of high-throughput sequencing technologies, and the associated new discoveries and developments, the fields of immunogenomics and adaptive immune receptor repertoire research are facing both opportunities and challenges. By leveraging biological and clinical heterogeneity across different populations in omics data and expanding the populations that are included in immunogenomics research, we can enhance our understanding of human adaptive immune responses, promote the development of effective diagnostics and treatments, and eventually advance precision medicine. However, challenges need to be overcome, including the high levels of copy number variation and segmental duplication in the BCR and TCR loci, and the need for protocols to validate novel allelic variants gleaned from short-read sequencing data 45, 77 Finally, we suggest the need for additional infrastructure and expertise in regions and countries with populations underrepresented in research, and to enhance collaborations between countries, which are critical in minimizing global health disparities.

abstract:
  With the recent advent of high-throughput sequencing technologies, and the associated new discoveries and developments, the fields of immunogenomics and adaptive immune receptor repertoire research are facing both opportunities and challenges. The majority of immunogenomics studies have been primarily conducted in cohorts of European ancestry, restricting the ability to detect and analyze variation in human adaptive immune responses across populations and limiting their applications. By leveraging biological and clinical heterogeneity across different populations in omics data and expanding the populations that are included in immunogenomics research, we can enhance our understanding of human adaptive immune responses, promote the development of effective diagnostics and treatments, and eventually advance precision medicine.


id: cord-176540-48mapwlq
title: COVID-19: A model for studying the evolution of contamination in Brazil
author: Schulz, Rodrigo A.
date: 2020-03-31
txt: ./txt/cord-176540-48mapwlq.txt
cache: ./cache/cord-176540-48mapwlq.txt
extension: .txt
mime: text/plain
url: https://arxiv.org/pdf/2003.13932v4.pdf
doi: nan
summary:
  The present work explores the building of a variation of the SIR model in order to cover relevant conditions present in the Brazilian context, such as: 1) daily mortality and daily birth rates (which change, over time, the population) and 2) the gradual reduction of the population susceptible to the disease in fuction of social distancing measures. And in respect to III, it is assumed that, with the evolution of the epidemic, people will begin to isolate themselves socially, whether by individual will or governmental determination, so that the susceptible population is also reduced due to this factor [8] . To correct the problematic points in assertions I, II and III, one can add terms in the equations (1), (2) and (3) in order to operate them according to the logic of a growing susceptible population, where there are reductions resulting from deaths and from social isolation processes, as well as an increase in the number of susceptible people due to the birth rate.

abstract:
  In the present article we introduce an epidemiological model for the investigation of the spread of epidemics caused by viruses. The model is applied specifically to COVID-19, the disease caused by the SARS-Cov-2 virus (aka"novel coronavirus"). The SIR (Susceptible - Infectious - Recovered) model is used as a basis for studying the evolution of the epidemic. Nevertheless, we have modified some of the model hypotheses in order to obtain an estimate of the contamination free of overestimated predictions. This extended model is then applied to the case of the recent advance of the epidemic in Brazil. In this regard, it is possible to obtain the evolution for the number of infectious significantly close to that provided by current data. Accordingly, we evaluate possible future scenarios for the disease spread. Regarding the population susceptibility, we consider different social behaviors in response to quarantine measures and precautions to avoid contagion. We conclude that the future scenario of the epidemic depends significantly on the social behavior adopted to date, as well as on the contagion control measures. The extent of such measures would be likely to cause thousands, millions or tens of millions of contaminations in the next few months.


id: cord-177001-ron8oqrn
author: Afshordi, Niayesh
date: 2020-07-01
txt: ./txt/cord-177001-ron8oqrn.txt
cache: ./cache/cord-177001-ron8oqrn.txt
extension: .txt
mime: text/plain
url: https://arxiv.org/pdf/2007.00159v1.pdf
doi: nan
summary:
  Compared to the linear model of the previous section (Table 1b) Diverse local epidemics reveal the distinct effects of population density, demographics, climate, depletion of susceptibles, and intervention in the first wave of COVID-19 in the United States individual''s probability of becoming infectious, and the distributions of incubation period and generation interval, all as a function of the median age of the population (see Supplementary Material). To obtain the simplest nontrivial incubation period, we assume that β(C) =β Θ(C − 1)where Θ(x) is the Heaviside step function -meaning Diverse local epidemics reveal the distinct effects of population density, demographics, climate, depletion of susceptibles, and intervention in the first wave of COVID-19 in the United States that an infected individual is only infectious once they reach stage C = 1, and the infection rate constant is otherwise unchanging.

title:
  Diverse local epidemics reveal the distinct effects of population density, demographics, climate, depletion of susceptibles, and intervention in the first wave of COVID-19 in the United States

abstract:
  The SARS-CoV-2 pandemic has caused significant mortality and morbidity worldwide, sparing almost no community. As the disease will likely remain a threat for years to come, an understanding of the precise influences of human demographics and settlement, as well as the dynamic factors of climate, susceptible depletion, and intervention, on the spread of localized epidemics will be vital for mounting an effective response. We consider the entire set of local epidemics in the United States; a broad selection of demographic, population density, and climate factors; and local mobility data, tracking social distancing interventions, to determine the key factors driving the spread and containment of the virus. Assuming first a linear model for the rate of exponential growth (or decay) in cases/mortality, we find that population-weighted density, humidity, and median age dominate the dynamics of growth and decline, once interventions are accounted for. A focus on distinct metropolitan areas suggests that some locales benefited from the timing of a nearly simultaneous nationwide shutdown, and/or the regional climate conditions in mid-March; while others suffered significant outbreaks prior to intervention. Using a first-principles model of the infection spread, we then develop predictions for the impact of the relaxation of social distancing and local climate conditions. A few regions, where a significant fraction of the population was infected, show evidence that the epidemic has partially resolved via depletion of the susceptible population (i.e.,"herd immunity"), while most regions in the United States remain overwhelmingly susceptible. These results will be important for optimal management of intervention strategies, which can be facilitated using our online dashboard.


id: cord-228049-1ttt1fgr
title: Urban Scaling of COVID-19 epidemics
author: Cardoso, Ben-Hur Francisco
date: 2020-05-15
txt: ./txt/cord-228049-1ttt1fgr.txt
cache: ./cache/cord-228049-1ttt1fgr.txt
extension: .txt
mime: text/plain
url: https://arxiv.org/pdf/2005.07791v1.pdf
doi: nan
summary:
  With this idea in mind, we present an analysis of a spreading-rate related measure of COVID-19 as a function of population density and population size for all US counties, as long as for Brazilian cities and German cities. Contrary to what is the common hypothesis in epidemics modeling, we observe a higher {em per-capita} contact rate for higher city''s population density and population size. The case of United states can be explained by the linear scaling between their county''s population size and population density, as show before in Fig. 1 . So, we expect that if we increase the geographical scale (counties → metropolitan areas → states), we reduce the dependence between contact rate and the population size. Our analysis and results give support to the validity of the population size driven contact rate for the COVID-19 pandemic.

abstract:
  Susceptible-Invective-Recovered (SIR) mathematical models are in high demand due to the COVID-19 pandemic. They are used in their standard formulation, or through the many variants, trying to fit and hopefully predict the number of new cases for the next days or weeks, in any place, city, or country. Such is key knowledge for the authorities to prepare for the health systems demand or to apply restrictions to slow down the infectives curve. Even when the model can be easily solved ---by the use of specialized software or by programming the numerical solution of the differential equations that represent the model---, the prediction is a non-easy task, because the behavioral change of people is reflected in a continuous change of the parameters. A relevant question is what we can use of one city to another; if what happened in Madrid could have been applied to New York and then, if what we have learned from this city would be of use for S~ao Paulo. With this idea in mind, we present an analysis of a spreading-rate related measure of COVID-19 as a function of population density and population size for all US counties, as long as for Brazilian cities and German cities. Contrary to what is the common hypothesis in epidemics modeling, we observe a higher {em per-capita} contact rate for higher city's population density and population size. Also, we find that the population size has a more explanatory effect than the population density. A contact rate scaling theory is proposed to explain the results.


id: cord-257969-2tax8ajw
title: COVID-19 zugzwang: potential public health moves towards population (herd) immunity
author: Bhopal, Raj S.
date: 2020-07-15
txt: ./txt/cord-257969-2tax8ajw.txt
cache: ./cache/cord-257969-2tax8ajw.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S2666535220300306
doi: 10.1016/j.puhip.2020.100031
summary:
  Outlining potential public health actions, including hygiene measures, social distancing and face masks, and realistic future advances, this paper focuses on the consequences of taking no public health action; the role of natural changes such as weather; the adverse public health consequences of lockdowns; testing for surveillance and research purposes; testing to identify cases and contacts, including the role of antibody tests; the public health value of treatments; mobilising people who have recovered; population (a synonym for herd) immunity through vaccination and through natural infection; involving the entire population; and the need for public debate. People in these groups could minimise their risk of exposure to COVID-19, await effective vaccination and benefit indirectly as population immunity through natural infection increases (Column 2, table 1). The pandemic needs to be prevented from returning year-on-year, potentially more severely, especially in young people and children, and mandating repeated lockdowns.(3) We urgently need to consider all reasonable public health actions and plans (table 1) .

abstract:
  Summary COVID-19 is pandemic, and likely to become endemic, possibly returning with greater virulence. Outlining potential public health actions, including hygiene measures, social distancing and face masks, and realistic future advances, this paper focuses on the consequences of taking no public health action; the role of natural changes such as weather; the adverse public health consequences of lockdowns; testing for surveillance and research purposes; testing to identify cases and contacts, including the role of antibody tests; the public health value of treatments; mobilising people who have recovered; population (a synonym for herd) immunity through vaccination and through natural infection; involving the entire population; and the need for public debate. Until there is a vaccine, population immunity is going to occur only from infection. Allowing infection in those at very low risk while making it safer for them and wider society needs consideration but is currently taboo. About 40-50% population immunity is sufficient to suppress an infection with a reproduction number of about 1 or slightly more. Importantly, in children and young people COVID-19 is currently rarely fatal, roughly comparable with influenza. The balance between the damage caused by COVID-19 and that caused by lockdowns needs quantifying. Public debate, including on population immunity, informed by epidemiological data, is now urgent.


id: cord-262846-1mhimfsf
author: Gray, Nicholas
date: 2020-10-21
txt: ./txt/cord-262846-1mhimfsf.txt
cache: ./cache/cord-262846-1mhimfsf.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1371/journal.pone.0240775
doi: 10.1371/journal.pone.0240775
summary:
  This strategy would involve detecting those who have successfully overcome the virus, and are likely to have some level of immunity (or at least reduced susceptibility to more serious illness if they are infected again), so are relatively safe to relax their personal lockdown measures. To explore the effect of imperfect testing on the disease dynamics when strategies testing regimes are employed to relax lockdown measures, three new classes were added to the model. implement quarantine in their model but do not incorporate the effects on the dynamics from imperfect testing, nor do they consider how the quality and scale of an available test affect the spread of a disease. Wide-scale screening for antibodies in the general population promises significant scientific value, and targeted antibody testing is likely to have value for reducing risks to NHS and care-sector staff, and other key workers who will need to have close contact with COVID-19 sufferers.

title:
  Is “no test is better than a bad test”? Impact of diagnostic uncertainty in mass testing on the spread of COVID-19

abstract:
  Testing is viewed as a critical aspect of any strategy to tackle epidemics. Much of the dialogue around testing has concentrated on how countries can scale up capacity, but the uncertainty in testing has not received nearly as much attention beyond asking if a test is accurate enough to be used. Even for highly accurate tests, false positives and false negatives will accumulate as mass testing strategies are employed under pressure, and these misdiagnoses could have major implications on the ability of governments to suppress the virus. The present analysis uses a modified SIR model to understand the implication and magnitude of misdiagnosis in the context of ending lockdown measures. The results indicate that increased testing capacity alone will not provide a solution to lockdown measures. The progression of the epidemic and peak infections is shown to depend heavily on test characteristics, test targeting, and prevalence of the infection. Antibody based immunity passports are rejected as a solution to ending lockdown, as they can put the population at risk if poorly targeted. Similarly, mass screening for active viral infection may only be beneficial if it can be sufficiently well targeted, otherwise reliance on this approach for protection of the population can again put them at risk. A well targeted active viral test combined with a slow release rate is a viable strategy for continuous suppression of the virus.


id: cord-263248-8y1u0h6y
title: Population heterogeneity is a critical factor of the kinetics of the COVID-19 epidemics
author: Ediev, D. M.
date: 2020-06-26
txt: ./txt/cord-263248-8y1u0h6y.txt
cache: ./cache/cord-263248-8y1u0h6y.txt
extension: .txt
mime: text/plain
url: http://medrxiv.org/cgi/content/short/2020.06.25.20140442v1?rss=1
doi: 10.1101/2020.06.25.20140442
summary:
  The lockdown presented in pane c (starts in day 39) is optimal for the more heterogeneous population that experiences, with the optimal lockdown timing, no second wave (and the total number infected is minimal at 4.9 percent). That lockdown, however, is yet too early for the less heterogeneous population where a moderate second epidemic wave develops and leads to a total of 15.8 percent infected (a substantially higher cost as compared to the minimal cost of 11 percent associated with the lockdown starting in day 44). Heterogeneous scenarios show much lower long-term costs of the epidemics and peak levels of the infected as compared to the traditional homogeneous case. With optimal lockdown strategy, the total number of infected people may be reduced to as low as five percent in the heterogeneous population.

abstract:
  The novel coronavirus pandemic generates extensive attention in political and scholarly domains. Its potentially lasting prospects, economic and social consequences call for a better understanding of its nature. The widespread expectations of large portions of the population to be infected or vaccinated before containing the COVID-19 epidemics rely on assuming a homogeneous population. In reality, people differ in the propensity to catch the infection and spread it further. Here, we incorporate population heterogeneity into the Kermack-McKendrick SIR compartmental model and show the cost of the pandemic may be much lower than usually assumed. We also indicate the crucial role of correctly planning lockdown interventions. We found that an efficient lockdown strategy may reduce the cost of the epidemic to as low as several percents in a heterogeneous population. That level is comparable to prevalences found in serological surveys. We expect that our study will be followed by more extensive data-driven research on epidemiological dynamics in heterogeneous populations.


id: cord-265357-3f0xph0y
author: Halczok, Tanja K.
date: 2017-01-05
txt: ./txt/cord-265357-3f0xph0y.txt
cache: ./cache/cord-265357-3f0xph0y.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28056776/
doi: 10.1186/s12862-016-0856-0
summary:
  RESULTS: We used 19 nuclear and one mitochondrial microsatellite loci to analyze the genetic population structure of the Natterer''s bat (Myotis nattereri) within and among populations at different geographical scales in Germany. CONCLUSIONS: The genetic population structure of the bat host suggests that mating sites where several local breeding colonies meet act as stepping-stones for gene flow. We studied patterns of population genetic structure and dispersal of Myotis nattereri within and among three geographic regions of Germany using both nuclear and mitochondrial microsatellite markers. We hypothesized that if virus transmission between host populations were associated with events linked to gene flow in the bats, e.g. mating [28] , genetic co-variation should be detectable between host populations and astroviruses on a larger scale (e.g. between geographic regions), even though not necessarily within a certain region. Using the 19 autosomal microsatellite loci, Structure inferred the presence of three distinct genetic clusters ( Fig. 2 ; Additional file 1: Figure S1 ), splitting our data set into the three sampled regions NRW, MV and BY.

title:
  Evidence for genetic variation in Natterer’s bats (Myotis nattereri) across three regions in Germany but no evidence for co-variation with their associated astroviruses

abstract:
  BACKGROUND: As bats have recently been described to harbor many different viruses, several studies have investigated the genetic co-variation between viruses and different bat species. However, little is known about the genetic co-variation of viruses and different populations of the same bat species, although such information is needed for an understanding of virus transmission dynamics within a given host species. We hypothesized that if virus transmission between host populations depends on events linked to gene flow in the bats, genetic co-variation should exist between host populations and astroviruses. RESULTS: We used 19 nuclear and one mitochondrial microsatellite loci to analyze the genetic population structure of the Natterer’s bat (Myotis nattereri) within and among populations at different geographical scales in Germany. Further, we correlated the observed bat population structure to that of partial astrovirus sequences (323–394 nt fragments of the RNA-dependent RNA polymerase gene) obtained from the same bat populations. Our analyses revealed that the studied bat colonies can be grouped into three distinct genetic clusters, corresponding to the three geographic regions sampled. Furthermore, we observed an overall isolation-by-distance pattern, while no significant pattern was observed within a geographic region. Moreover, we found no correlation between the genetic distances among the bat populations and the astrovirus sequences they harbored. Even though high genetic similarity of some of the astrovirus haplotypes found in several different regions was detected, identical astrovirus haplotypes were not shared between different sampled regions. CONCLUSIONS: The genetic population structure of the bat host suggests that mating sites where several local breeding colonies meet act as stepping-stones for gene flow. Identical astrovirus haplotypes were not shared between different sampled regions suggesting that astroviruses are mostly transmitted among host colonies at the local scale. Nevertheless, high genetic similarity of some of the astrovirus haplotypes found in several different regions implies that occasional transmission across regions with subsequent mutations of the virus haplotypes does occur. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12862-016-0856-0) contains supplementary material, which is available to authorized users.


id: cord-265705-b6xuzkbb
title: On Urgent Socioeconomic Measures During The Corona Crisis
author: Fal’tsman, V. K.
date: 2020-09-24
txt: ./txt/cord-265705-b6xuzkbb.txt
cache: ./cache/cord-265705-b6xuzkbb.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1134/s1075700720050056
doi: 10.1134/s1075700720050056
summary:
  In anticipation of the impending crisis, the article considers two branches of anticrisis measures: 1) the creation of an economic structure that ensures the accelerated growth of small and medium-sized enterprises, the products of which can partially offset the loss of income from the export of hydrocarbons due to import substitution and export of manufacturing goods and services; 2) social protection of the poorest segments of the population from the possible increase in unemployment and poverty. Among the most important of them, in our opinion, is a deep institutional reform of the economy, aimed at creating a special economic structure for the accelerated development of small and medium-sized enterprises (SMEs). The development of production at SME enterprises should be aimed at compensating for possible losses from the reduction in sales of oil, natural gas and other traditional goods and services of the Russian economy.

abstract:
  In anticipation of the impending crisis, the article considers two branches of anticrisis measures: 1) the creation of an economic structure that ensures the accelerated growth of small and medium-sized enterprises, the products of which can partially offset the loss of income from the export of hydrocarbons due to import substitution and export of manufacturing goods and services; 2) social protection of the poorest segments of the population from the possible increase in unemployment and poverty.


id: cord-271687-sxl8g85p
title: Chapter 8 Zoonoses in Wildlife: Integrating Ecology into Management
author: Mathews, Fiona
date: 2009-03-14
txt: ./txt/cord-271687-sxl8g85p.txt
cache: ./cache/cord-271687-sxl8g85p.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0065308X08006088
doi: 10.1016/s0065-308x(08)00608-8
summary:
  This review examines the pathways linking zoonoses in wildlife with infection in other hosts, using examples from a range of key zoonoses, including European bat lyssaviruses and bovine tuberculosis. For example, bovine tuberculosis (bTB) in the United Kingdom undoubtedly has a reservoir in wild badger populations, and the direct cost of the disease to agriculture is projected to reach £1 billion by 2011 (Department for Environment, Food and Rural Affairs (DEFRA), 2004). Examples of recent successes include the control of canine distemper virus in black-footed ferrets (Mustela nigripes) (Williams et al., 1988) , and rabies in African wild dogs (Lycaon pictus) (Hofmayer et al., 2004) and Ethiopian wolves (Canis simensis) (Haydon et al., 2004) . It proposes that a shift to ecologically based control, explicitly considering the natural history of wildlife hosts and their pathogens, is crucial in minimising the risk presented to humans, domestic animals and endangered species from zoonoses.

abstract:
  Zoonoses in wildlife not only play an important ecological role, but pose significant threats to the health of humans, domestic animals and some endangered species. More than two‐thirds of emerging, or re‐emerging, infectious diseases are thought to originate in wildlife. Despite this, co‐ordinated surveillance schemes are rare, and most efforts at disease control operate at the level of crisis management. This review examines the pathways linking zoonoses in wildlife with infection in other hosts, using examples from a range of key zoonoses, including European bat lyssaviruses and bovine tuberculosis. Ecologically based control, including the management of conditions leading to spill‐overs into target host populations, is likely to be more effective and sustainable than simple reductions in wildlife populations alone.


id: cord-272319-jtr7wi6c
author: Psy, David Lazzari
date: 2020-05-13
txt: ./txt/cord-272319-jtr7wi6c.txt
cache: ./cache/cord-272319-jtr7wi6c.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0889159120308813?v=s5
doi: 10.1016/j.bbi.2020.05.036
abstract: nan
summary:
  A recent survey conducted on the Italian population during the pandemic showed there is a widespread state of psychological distress among them (i.e. anxiety, depression, sleep disorders and more) , as confirmed in other survey involving three Europe countries: Italy, Spain and United Kingdom (see Tab. 1). Moreover, predictive analyses showed that mental health of a large proportion of the population in Italy, United Kingdom and Spain is at high risk for stress, anxiety and depression (41%, 42% and 46% respectively), due to socio-economic vulnerability and worsened conditions since the pandemic onset (Open Evidence, 2020). We believe that a rational approach based on psychoneuroendocrineimmunology (PNEI), the paradigm built on the two-way relationship between the psychological and biological systems in environmental and social contexts (Ader, 2007; Bottaccioli & Bottaccioli, 2020) , could provide an appropriate model for the identification of risk and resilience factors in the context of SARS-CoV-2 infection.

title:
  Letter to the Editor: Kim, S-W., Su, K-P. (2020) Using psychoneuroimmunity against COVID-19, Brain, Behavior, and Immunity (2020), doi: https://doi.org/10.1016/j.bbi.2020.03.025


id: cord-274019-dao10kx9
title: Phylodynamic applications in 21(st) century global infectious disease research
author: Rife, Brittany D
date: 2017-05-08
txt: ./txt/cord-274019-dao10kx9.txt
cache: ./cache/cord-274019-dao10kx9.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s41256-017-0034-y
doi: 10.1186/s41256-017-0034-y
summary:
  These innovative tools have greatly enhanced scientific investigations of the temporal and geographical origins, evolutionary history, and ecological risk factors associated with the growth and spread of viruses such as human immunodeficiency virus (HIV), Zika, and dengue and bacteria such as Methicillin-resistant Staphylococcus aureus. CONCLUSIONS: Capitalizing on an extensive review of the literature, we discuss the evolution of the field of infectious disease epidemiology and recent accomplishments, highlighting the advancements in phylodynamics, as well as the challenges and limitations currently facing researchers studying emerging pathogen epidemics across the globe. The reliance on phylodynamic methods for estimating a pathogen''s population-level characteristics (e.g., effective population size) and their relationships with epidemiological data suffers from a high costincreasing the number of inference models, and thus parameters associated with these models, requires an even greater increase in the information content, or phylogenetic resolution, of the sequence alignment and associated phenotypic data.

abstract:
  BACKGROUND: Phylodynamics, the study of the interaction between epidemiological and pathogen evolutionary processes within and among populations, was originally defined in the context of rapidly evolving viruses and used to characterize transmission dynamics. The concept of phylodynamics has evolved since the early 21(st) century, extending its reach to slower-evolving pathogens, including bacteria and fungi, and to the identification of influential factors in disease spread and pathogen population dynamics. RESULTS: The phylodynamic approach has now become a fundamental building block for the development of comparative phylogenetic tools capable of incorporating epidemiological surveillance data with molecular sequences into a single statistical framework. These innovative tools have greatly enhanced scientific investigations of the temporal and geographical origins, evolutionary history, and ecological risk factors associated with the growth and spread of viruses such as human immunodeficiency virus (HIV), Zika, and dengue and bacteria such as Methicillin-resistant Staphylococcus aureus. CONCLUSIONS: Capitalizing on an extensive review of the literature, we discuss the evolution of the field of infectious disease epidemiology and recent accomplishments, highlighting the advancements in phylodynamics, as well as the challenges and limitations currently facing researchers studying emerging pathogen epidemics across the globe. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s41256-017-0034-y) contains supplementary material, which is available to authorized users.


id: cord-280048-b4dz1lnn
title: Viral quasispecies
author: Domingo, Esteban
date: 2019-10-17
txt: ./txt/cord-280048-b4dz1lnn.txt
cache: ./cache/cord-280048-b4dz1lnn.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/31622336/
doi: 10.1371/journal.pgen.1008271
summary:
  Research on quasispecies has proceeded through several theoretical and experimental avenues that include continuing studies on evolutionary optimization and the origin of life, RNA-RNA interactions and replicator networks, the error threshold in variable fitness landscapes, consideration of chemical mutagenesis and proofreading mechanisms, evolution of tumor cells, bacterial populations or stem cells, chromosomal instability, drug resistance, and conformation distributions in prions (a class of proteins with conformation-dependent pathogenic potential; in this case the quasispecies is defined by a distribution of conformations) [16, 20] . Adaptability of RNA viruses is linked to parameters that facilitate exploration of sequence space: genome size (1.8 to 33 Kb), population size (variable but that can attain an impressive 10 12 individual genomes in an infected host at a given time), replication rate, mutation rate, fecundity (yield of viral particles per cell), and number of mutations required for a phenotypic change (surprisingly low for several relevant traits) (see [49] ).

abstract:
  Viral quasispecies refers to a population structure that consists of extremely large numbers of variant genomes, termed mutant spectra, mutant swarms or mutant clouds. Fueled by high mutation rates, mutants arise continually, and they change in relative frequency as viral replication proceeds. The term quasispecies was adopted from a theory of the origin of life in which primitive replicons) consisted of mutant distributions, as found experimentally with present day RNA viruses. The theory provided a new definition of wild type, and a conceptual framework for the interpretation of the adaptive potential of RNA viruses that contrasted with classical studies based on consensus sequences. Standard clonal analyses and deep sequencing methodologies have confirmed the presence of myriads of mutant genomes in viral populations, and their participation in adaptive processes. The quasispecies concept applies to any biological entity, but its impact is more evident when the genome size is limited and the mutation rate is high. This is the case of the RNA viruses, ubiquitous in our biosphere, and that comprise many important pathogens. In virology, quasispecies are defined as complex distributions of closely related variant genomes subjected to genetic variation, competition and selection, and that may act as a unit of selection. Despite being an integral part of their replication, high mutation rates have an upper limit compatible with inheritable information. Crossing such a limit leads to RNA virus extinction, a transition that is the basis of an antiviral design termed lethal mutagenesis.


id: cord-287133-2mldz987
title: Assembling evidence for identifying reservoirs of infection
author: Viana, Mafalda
date: 2014-05-17
txt: ./txt/cord-287133-2mldz987.txt
cache: ./cache/cord-287133-2mldz987.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/24726345/
doi: 10.1016/j.tree.2014.03.002
summary:
  Our central thesis is that interventions that are meticulously planned to optimise both the immediate short-term benefits to the target population and the longer-term understanding of how reservoirs function, applied together with a formal integration of data and methods [13] , can provide powerful new opportunities for studying complex multihost systems (e.g., [14] ). Trends in Ecology & Evolution May 2014, Vol. 29, No. 5 Target populations in which limited transmission can occur but R 0,T <1 will, when the force of infection from the source is low, exhibit the classic ''stuttering chain'' dynamics ( Figure 1 , zone C) in which outbreak sizes follow an overdispersed distribution [16] . Although still in early stages of development, advanced modelling techniques, such as Bayesian process models, can enable inferences of timing of exposure from ageseroprevalence data, accounting for non-stationary epidemiological dynamics [26] , and/or detect cross-species transmission [27] , to identify which host species is the most likely source of infection.

abstract:
  Many pathogens persist in multihost systems, making the identification of infection reservoirs crucial for devising effective interventions. Here, we present a conceptual framework for classifying patterns of incidence and prevalence, and review recent scientific advances that allow us to study and manage reservoirs simultaneously. We argue that interventions can have a crucial role in enriching our mechanistic understanding of how reservoirs function and should be embedded as quasi-experimental studies in adaptive management frameworks. Single approaches to the study of reservoirs are unlikely to generate conclusive insights whereas the formal integration of data and methodologies, involving interventions, pathogen genetics, and contemporary surveillance techniques, promises to open up new opportunities to advance understanding of complex multihost systems.


id: cord-296179-hobh6akq
title: Does genetic diversity limit disease spread in natural host populations?
author: King, K C
date: 2012-06-20
txt: ./txt/cord-296179-hobh6akq.txt
cache: ./cache/cord-296179-hobh6akq.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1038/hdy.2012.33
doi: 10.1038/hdy.2012.33
summary:
  (2004) confirmed that the increase in disease susceptibility resulted from a lower frequency of resistance alleles in the population, and not by generalized inbreeding effects. Two models suggest that genetic variation in host susceptibility would not affect infectious disease spread (Springbett et al., 2003; Yates et al., 2006) , but it might reduce the severity of infection (Springbett et al., 2003) . In contrast, Lively (2010a) found that host genetic diversity could reduce the risk of disease spread, assuming that each host genotype was susceptible to a different parasite genotype. The more recent model suggests that increases in the genetic diversity of host populations could have a large effect on disease spread and prevalence at equilibrium (Lively, 2010a) . The available data and the model are consistent with the idea that genetic diversity in host populations can reduce the spread of disease.

abstract:
  It is a commonly held view that genetically homogenous host populations are more vulnerable to infection than genetically diverse populations. The underlying idea, known as the ‘monoculture effect,' is well documented in agricultural studies. Low genetic diversity in the wild can result from bottlenecks (that is, founder effects), biparental inbreeding or self-fertilization, any of which might increase the risk of epidemics. Host genetic diversity could buffer populations against epidemics in nature, but it is not clear how much diversity is required to prevent disease spread. Recent theoretical and empirical studies, particularly in Daphnia populations, have helped to establish that genetic diversity can reduce parasite transmission. Here, we review the present theoretical work and empirical evidence, and we suggest a new focus on finding ‘diversity thresholds.'


id: cord-297530-7zbvgvk8
title: Phylogenetic and epidemic modeling of rapidly evolving infectious diseases
author: Kühnert, Denise
date: 2011-08-31
txt: ./txt/cord-297530-7zbvgvk8.txt
cache: ./cache/cord-297530-7zbvgvk8.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S156713481100284X
doi: 10.1016/j.meegid.2011.08.005
summary:
  By using Kingman''s coalescent as a prior density on trees, Bayesian inference can be used to simultaneously estimate the phylogeny of the viral sequences and the demographic history of the virus population (Drummond et al., 2002 (Drummond et al., , 2005 , see Box 1). A maximum likelihood based method (the single rate dated tips (SRDT) model; Rambaut, 2000) , estimates ancestral divergence times and overall substitution rate on a fixed tree, assuming a strict molecular clock. While the generalized skyline plot is a good tool for data exploration, and to assist in model selection (e.g., Pybus et al., 2003; Lemey et al., 2004) , it infers demographic history based on a single input tree and therefore does not account for sampling error produced by phylogenetic reconstruction nor for the intrinsic stochasticity of the coalescent process.

abstract:
  Epidemic modeling of infectious diseases has a long history in both theoretical and empirical research. However the recent explosion of genetic data has revealed the rapid rate of evolution that many populations of infectious agents undergo and has underscored the need to consider both evolutionary and ecological processes on the same time scale. Mathematical epidemiology has applied dynamical models to study infectious epidemics, but these models have tended not to exploit – or take into account – evolutionary changes and their effect on the ecological processes and population dynamics of the infectious agent. On the other hand, statistical phylogenetics has increasingly been applied to the study of infectious agents. This approach is based on phylogenetics, molecular clocks, genealogy-based population genetics and phylogeography. Bayesian Markov chain Monte Carlo and related computational tools have been the primary source of advances in these statistical phylogenetic approaches. Recently the first tentative steps have been taken to reconcile these two theoretical approaches. We survey the Bayesian phylogenetic approach to epidemic modeling of infection diseases and describe the contrasts it provides to mathematical epidemiology as well as emphasize the significance of the future unification of these two fields.


id: cord-297777-lnr4w3ek
title: The mental health impact of the COVID-19 epidemic on immigrants and racial and ethnic minorities
author: Rothman, S
date: 2020-06-17
txt: ./txt/cord-297777-lnr4w3ek.txt
cache: ./cache/cord-297777-lnr4w3ek.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32591836/
doi: 10.1093/qjmed/hcaa203
abstract: nan
summary:
  Disease spread has been tracked by the CDC and geographic differences can be viewed through the lens of epidemiologic and population-level factors which include: the timing of COVID-19 introductions, population density, age distribution and prevalence of underlying medical conditions among COVID-19 patients, the timing and extent of community mitigation measures, diagnostic testing capacity and finally, public health reporting practices. 3 In New York City, specifically in the Bronx where it is estimated that 29% of individuals live below poverty level 4 and the population is composed mainly of Hispanics and African Americans who may have a number of psychosocial issues including: poverty, homelessness, issues with access to health care, education and immigration concerns. Many of these workers are young and healthy, however diabetes affects 22% of the Latino population and this medical comorbidity is a significant risk factor for severe COVID-19 disease course.


id: cord-298009-0iv9fdof
author: Hori, Keiko
date: 2020-08-06
txt: ./txt/cord-298009-0iv9fdof.txt
cache: ./cache/cord-298009-0iv9fdof.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s11625-020-00835-5
doi: 10.1007/s11625-020-00835-5
summary:
  Based on the Japanese depopulation context and the country''s National Spatial Strategy, the compact scenario predicts the formation of medium-scale regional urban areas (population centers located across Japan) and the concentration of people on high-density population areas within municipalities. The aim of this study was to develop a population distribution projection model under conditions of depopulation, expressing migration at multiple levels, to conduct scenario analyses that assume compactification and dispersion of Japan''s population. In contrast, based on the central city''s requirements of "Self-Support Settlement Region" (MIC b), municipalities located outside of Japan''s three major metropolitan areas, with populations of more than 40,000, and with daytime/night-time population ratios of more than 1 were selected as regional urban centers in the dispersed scenario.

title:
  Projecting population distribution under depopulation conditions in Japan: scenario analysis for future socio-ecological systems

abstract:
  This study develops a projection model of future population distribution on the basis of Japan’s current depopulation trend and applies this model to scenario analyses that assume population compactification and dispersion. The model enables a description of population migration at two levels. First, municipal populations are projected using the cohort-component method, and second, the spatial distribution of populations within municipalities is projected at a 500 m grid resolution with the use of the gravity model. Based on the Japanese depopulation context and the country’s National Spatial Strategy, the compact scenario predicts the formation of medium-scale regional urban areas (population centers located across Japan) and the concentration of people on high-density population areas within municipalities. Meanwhile, the dispersed scenario predicts the formation of more but smaller regional urban areas and the dispersion of the population to low-density areas. The simulated population distribution for 2050 reveals spatial change in population density and age structure, as well as an abundance of areas that were inhabited in 2015 but will be zero population areas by 2050. Overlay analysis of future land use maps and the simulated population distribution maps can contribute toward identifying areas where natural capital such as farmland and forest plantation should be managed but where there will be significant population loss by 2050. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11625-020-00835-5) contains supplementary material, which is available to authorized users.


id: cord-299261-ew99nraq
title: IMPACT OF UNIVERSITY RE-OPENING ON TOTAL COMMUNITY COVID-19 BURDEN
author: Cipriano, L. E.
date: 2020-09-18
txt: ./txt/cord-299261-ew99nraq.txt
cache: ./cache/cord-299261-ew99nraq.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.09.18.20197467
doi: 10.1101/2020.09.18.20197467
summary:
  In a scenario in which students immediately engage in a 24% contact reduction compared to pre-COVID levels, the total number of infections in the community increases by 87% (from 3,900 without the students to 7,299 infections with the students), with 71% of the incremental infections occurring in the general population, causing social and economic restrictions to be re-engaged 3 weeks earlier and an incremental 17 COVID-19 deaths. The timing and magnitude of the city''s COVID-19 outbreak, excluding any impacts from students, is determined by the initial number of COVID-19 infections in the community, the level of participation in physical distancing, the responsiveness of the community to increasing critical care cases and COVID-19 deaths, and the proportion of contacts that are protected with mask wearing (Appendix Figures 5-7) . 16 In the base case, we also assume that students are equally responsive as the general population to COVID-19 outcomes in the community reducing their contacts in response to high numbers of critical care hospitalizations and deaths.

abstract:
  Purpose: Post-secondary students have higher than average contacts than the general population due to congregate living, use of public transit, high-density academic and social activities, and employment in the services sector. We evaluated the impact of a large student population returning to a mid-sized city currently experiencing a low rate of COVID-19 on community health outcomes. We consider whether targeted routine or one-time screening in this population can mitigate community COVID-19 impacts. Methods: We developed a dynamic transmission model of COVID-19 subdivided into three interacting populations: general population, university students, and long-term care residents. We parameterized the model using the medical literature and expert opinion. We calibrated the model to the observed outcomes in a mid-sized Canadian city between March 1 and August 15, 2020 prior to the arrival of a relatively large post-secondary student population. We evaluated the impact of the student population (20,000 people arriving on September 1) on cumulative COVID-19 infections over the fall semester, the timing of peak infections, the timing and peak level of critical care occupancy, and the timing of re-engaged social and economic restrictions. We consider multiple scenarios with different student and general population COVID-19 prevention behaviours as well as different COVID-19 screening strategies in students. Results: In a city with low levels of COVID-19 activity, the return of a relatively large student population substantially increases the total number of COVID-19 infections in the community. In a scenario in which students immediately engage in a 24% contact reduction compared to pre-COVID levels, the total number of infections in the community increases by 87% (from 3,900 without the students to 7,299 infections with the students), with 71% of the incremental infections occurring in the general population, causing social and economic restrictions to be re-engaged 3 weeks earlier and an incremental 17 COVID-19 deaths. Scenarios in which students have an initial, short-term increase in contacts with other students before engaging in contact reduction behaviours can increase infections in the community by 150% or more. In such scenarios, screening asymptomatic students every 5 days reduces the number of infections attributable to the introduction of the university student population by 42% and delays the re-engagement of social and economic restrictions by 1 week. Compared to screening every 5 days, one-time mass screening of students prevents fewer infections, but is highly efficient in terms of infections prevented per screening test performed. Discussion: University students are highly inter-connected with the city communities in which they live and go to school, and they have a higher number of contacts than the general population. High density living environments, enthusiasm for the new school year, and relatively high rates of asymptomatic presentation may decrease their self-protective behaviours and contribute to increased community transmission of COVID-19 affecting at-risk members of the city community. Screening targeted at this population provides significant public health benefits to the community through averted infections, critical care admissions, and COVID-19 deaths.


id: cord-299828-fb84rtmx
title: Taming wildlife disease: bridging the gap between science and management
author: Joseph, Maxwell B.
date: 2013-04-16
txt: ./txt/cord-299828-fb84rtmx.txt
cache: ./cache/cord-299828-fb84rtmx.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/1365-2664.12084
doi: 10.1111/1365-2664.12084
summary:
  Despite the wealth of empirical WDM research, management outcomes can be difficult to predict because system-specific information is lacking for novel pathogens and many theoretical concepts in disease ecology (see Table 1 for a subset) have not been widely tested in the field, leading to uncertainty in their generality. Corridor vaccination can reduce disease in metapopulations; movement controls are unlikely to work for chronic infections Keeling & Eames (2005) Transmission increases with host density Host density reductions may reduce disease transmission, and density thresholds for disease persistence may exist Anderson & May (1979) Transmission increases with disease prevalence independent of host density Transmission associated with sexual interactions is more likely to cause host extinction, and non-selective culling may not reduce transmission Getz & Pickering (1983) Predation as a regulator of host population and disease We use a quantitative, case-based approach to provide a critical retrospective of WDM over the last four decades to: (i) quantify how frequently specific theoretical concepts from disease ecology have been applied in the literature, (ii) identify prevailing management objectives, groups and reported outcomes and (iii) assess taxonomic biases in WDM literature.

abstract:
  1. Parasites and pathogens of wildlife can threaten biodiversity, infect humans and domestic animals, and cause significant economic losses, providing incentives to manage wildlife diseases. Recent insights from disease ecology have helped transform our understanding of infectious disease dynamics and yielded new strategies to better manage wildlife diseases. Simultaneously, wildlife disease management (WDM) presents opportunities for large‐scale empirical tests of disease ecology theory in diverse natural systems. 2. To assess whether the potential complementarity between WDM and disease ecology theory has been realized, we evaluate the extent to which specific concepts in disease ecology theory have been explicitly applied in peer‐reviewed WDM literature. 3. While only half of WDM articles published in the past decade incorporated disease ecology theory, theory has been incorporated with increasing frequency over the past 40 years. Contrary to expectations, articles authored by academics were no more likely to apply disease ecology theory, but articles that explain unsuccessful management often do so in terms of theory. 4. Some theoretical concepts such as density‐dependent transmission have been commonly applied, whereas emerging concepts such as pathogen evolutionary responses to management, biodiversity–disease relationships and within‐host parasite interactions have not yet been fully integrated as management considerations. 5. Synthesis and applications. Theory‐based disease management can meet the needs of both academics and managers by testing disease ecology theory and improving disease interventions. Theoretical concepts that have received limited attention to date in wildlife disease management could provide a basis for improving management and advancing disease ecology in the future.


id: cord-301856-71syce4n
title: Impact of Historic Migrations and Evolutionary Processes on Human Immunity
author: Domínguez-Andrés, Jorge
date: 2019-11-27
txt: ./txt/cord-301856-71syce4n.txt
cache: ./cache/cord-301856-71syce4n.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.it.2019.10.001
doi: 10.1016/j.it.2019.10.001
summary:
  With the burst of next-generation sequencing and the development of cutting-edge technologies such as transcriptomics, proteomics, and systems biology, we are starting to witness the great impact of evolutionary processes on human immunity and how the interactions between microorganisms and humans that took place millennia ago might play a fundamental role not only in the response against modern pathogenic threats, but also in the emergence of autoimmune and inflammatory diseases observed in modern populations worldwide. Specific genetic variants selected throughout different periods of human history may have influenced immune responses of present-day populations against pathogenic microorganisms and may have played a role in the development of certain inflammatory and autoimmune diseases. Patients with African ancestry present a higher frequency of MTB-related genetic variants than individuals from other populations, including variants in the gene encoding for Toll-like receptor 6 (TLR6), mediating cellular responses to bacterial Malaria is one of the greatest causes of morbidity and mortality in the history of humanity.

abstract:
  The evolution of mankind has constantly been influenced by the pathogens encountered. The various populations of modern humans that ventured out of Africa adapted to different environments and faced a large variety of infectious agents, resulting in local adaptations of the immune system for these populations. The functional variation of immune genes as a result of evolution is relevant in the responses against infection, as well as in the emergence of autoimmune and inflammatory diseases observed in modern populations. Understanding how host–pathogen interactions have influenced the human immune system from an evolutionary perspective might contribute to unveiling the causes behind different immune-mediated disorders and promote the development of new strategies to detect and control such diseases.


id: cord-302056-wvf6cpib
title: Estimating COVID-19 Prevalence in the United States: A Sample Selection Model Approach
author: Benatia, D.
date: 2020-04-30
txt: ./txt/cord-302056-wvf6cpib.txt
cache: ./cache/cord-302056-wvf6cpib.txt
extension: .txt
mime: text/plain
url: http://medrxiv.org/cgi/content/short/2020.04.20.20072942v1?rss=1
doi: 10.1101/2020.04.20.20072942
summary:
  Background: Public health efforts to determine population infection rates from coronavirus disease 2019 (COVID-19) have been hampered by limitations in testing capabilities and the large shares of mild and asymptomatic cases. Public health efforts to determine population infection rates from coronavirus disease 2019 (COVID -19) have been hampered by limitations in testing capabilities and the large shares of mild and asymptomatic cases. We developed a methodology that corrects observed positive test rates for non-random sampling to estimate population infection rates across U.S. states from March 31 to April 7. We developed a methodology that corrects observed positive test rates for non-random sampling to estimate population infection rates across U.S. states from March 31 to April 7. Because the severity of sample selection bias depends on the extent of testing, these disparities create large uncertainty regarding the relative disease prevalence across jurisdictions, and may contribute to the wide differences in estimated case fatality rates [10, 11] .

abstract:
  Background: Public health efforts to determine population infection rates from coronavirus disease 2019 (COVID-19) have been hampered by limitations in testing capabilities and the large shares of mild and asymptomatic cases. We developed a methodology that corrects observed positive test rates for non-random sampling to estimate population infection rates across U.S. states from March 31 to April 7. Methods We adapted a sample selection model that corrects for non-random testing to estimate population infection rates. The methodology compares how the observed positive case rate vary with changes in the size of the tested population, and applies this gradient to infer total population infection rates. Model identification requires that variation in testing rates be uncorrelated with changes in underlying disease prevalence. To this end, we relied on data on day-to-day changes in completed tests across U.S. states for the period March 31 to April 7, which were primarily influenced by immediate supply-side constraints. We used this methodology to construct predicted infection rates across each state over the sample period. We also assessed the sensitivity of the results to controls for state-specific daily trends in infection rates. Results The median population infection rate over the period March 31 to April 7 was 0.9% (IQR 0.64 1.77). The three states with the highest prevalence over the sample period were New York (8.5%), New Jersey (7.6%), and Louisiana (6.7%). Estimates from models that control for state-specific daily trends in infection rates were virtually identical to the baseline findings. The estimates imply a nationwide average of 12 population infections per diagnosed case. We found a negative bivariate relationship (corr. = -0.51) between total per capita state testing and the ratio of population infections per diagnosed case. Interpretation The effectiveness of the public health response to the coronavirus pandemic will depend on timely information on infection rates across different regions. With increasingly available high frequency data on COVID-19 testing, our methodology could be used to estimate population infection rates for a range of countries and subnational districts. In the United States, we found widespread undiagnosed COVID-19 infection. Expansion of rapid diagnostic and serological testing will be critical in preventing recurrent unobserved community transmission and identifying the large numbers individuals who may have some level of viral immunity.


id: cord-303165-ikepr2p2
title: Expanding the Concept of Public Health
author: Tulchinsky, Theodore H.
date: 2014-10-10
txt: ./txt/cord-303165-ikepr2p2.txt
cache: ./cache/cord-303165-ikepr2p2.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/B9780124157668000021
doi: 10.1016/b978-0-12-415766-8.00002-1
summary:
  It also demands special attention through health promotion activities of all kinds at national and local societal levels to provide access for groups with special risks and needs to medical and community health care with the currently available and newly developing knowledge and technologies. 5. Environmental, biological, occupational, social, and economic factors that endanger health and human life, addressing: (a) physical and mental illness, diseases and infirmity, trauma and injuries (b) local and global sanitation and environmental ecology (c) healthful nutrition and food security including availability, quality, safety, access, and affordability of food products (d) disasters, natural and human-made, including war, terrorism, and genocide (e) population groups at special risk and with specific health needs. It acts to improve health and social welfare, and to reduce specific determinants of diseases and risk factors that adversely affect the health, well-being, and productive capacities of an individual or society, setting targets based on the size of the problem but also the feasibility of successful intervention, in a cost-effective way.

abstract:
  Ancient societies recognized the needs of sanitation, food safety, workers’ health, and medical care to protect against disease and to promote well-being and civic prosperity. New energies and knowledge since the eighteenth century produced landmark discoveries such as prevention of scurvy and vaccination against smallpox. The biological germ theory and competing miasma theory each proved effective in sanitation, and immunization in control of infectious diseases. Non-communicable diseases as the leading causes of mortality have responded to innovative preventive care of health risk factors, smoking, hypertension, obesity, physical inactivity, unhealthful diets, and diabetes mellitus. Health promotion proved effective to modern public health in tackling disease origins, individual behavior, and social and economic conditions. The global burden of infectious and non-communicable diseases, aging and chronic illness faces rising costs and still inadequate prevention. The evolution of concepts of public health will have to address these new challenges of population health.


id: cord-303187-ny4qr2a2
author: Belo, Vinícius Silva
date: 2017-11-01
txt: ./txt/cord-303187-ny4qr2a2.txt
cache: ./cache/cord-303187-ny4qr2a2.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/29091961/
doi: 10.1371/journal.pone.0187233
summary:
  Despite the perceived need and usefulness of such parameter estimates and recommendations for the most appropriate approaches applicable under such study designs [30] , survival and recruitment estimates of free-ranging dogs had not been obtained using methods of capture and recapture. In this study, we present estimates of abundance, survival and recruitment rates, and the probabilities of capture of two free-roaming dog populations by means of analytical models for open populations, so far unexplored in previous studies. We estimated critical parameters (survival, recruitment and abundance) that describe the population dynamics of free-roaming dogs based on a capture and recapture study design and on models suitable for open populations. Our study demonstrated the increase in population size in both areas, the predominance and greater recruitment of males, the temporal variability in recruitment and in survival probabilities, the lack of effect of sterilization on population dynamics, the influence of abandon and of density-independent factors and a high demographic turnover.

title:
  Abundance, survival, recruitment and effectiveness of sterilization of free-roaming dogs: A capture and recapture study in Brazil

abstract:
  The existence of free-roaming dogs raises important issues in animal welfare and in public health. A proper understanding of these animals’ ecology is useful as a necessary input to plan strategies to control these populations. The present study addresses the population dynamics and the effectiveness of the sterilization of unrestricted dogs using capture and recapture procedures suitable for open animal populations. Every two months, over a period of 14 months, we captured, tagged, released and recaptured dogs in two regions in a city in the southeast region of Brazil. In one of these regions the animals were also sterilized. Both regions had similar social, environmental and demographic features. We estimated the presence of 148 females and 227 males during the period of study. The average dog:man ratio was 1 dog for each 42 and 51 human beings, in the areas without and with sterilization, respectively. The animal population size increased in both regions, due mainly to the abandonment of domestic dogs. Mortality rate decreased throughout the study period. Survival probabilities did not differ between genders, but males entered the population in higher numbers. There were no differences in abundance, survival and recruitment between the regions, indicating that sterilization did not affect the population dynamics. Our findings indicate that the observed animal dynamics were influenced by density-independent factors, and that sterilization might not be a viable and effective strategy in regions where availability of resources is low and animal abandonment rates are high. Furthermore, the high demographic turnover rates observed render the canine free-roaming population younger, thus more susceptible to diseases, especially to rabies and leishmaniasis. We conclude by stressing the importance of implementing educational programs to promote responsible animal ownership and effective strategies against abandonment practices.


id: cord-303700-rrwy3osd
title: How urbanization affects the epidemiology of emerging infectious diseases
author: Neiderud, Carl-Johan
date: 2015-06-24
txt: ./txt/cord-303700-rrwy3osd.txt
cache: ./cache/cord-303700-rrwy3osd.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3402/iee.v5.27060
doi: 10.3402/iee.v5.27060
summary:
  The lack of a universal definition makes it hard to compare different countries and cities in regard to public health and the burden and impact of infectious diseases (4) . Many of the lower income countries are expected to have a major growth among the urban population, which leads to considerable challenges for the governments and health care to keep up to pace and develop their social services and health care as these regions grow. The environment in urban cities has proven to be favourable for the rat population (Rattus spp.) and close encounters between rats and humans can lead to transmission of zoonotic infectious diseases. LF still has its major impact in rural settings, but the increasing urbanization in the developing world has made LF an infectious disease that also has to be considered elsewhere.

abstract:
  The world is becoming more urban every day, and the process has been ongoing since the industrial revolution in the 18th century. The United Nations now estimates that 3.9 billion people live in urban centres. The rapid influx of residents is however not universal and the developed countries are already urban, but the big rise in urban population in the next 30 years is expected to be in Asia and Africa. Urbanization leads to many challenges for global health and the epidemiology of infectious diseases. New megacities can be incubators for new epidemics, and zoonotic diseases can spread in a more rapid manner and become worldwide threats. Adequate city planning and surveillance can be powerful tools to improve the global health and decrease the burden of communicable diseases.


id: cord-304399-7t2mu13s
author: Wynne, Keona Jeane
date: 2020-06-19
txt: ./txt/cord-304399-7t2mu13s.txt
cache: ./cache/cord-304399-7t2mu13s.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1136/medethics-2019-105943
doi: 10.1136/medethics-2019-105943
summary:
  Many healthcare professionals, emergency services staff and humanitarian workers, as well as organisational leaders and policy-makers are shaken by powerlessness, guilt and fear from witnessing COVID-19 deaths which could have been avoided with better preparation; from being aware of the suffering and loneliness of those who are dying, while all available staff are needed to fight for the lives of those with higher chances of survival; or, with a growing likelihood, from contemplating decisions about withholding or withdrawing critical treatment because of severe resource limitations. Yet until the COVID-19 pandemic, these challenges were not openly discussed in the context of palliative care-including in the WHO guide which is our main focuseven if they were a way of life for many humanitarian and emergency workers and intuitively sensed by individuals external to the sectors.

title:
  Dying individuals and suffering populations: applying a population-level bioethics lens to palliative care in humanitarian contexts: before, during and after the COVID-19 pandemic

abstract:
  BACKGROUND: Humanitarian crises and emergencies, events often marked by high mortality, have until recently excluded palliative care—a specialty focusing on supporting people with serious or terminal illness or those nearing death. In the COVID-19 pandemic, palliative care has received unprecedented levels of societal attention. Unfortunately, this has not been enough to prevent patients dying alone, relatives not being able to say goodbye and palliative care being used instead of intensive care due to resource limitations. Yet global guidance was available. In 2018, the WHO released a guide on ‘Integrating palliative care and symptom relief into the response to humanitarian emergencies and crises’—the first guidance on the topic by an international body. AIMS: This paper argues that while a landmark document, the WHO guide took a narrowly clinical bioethics perspective and missed crucial moral dilemmas. We argue for adding a population-level bioethics lens, which draws forth complex moral dilemmas arising from the fact that groups having differential innate and acquired resources in the context of social and historical determinants of health. We discuss dilemmas concerning: limitations of material and human resources; patient prioritisation; euthanasia; and legacy inequalities, discrimination and power imbalances. IMPLICATIONS: In parts of the world where opportunity for preparation still exists, and as countries emerge from COVID-19, planners must consider care for the dying. Immediate steps to support better resolutions to ethical dilemmas of the provision of palliative care in humanitarian and emergency contexts will require honest debate; concerted research effort; and international, national and local ethical guidance.


id: cord-305472-w33k8pdu
author: Ojosnegros, Samuel
date: 2008-07-17
txt: ./txt/cord-305472-w33k8pdu.txt
cache: ./cache/cord-305472-w33k8pdu.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/1471-2148-8-207
doi: 10.1186/1471-2148-8-207
summary:
  Here we apply for the first time phylogenetic methods and Partition Analysis of Quasispecies (PAQ) to monitor genetic distances and intra-population structures of mutant spectra of foot-and-mouth disease virus (FMDV) quasispecies subjected to mutagenesis by base and nucleoside analogues. In the course of the studies on lethal mutagenesis of FMDV, biological clones of the virus were subjected to serial cytolytic passages in cell culture in the absence or presence of the mutagenic bases or nucleoside analogues 5-fluorouracil (FU), ribavirin (1-β-D ribofuranosyl-1, 2, 3-triazole-3 carboxamide) (R), or 5-azacytidine (AZC) [32, [38] [39] [40] [41] . Comparison of the phylogenetic trees derived from nucleotide sequences of the different FMDV clonal populations passaged 1 and 25 times in the absence or the presence of AZC or FU shows an expansion of genetic distances among components of the mutant spectrum of the mutated populations compared to the respective control populations passaged in the absence of drug.

title:
  Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selection

abstract:
  BACKGROUND: The molecular events and evolutionary forces underlying lethal mutagenesis of virus (or virus extinction through an excess of mutations) are not well understood. Here we apply for the first time phylogenetic methods and Partition Analysis of Quasispecies (PAQ) to monitor genetic distances and intra-population structures of mutant spectra of foot-and-mouth disease virus (FMDV) quasispecies subjected to mutagenesis by base and nucleoside analogues. RESULTS: Phylogenetic and PAQ analyses have revealed a highly dynamic variation of intrapopulation diversity of FMDV quasispecies. The population diversity first suffers striking expansions in the presence of mutagens and then compressions either when the presence of the mutagenic analogue was discontinued or when a mutation that decreased sensitivity to a mutagen was selected. The pattern of mutations found in the populations was in agreement with the behavior of the corresponding nucleotide analogues with FMDV in vitro. Mutations accumulated at preferred genomic sites, and dn/ds ratios indicate the operation of negative (or purifying) selection in populations subjected to mutagenesis. No evidence of unusually elevated genetic distances has been obtained for FMDV populations approaching extinction. CONCLUSION: Phylogenetic and PAQ analysis provide adequate procedures to describe the evolution of viral sequences subjected to lethal mutagenesis. These methods define the changes of intra-population structure more precisely than mutation frequencies and Shannon entropies. PAQ is very sensitive to variations of intrapopulation genetic distances. Strong negative (or purifying) selection operates in FMDV populations subjected to enhanced mutagenesis. The quantifications provide evidence that extinction does not imply unusual increases of intrapopulation complexity, in support of the lethal defection model of virus extinction.


id: cord-310648-oqiwnjpp
author: Cainzos-Achirica, Miguel
date: 2020-05-20
url: https://api.elsevier.com/content/article/pii/S0002934320304204
doi: 10.1016/j.amjmed.2020.04.017
abstract: nan
title:
  Polypill for Population-Level Primary Cardiovascular Prevention in Underserved Populations at Heterogeneous Risk — A Social Epidemiology Counterargument


id: cord-312366-8qg1fn8f
title: Mathematical Models for COVID-19 Pandemic: A Comparative Analysis
author: Adiga, Aniruddha
date: 2020-10-30
txt: ./txt/cord-312366-8qg1fn8f.txt
cache: ./cache/cord-312366-8qg1fn8f.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s41745-020-00200-6
doi: 10.1007/s41745-020-00200-6
summary:
  As the pandemic takes hold, researchers begin investigating: (i) various intervention and control strategies; usually pharmaceutical interventions do not work in the event of a pandemic and thus nonpharmaceutical interventions are most appropriate, (ii) forecasting the epidemic incidence rate, hospitalization rate and mortality rate, (iii) efficiently allocating scarce medical resources to treat the patients and (iv) understanding the change in individual and collective behavior and adherence to public policies. Like projection approaches, models for epidemic forecasting can be broadly classified into two broad groups: (i) statistical and machine learning-based data-driven models, (ii) causal or mechanistic models-see 29, 30, 2, 31, 32, 6, 33 and the references therein for the current state of the art in this rapidly evolving field. In the context of COVID-19 case count modeling and forecasting, a multitude of models have been developed based on different assumptions that capture specific aspects of the disease dynamics (reproduction number evolution, contact network construction, etc.).

abstract:
  COVID-19 pandemic represents an unprecedented global health crisis in the last 100 years. Its economic, social and health impact continues to grow and is likely to end up as one of the worst global disasters since the 1918 pandemic and the World Wars. Mathematical models have played an important role in the ongoing crisis; they have been used to inform public policies and have been instrumental in many of the social distancing measures that were instituted worldwide. In this article, we review some of the important mathematical models used to support the ongoing planning and response efforts. These models differ in their use, their mathematical form and their scope.


id: cord-312885-d4ku8dyz
title: Global, regional, and national estimates of target population sizes for COVID-19 vaccination
author: Wang, W.
date: 2020-09-30
txt: ./txt/cord-312885-d4ku8dyz.txt
cache: ./cache/cord-312885-d4ku8dyz.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.09.29.20200469
doi: 10.1101/2020.09.29.20200469
summary:
  Here, we provide global, regional, and national estimates of the size of the COVID-19 vaccine recipient population by priority group under the allocation frameworks proposed by various international teams (8, (10) (11) (12) . preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in In main analysis, to consider vaccine programs tailored the epidemiological situation of individual countries, we also used COVID-19 case counts (as of September 13, 2020) and serology data to estimate the size of the population already infected, who may be at lower priority for vaccination.

abstract:
  Abstract Background COVID-19 vaccine prioritization and allocation strategies that maximize health benefit through efficient use of limited resources are urgently needed. We aimed to provide global, regional, and national estimates of target population sizes for COVID-19 vaccination to inform country-specific immunization strategies on a global scale. Methods Based on a previous study of international allocation for pandemic COVID-19 vaccines, we classified the entire world population into eleven priority groups. Information on priority groups was derived from a multi-pronged search of official websites, media sources and academic journal articles. The sizes of different priority groups were projected for 194 countries globally. Results Overall, the size of COVID-19 vaccine recipient population varied markedly by goals of the vaccination program and geography. The general population aged <60 years without any underlying condition accounts for the majority of the total population (5.2 billion people, 68%), followed by 2.3 billion individuals at risk of severe disease, and 46.9 million essential workers which are critical to maintaining a functional society. Differences in the demographic structure, presence of underlying conditions, and number of essential workers led to highly variable estimates of target populations both at the WHO region and country level. In particular, Europe has the highest share of essential workers (6.8%) and the highest share of individuals with underlying conditions (37.8%), two priority categories to maintain societal functions and reduce severe burden. In contrast, Africa has the highest share of healthy adults, school-age individuals, and infants (77.6%), which are the key groups to target to reduce community transmission. Interpretation The sizeable distribution of target groups on a country and regional bases underlines the importance of equitable and efficient vaccine prioritization and allocation globally. The direct and indirect benefits of COVID-19 vaccination should be balanced by considering local differences in demography and health.


id: cord-313869-3x2qf3yu
author: Bin, Sheng
date: 2019-11-25
txt: ./txt/cord-313869-3x2qf3yu.txt
cache: ./cache/cord-313869-3x2qf3yu.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/ijerph16234683
doi: 10.3390/ijerph16234683
summary:
  Based on the ability of cellular automata to model complex problems, this paper considered that, in real society, population mobility is caused by economic development, living environment, education level, and other factors, and that population density, sex ratio, and age structure of area also have some influence on the spread of infectious diseases. In order to study and analyze the influence of population density on infectious disease spread, each individual is mapped into a cell in the cellular automata model. Without considering other factors, this paper focused on the influence of three factors, namely, population density, individual heterogeneity, and mobility on infectious disease spread, and the SLIRDS model based on cellular automata was constructed. Without considering other factors, this paper focused on the influence of three factors, namely, population density, individual heterogeneity, and mobility on infectious disease spread, and the SLIRDS model based on cellular automata was constructed.

title:
  Spread of Infectious Disease Modeling and Analysis of Different Factors on Spread of Infectious Disease Based on Cellular Automata

abstract:
  Infectious diseases are an important cause of human death. The study of the pathogenesis, spread regularity, and development trend of infectious diseases not only provides a theoretical basis for future research on infectious diseases, but also has practical guiding significance for the prevention and control of their spread. In this paper, a controlled differential equation and an objective function of infectious diseases were established by mathematical modeling. Based on cellular automata theory and a compartmental model, the SLIRDS (Susceptible-Latent-Infected-Recovered-Dead-Susceptible) model was constructed, a model which can better reflect the actual infectious process of infectious diseases. Considering the spread of disease in different populations, the model combines population density, sex ratio, and age structure to set the evolution rules of the model. Finally, on the basis of the SLIRDS model, the complex spread process of pandemic influenza A (H1N1) was simulated. The simulation results are similar to the macroscopic characteristics of pandemic influenza A (H1N1) in real life, thus the accuracy and rationality of the SLIRDS model are confirmed.


id: cord-314325-nquov2i0
title: Epidemiology of Human and Animal Viral Diseases
author: Murphy, F.A.
date: 2008-07-30
txt: ./txt/cord-314325-nquov2i0.txt
cache: ./cache/cord-314325-nquov2i0.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/B9780123744104003903
doi: 10.1016/b978-012374410-4.00390-3
summary:
  Viral disease epidemiology has come to have a major role in clarifying the etiologic role of particular viruses and viral variants as the cause of specific diseases, in improving our understanding of the overall nature of specific viral diseases, and in determining factors affecting host susceptibility and immunity, in unraveling modes of transmission, in clarifying the interaction of viruses with environmental determinants of disease, in determining the safety, efficacy, and utility of vaccines and antiviral drugs, and especially in alerting and directing disease prevention and control actions. Epidemiology is also effective in (1) clarifying the role of particular viruses and viral variants as the cause of disease, (2) clarifying the interaction of viruses with environmental determinants of disease, (3) determining factors affecting host susceptibility, (4) unraveling modes of transmission, and (5) field testing of vaccines and antiviral drugs.

abstract:
  Viral disease epidemiology is the study of the determinants, dynamics, and distribution of viral diseases in populations. The risk of infection or disease in a population is determined by characteristics of the virus, the host, and the host population, as well as behavioral, environmental, and ecological factors that affect virus transmission from one host to another. Viral disease epidemiology has come to have a major role in clarifying the etiologic role of particular viruses and viral variants as the cause of specific diseases, in improving our understanding of the overall nature of specific viral diseases, and in determining factors affecting host susceptibility and immunity, in unraveling modes of transmission, in clarifying the interaction of viruses with environmental determinants of disease, in determining the safety, efficacy, and utility of vaccines and antiviral drugs, and especially in alerting and directing disease prevention and control actions. Information on incidence, prevalence, and morbidity and mortality rates contributes directly to the establishment of priorities for prevention and control programs, whether this involves vaccine or drug development and delivery, environmental and hygienic improvements, enhancement of nutritional status, personal or community behavior, agricultural and food processing enhancements, reservoir host and vector control, and international cooperation and communication.


id: cord-314488-x8mqxif9
title: Genetics research at the "Centenary of human population genetics" conference and SBB-2019
author: Tatarinova, Tatiana V.
date: 2020-10-22
txt: ./txt/cord-314488-x8mqxif9.txt
cache: ./cache/cord-314488-x8mqxif9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33092531/
doi: 10.1186/s12863-020-00906-7
abstract: nan
summary:
  We open up this Special Issue by the human population genetics study in Africa by the article by Sandra Walsh and colleagues [10] (this issue). Role of gene regulatory regions in the human genome were discussed in [16] as part of special postconference Supplement issues at BioMed Central Distribution of haplotypes in the putative enhancer region has been assessed using the data on four continental super groups from the 1000 Genomes Project. Rosa Tiis and co-authors [20] (this issue) studied polymorphic variants of the NAT2 (N-acetyltransferase 2) gene in native populations of Siberia. Genetic predispositions to diabetes and related diseases among native Mongolian populations were studied by the authors'' group earlier in [22, 23] . The authors continued study on singlenucleotide polymorphisms (SNP) in TATA-binding protein binding sites in human gene promoters [25, 26] . Genetics studies on model organisms have new value in relation to the infectious disease resistance, adaptations of human populations to environment, and natural polymorphism.


id: cord-314992-vhjuus50
title: On biological evolution and environmental solutions
author: Matthews, Blake
date: 2020-07-01
txt: ./txt/cord-314992-vhjuus50.txt
cache: ./cache/cord-314992-vhjuus50.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.scitotenv.2020.138194
doi: 10.1016/j.scitotenv.2020.138194
summary:
  Drug treatment is often the default approach used to control emergent bacterial and fungal diseases, but in some cases a single new drug can cause strong natural selection, and, combined with the high evolutionary potential of pathogens, this means that the expected time until drug resistance evolves can be short (Fisher et al., 2018; Kennedy and Read, 2018) . A better understanding of the evolutionary dynamics of such systems, gained, for example, by tracking environmental change in real-time and linking those changes with environmental sources of natural selection, could help us predict the outbreaks of toxic algae. Predictions about complex ecological systems are challenging and require solid understanding of ecological and evolutionary mechanisms behind population growth, genetic and trait diversity, trait-environmental relationships, trade-offs, and community dynamics.

abstract:
  Drawing insights from multiple disciplines is essential for finding integrative solutions that are required to tackle complex environmental problems. Human activities are causing unprecedented influence on global ecosystems, culminating in the loss of species and fundamental changes in the selective environments of organisms across the tree of life. Our collective understanding about biological evolution can help identify and mitigate many of the environmental problems in the Anthropocene. To this end, we propose a stronger integration of environmental sciences with evolutionary biology.


id: cord-315449-kt4m3247
title: Public and Population Health Genomics
author: Wise, A.L.
date: 2016-06-10
txt: ./txt/cord-315449-kt4m3247.txt
cache: ./cache/cord-315449-kt4m3247.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/B978012420196500023X
doi: 10.1016/b978-0-12-420196-5.00023-x
summary:
  In this chapter we will survey the three major disciplines contributing to population genomics (genomics, population, and social sciences) and explore two cross-cutting issues: global health and population versus individual health, using specific examples from diseases such as asthma, colon cancer, and cystic fibrosis. This aspect of the emerging field of population genomics is discussed in this chapter using specific examples from diverse diseases such as breast cancer, colorectal cancer, bronchial asthma, Crohn disease, Alzheimer dementia, and cystic fibrosis. Population variation is an important consideration when studying common complex conditions that are influenced by multiple genetic, environmental, and social risk factors, such as bronchial asthma. For example, the prevalence of type 2 diabetes mellitus is increasing globally and has been associated with multiple genetic (more than 60 genes to date), epigenetic (such as methylation or histone modification), environmental (such as diet), and social factors (such as exercise), all of which contribute to this complex disease [42] .

abstract:
  Public health seeks to improve health at a population level through interventions that increase the net health benefit to the population as a whole. Advances in genomics knowledge and technologies can add to this endeavor, but also pose a challenge when faced with often conflicting public health (population) and genomic medicine (individual) perspectives. Combining the fields of genomic, population, and social sciences, population genomics or public health genomics looks at the promotion of health and prevention of disease using genomic knowledge through the lens of populations rather than individuals. In this chapter we will survey the three major disciplines contributing to population genomics (genomics, population, and social sciences) and explore two cross-cutting issues: global health and population versus individual health, using specific examples from diseases such as asthma, colon cancer, and cystic fibrosis.


id: cord-322982-c4xhg567
title: Low genetic diversity in the masked palm civet Paguma larvata (Viverridae)
author: Patou, M.‐L.
date: 2009-04-17
txt: ./txt/cord-322982-c4xhg567.txt
cache: ./cache/cord-322982-c4xhg567.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/j.1469-7998.2009.00570.x
doi: 10.1111/j.1469-7998.2009.00570.x
summary:
  Results indicated a low genetic variability and suggested a lack of a phylogeographic structure in this species, which do not allow inferring the geographic origin of samples of unknown origin, although it is possible to distinguish individuals from China and the Sundaic region. For this purpose, we sequenced a portion of two mitochondrial genes, the cytochrome b (Cytb) and the control region (CR), both shown to be suitable markers for carnivore species phylogeography (e.g. Li et al., 2005a,b; Marmi et al., 2006; Cosson et al., 2007; Veron et al., 2007) , and analysed five polymorphic microsatellite markers in Chinese wild and farmed populations. We used the Arlequin 2.0 software (Excoffier, Laval & Schneider, 2005) to carry out several analyses: (1) analysis of molecular variance (AMOVA, Excoffier, Smouse & Quattro, 1992) to test for genetic differentiation between putative geographical regions and (2) computation of haplotypic as well as nucleotidic diversity (p) for each of the groups.

abstract:
  The masked palm civet is distributed through south‐east Asia, China and the Himalayas. Because of its potential role in the severe acute respiratory syndrome (SARS) epidemic, it has become important to gather information on this species, and notably to provide a tool to determine the origin of farm and market animals. For this purpose, we studied the genetic variability and the phylogeographic pattern of the masked palm civet Paguma larvata. First, two portions of mitochondrial genes, cytochrome b and the control region, were sequenced for a total of 76 individuals sampled from China, the Indochinese region and the Sundaic region. Results indicated a low genetic variability and suggested a lack of a phylogeographic structure in this species, which do not allow inferring the geographic origin of samples of unknown origin, although it is possible to distinguish individuals from China and the Sundaic region. This low variation is in contrast to the well‐marked morphological differentiation between the populations in the Sundaic and Chinese–Indochinese regions. We also used five microsatellite loci to genotype 149 samples from two wild and four farmed populations in China, where the masked palm civet is farmed and where the SARS coronavirus was isolated. These analyses also showed a reduced variability in Chinese civets and showed that farmed populations did not exhibit a lower genetic diversity than wild populations, suggesting frequent introductions of wild individuals into farms.


id: cord-324435-qpufvt3o
title: Targeted adaptive isolation strategy for COVID-19 pandemic
author: Neufeld, Zoltan
date: 2020-06-05
txt: ./txt/cord-324435-qpufvt3o.txt
cache: ./cache/cord-324435-qpufvt3o.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S2468042720300142
doi: 10.1016/j.idm.2020.04.003
summary:
  We show that an alternative or complementary approach based on targeted isolation of the vulnerable sub-population may provide a more efficient and robust strategy at a lower economic and social cost within a shorter timeframe resulting in a collectively immune population. The so called "social distancing" strategy aims to reduce social interactions within the population decreasing the probability of transmission of the infection, represented by the parameter k in the model. • if R 0 remains > 1, the social distancing can significantly extend the duration of the epidemic, making it difficult to maintain the reduced transmission rate over a long time period in a large population. To take into account the markedly different age-dependent outcome of the COVID-19 infection, we extend the standard SIR model by separating the population into two compartments: the lowrisk majority population with mild symptoms, and a vulnerable, mainly older population, where infection is more likely to lead to hospitalization and death; see Fig. 2 (a).

abstract:
  We investigate the effects of social distancing in controlling the impact of the COVID-19 epidemic using a simple susceptible-infected-removed epidemic model. We show that an alternative or complementary approach based on targeted isolation of the vulnerable sub-population may provide a more efficient and robust strategy at a lower economic and social cost within a shorter timeframe resulting in a collectively immune population.


id: cord-328865-ekgqdjlk
author: Anand, Shuchi
date: 2020-09-25
txt: ./txt/cord-328865-ekgqdjlk.txt
cache: ./cache/cord-328865-ekgqdjlk.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0140673620320092
doi: 10.1016/s0140-6736(20)32009-2
summary:
  METHODS: For this cross-sectional study, in partnership with a central laboratory that receives samples from approximately 1300 dialysis facilities across the USA, we tested the remainder plasma of 28 503 randomly selected adult patients receiving dialysis in July, 2020, using a spike protein receptor binding domain total antibody chemiluminescence assay (100% sensitivity, 99·8% specificity). 12 Testing remainder plasma from monthly samples obtained for routine care of patients on dialysis for SARS-CoV-2 antibodies therefore represents a practical approach to a population-representative surveillance strat egy, 13 informing risks faced by a susceptible population while ensuring representation from racial and ethnic minorities. In our analysis of seroprevalence of SARS-CoV-2 spike protein receptor binding antibodies from a nationwide representative sample of patients receiving dialysis, we find that despite the USA contemporaneously leading the world in the numbers of diagnosed cases, overall, fewer than 10% of US adults had evidence of seroconversion in July, 2020.

title:
  Prevalence of SARS-CoV-2 antibodies in a large nationwide sample of patients on dialysis in the USA: a cross-sectional study

abstract:
  BACKGROUND: Many patients receiving dialysis in the USA share the socioeconomic characteristics of underserved communities, and undergo routine monthly laboratory testing, facilitating a practical, unbiased, and repeatable assessment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroprevalence. METHODS: For this cross-sectional study, in partnership with a central laboratory that receives samples from approximately 1300 dialysis facilities across the USA, we tested the remainder plasma of 28 503 randomly selected adult patients receiving dialysis in July, 2020, using a spike protein receptor binding domain total antibody chemiluminescence assay (100% sensitivity, 99·8% specificity). We extracted data on age, sex, race and ethnicity, and residence and facility ZIP codes from the anonymised electronic health records, linking patient-level residence data with cumulative and daily cases and deaths per 100 000 population and with nasal swab test positivity rates. We standardised prevalence estimates according to the overall US dialysis and adult population, and present estimates for four prespecified strata (age, sex, region, and race and ethnicity). FINDINGS: The sampled population had similar age, sex, and race and ethnicity distribution to the US dialysis population, with a higher proportion of older people, men, and people living in majority Black and Hispanic neighbourhoods than in the US adult population. Seroprevalence of SARS-CoV-2 was 8·0% (95% CI 7·7–8·4) in the sample, 8·3% (8·0–8·6) when standardised to the US dialysis population, and 9·3% (8·8–9·9) when standardised to the US adult population. When standardised to the US dialysis population, seroprevalence ranged from 3·5% (3·1–3·9) in the west to 27·2% (25·9–28·5) in the northeast. Comparing seroprevalent and case counts per 100 000 population, we found that 9·2% (8·7–9·8) of seropositive patients were diagnosed. When compared with other measures of SARS-CoV-2 spread, seroprevalence correlated best with deaths per 100 000 population (Spearman's ρ=0·77). Residents of non-Hispanic Black and Hispanic neighbourhoods experienced higher odds of seropositivity (odds ratio 3·9 [95% CI 3·4–4·6] and 2·3 [1·9–2·6], respectively) compared with residents of predominantly non-Hispanic white neighbourhoods. Residents of neighbourhoods in the highest population density quintile experienced increased odds of seropositivity (10·3 [8·7–12·2]) compared with residents of the lowest density quintile. County mobility restrictions that reduced workplace visits by at least 5% in early March, 2020, were associated with lower odds of seropositivity in July, 2020 (0·4 [0·3–0·5]) when compared with a reduction of less than 5%. INTERPRETATION: During the first wave of the COVID-19 pandemic, fewer than 10% of the US adult population formed antibodies against SARS-CoV-2, and fewer than 10% of those with antibodies were diagnosed. Public health efforts to limit SARS-CoV-2 spread need to especially target racial and ethnic minority and densely populated communities. FUNDING: Ascend Clinical Laboratories.


id: cord-329244-z28twpb1
title: Wildlife cancer: a conservation perspective
author: McAloose, Denise
date: 2009
txt: ./txt/cord-329244-z28twpb1.txt
cache: ./cache/cord-329244-z28twpb1.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1038/nrc2665
doi: 10.1038/nrc2665
summary:
  However, over the past few decades wildlife health monitoring has increased and we are now gaining an improved -and occasionally alarming -perspective about the presence and impact of cancer in endangered species, such as the Tasmanian devil, western barred bandicoot (Perameles bougainville) and Attwater''s prairie chicken (Tympanuchus cupido Attwateri), and non-endangered species, such as the beluga whale (Delphinapterus leucas). However, with the identification of Tasmanian devil facial tumour disease, sea turtle fibropapillomatosis and sea lion genital carcinoma, it has become apparent that neoplasia can be highly prevalent and have considerable effects on some species. However, with the identification of Tasmanian devil facial tumour disease, sea turtle fibropapillomatosis and sea lion genital carcinoma, it has become apparent that neoplasia can be highly prevalent and have considerable effects on some species.

abstract:
  Until recently, cancer in wildlife was not considered to be a conservation concern. However, with the identification of Tasmanian devil facial tumour disease, sea turtle fibropapillomatosis and sea lion genital carcinoma, it has become apparent that neoplasia can be highly prevalent and have considerable effects on some species. It is also clear that anthropogenic activities contribute to the development of neoplasia in wildlife species, such as beluga whales and bottom-dwelling fish, making them sensitive sentinels of disturbed environments.


id: cord-331608-ezf9r8l4
title: Effectiveness of population density as natural social distancing in COVID19 spreading
author: Jawad, A.J.
date: 2020-08-20
txt: ./txt/cord-331608-ezf9r8l4.txt
cache: ./cache/cord-331608-ezf9r8l4.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S2352552520300943
doi: 10.1016/j.jemep.2020.100556
summary:
  In our study, a new view of the importance of social distancing to prevent the spread of coronavirus has been presented in terms of the relationship between peak day and peak period and population density of nine countries. analysis of that data with population density was evaluated to indicate there are significant effects of population density on peak day and peak period times which explain the importance of social distancing between people to manage and control that. analysis of that data with population density was evaluated to indicate there are significant effects of population density on peak day and peak period times which explain the importance of social distancing between people to manage and control that. In our work, we try to analyse the relationship between population density and sizes on COVID19 spreading in the terms of peak day and period times in nine different countries.

abstract:
  Recently, many countries have decided to reopen gradually and some of them have thought that social distancing has not had a significant effect. In our study, a new view of the importance of social distancing to prevent the spread of coronavirus has been presented in terms of the relationship between peak day and peak period and population density of nine countries. Data for nine different countries in different coronavirus situations have been analyzed. The analysis process was applied by using three programs, namely; WebPlotDigitizer, WSxM and Origin. The results provide evidence of the effectiveness of social distancing by calculation of the effect of population density on coronavirus infection. That was applied by two stages, the first one by determination of two different groups of countries depending on the rate and range of coronavirus spread. These two groups were countries with developed and developing COVID19 which lead to calculate the peak day and the period times of developed groups. Then, analysis of that data with population density was evaluated to indicate there are significant effects of population density on peak day and peak period times which explain the importance of social distancing between people to manage and control that. The results showed that there are increasing in peak day and peak period times with increasing the population density.


id: cord-331879-w7008uyy
author: Iversen, Jenny
date: 2020-10-01
txt: ./txt/cord-331879-w7008uyy.txt
cache: ./cache/cord-331879-w7008uyy.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1002/jia2.25632
doi: 10.1002/jia2.25632
summary:
  However, the conditions faced by specific populations vary according to social, structural and environmental factors, including stigma and discrimination, criminalization, social and economic safety nets and the local epidemiology of HIV and COVID‐19, which determine risk of exposure and vulnerability to adverse health outcomes, as well as the ability to comply with measures such as physical distancing. Significant heterogeneity in the COVID‐19 pandemic, the underlying HIV epidemic and the ability of key populations to protect themselves means that people who inject drugs and sex workers face particular challenges, including indirect impacts as a result of police targeting, loss of income and sometimes both. Global networks, including the International Network of People who use Drugs (INPUD), the Global Network of Sex Work Projects (NSWP), the Global Network of People Living with HIV (GNP+) and MPact Global Action for Gay Men''s Health and Rights have issued statements calling for urgent action to protect their communities and to address population-specific needs for prevention, care and treatment [9,18-20].

title:
  COVID‐19, HIV and key populations: cross‐cutting issues and the need for population‐specific responses

abstract:
  INTRODUCTION: Key populations at elevated risk to contract or transmit HIV may also be at higher risk of COVID‐19 complications and adverse outcomes associated with public health prevention measures. However, the conditions faced by specific populations vary according to social, structural and environmental factors, including stigma and discrimination, criminalization, social and economic safety nets and the local epidemiology of HIV and COVID‐19, which determine risk of exposure and vulnerability to adverse health outcomes, as well as the ability to comply with measures such as physical distancing. This commentary identifies common vulnerabilities and cross‐cutting themes in terms of the impacts of COVID‐19 on key populations before addressing issues and concerns specific to particular populations. DISCUSSION: Cross‐cutting themes include direct impacts such as disrupted access to essential medicines, commodities and services such as anti‐retroviral treatment, HIV pre‐exposure prophylaxis, opioid agonist treatment, viral load monitoring, HIV and sexually transmitted infections testing, condoms and syringes. Indirect impacts include significant collateral damage arising from prevention measures which restrict human rights, increase or impose criminal penalties, and expand police powers to target vulnerable and criminalized populations. Significant heterogeneity in the COVID‐19 pandemic, the underlying HIV epidemic and the ability of key populations to protect themselves means that people who inject drugs and sex workers face particular challenges, including indirect impacts as a result of police targeting, loss of income and sometimes both. Geographical variations mean that transgender people and men who have sex with men in regions like Africa and the middle east remain criminalized, as well as stigmatized and discriminated against, increasing their vulnerability to adverse outcomes in relation to COVID‐19. CONCLUSIONS: Disruptions to both licit and illicit supply chains, loss of income and livelihoods and changes in behaviour as a result of lockdowns and physical distancing have the potential to exacerbate the impacts of the COVID‐19 pandemic on key populations. While these impacts will vary significantly, human‐rights approaches to COVID‐19 emergency laws and public health prevention measures that are population‐specific and sensitive, will be key to reducing adverse health outcomes and ensuring that no one is left behind.


id: cord-337703-637xgk6g
title: Equity in Health: Consideration of Race and Ethnicity in Precision Medicine
author: Edwards, Todd L.
date: 2020-07-22
txt: ./txt/cord-337703-637xgk6g.txt
cache: ./cache/cord-337703-637xgk6g.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0168952520301670
doi: 10.1016/j.tig.2020.07.001
summary:
  The causes for disparities in implementation of precision medicine are complex, due in part to differences in clinical care and a lack of engagement and recruitment of under-represented populations in studies. The causes for disparities in implementation of precision medicine are complex, due in part to differences in clinical care and a lack of engagement and recruitment of under-represented populations in studies. The development of precision medicine approaches to improve accuracy of diagnoses, understand biological and environmental elements of disease risk, and improve safety and efficacy of treatments has been relatively slow within minority and disadvantaged populations. The reasons minorities and economically disadvantaged populations have had limited access to personalized medicine are complex and directly tied to the causes of health disparities. These causes are described earlier, and also include distrust of researchers combined with a lack of consistent long-term community engagement and other strategies to increase diversity in recruitment from under-represented populations for clinical studies.

abstract:
  The causes for disparities in implementation of precision medicine are complex, due in part to differences in clinical care and a lack of engagement and recruitment of under-represented populations in studies. New tools and large genetic cohorts can change these circumstances and build access to personalized medicine for disadvantaged populations.


id: cord-341879-vubszdp2
title: Genomic analysis of emerging pathogens: methods, application and future trends
author: Li, Lucy M
date: 2014-11-22
txt: ./txt/cord-341879-vubszdp2.txt
cache: ./cache/cord-341879-vubszdp2.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25418281/
doi: 10.1186/s13059-014-0541-9
summary:
  In this review, we evaluate methods that exploit pathogen sequences and the contribution of genomic analysis to understand the epidemiology of recently emerged infectious diseases. In this review, we provide an overview of recent developments in genomic methods in the context of infectious diseases, evaluate integrative methods that incorporate genetic data in epidemiological analysis, and discuss the application of these methods to EIDs. Over the last two decades, sequence data have increased in quality, length and volume due to improvements in the underlying technology and decreasing costs. In recent cases of EIDs, genomic data have helped to classify and characterize the pathogen, uncover the population history of the disease, and produce estimates of epidemiological parameters. Just as compartmental models can be fitted to surveillance data to infer the epidemiological dynamics of an infectious disease (Box 1), the coalescent framework allows inference of population history from pathogen sequences.

abstract:
  The number of emerging infectious diseases is increasing. Characterizing novel or re-emerging infections is aided by the availability of pathogen genomes. In this review, we evaluate methods that exploit pathogen sequences and the contribution of genomic analysis to understand the epidemiology of recently emerged infectious diseases.


id: cord-342181-x14iywtr
title: Population-scale testing can suppress the spread of COVID-19
author: Taipale, J.
date: 2020-05-01
txt: ./txt/cord-342181-x14iywtr.txt
cache: ./cache/cord-342181-x14iywtr.txt
extension: .txt
mime: text/plain
url: http://medrxiv.org/cgi/content/short/2020.04.27.20078329v1?rss=1
doi: 10.1101/2020.04.27.20078329
summary:
  Our model also indicates that unlike sampling-based tests, population-scale testing does not need to be very accurate: false negative rates up to 15% could be tolerated if 80% comply with testing every ten days, and false positives can be almost arbitrarily high when a high fraction of the population is already effectively quarantined. Using the standard (continuous, deterministic) SIR model, the equations in Fig. 2A and Methods show that the optimal population-scale testing strategy will succeed if at least two thirds of all new COVID-19 cases are immediately identified and quarantined. Although a population-scale test does not need to be as accurate as a clinical-grade qRT-PCR test (see above), apart from a potential increase in errors due to sample collection, there is no theoretical reason why a self-test based on isothermal amplification would not achieve the false negative and positive rates that are equivalent to the current state-of-the-art methodology.

abstract:
  We propose an additional intervention that would contribute to the control of the COVID-19 pandemic, offer more protection for people working in essential jobs, and help guide an eventual reopening of society. The intervention is based on: (1) testing every individual (2) repeatedly, and (3) self-quarantine of infected individuals. Using a standard epidemiological model (SIR), we show here that by identification and isolation of the majority of infectious individuals, including those who may be asymptomatic, the reproduction number R0 of SARS-CoV-2 would be reduced well below 1.0, and the epidemic would collapse. We replicate these observations in a more complex stochastic dynamic model on a social network graph. We also find that the testing regime would be additive to other interventions, and be effective at any level of prevalence. If adopted as a policy, any industrial society could sustain the regime for as long as it takes to find a safe and effective cure or vaccine. Our model also indicates that unlike sampling-based tests, population-scale testing does not need to be very accurate: false negative rates up to 15% could be tolerated if 80% comply with testing every ten days, and false positives can be almost arbitrarily high when a high fraction of the population is already effectively quarantined. Testing at the required scale would be feasible if existing qPCR-based methods are scaled up and multiplexed. A mass produced, low throughput field test kit could also be carried out at home. Economic analysis also supports the feasibility of the approach: current reagent costs for tests are in the range of a dollar or less, and the estimated benefits for population-scale testing are so large that the policy would be cost-effective even if the costs were larger by more than two orders of magnitude. To identify both active and previous infections, both viral RNA and antibodies could be tested. All technologies to build such test kits, and to produce them in the scale required to test the entire world's population exist already. Integrating them, scaling up production, and implementing the testing regime will require resources and planning, but at a scale that is very small compared to the effort that every nation would devote to defending itself against a more traditional foe.


id: cord-344009-hm36pepp
title: Virus perpetuation in populations: biological variables that determine persistence or eradication
author: Nathanson, N.
date: 2005
txt: ./txt/cord-344009-hm36pepp.txt
cache: ./cache/cord-344009-hm36pepp.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16355865/
doi: 10.1007/3-211-29981-5_2
summary:
  However, small animal populations can turnover significantly each year, permitting the perpetuation of some viruses that cause acute infections. Measles has several attributes that -in the aggregate -are not seen for other common viral diseases: (i) There are longterm records of measles incidence, collected by many health departments in the United States and other countries; (ii) 95% of all measles infections manifest as illness (in contrast to 1% for poliomyelitis for example); (iii) the symptoms of measles are sufficiently pathognomonic so that it can be distinguished from other viral infections by clinical observers; and (iv) population-wide reports can be corrected for under-reporting (about 15% of measles cases were reported in most cities in the United States prior to the introduction of measles vaccine in 1963). Vaccine-induced reduction of susceptible individuals in such a population can be guesstimated to reduce the number of new infections per trough generation period below the threshold for virus perpetuation.

abstract:
  In this review, I use the term “perpetuation” for persistence of a virus in a population, since this is a different phenomenon from persistence of a virus in an infected host. Important variables that influence perpetuation differ in small (<1,000 individuals) and large (>10,000) populations: in small populations, two important variables are persistence in individuals, and turnover of the population, while in large populations important variables are transmissibility, generation time, and seasonality. In small populations, viruses such as poliovirus that cause acute infections cannot readily be perpetuated, in contrast to viruses such as hepatitis B virus, that cause persistent infections. However, small animal populations can turnover significantly each year, permitting the perpetuation of some viruses that cause acute infections. Large populations of humans are necessary for the perpetuation of acute viruses; for instance, measles required a population of 500,000 for perpetuation in the pre-measles vaccine era. Furthermore, if an acute virus, such as poliovirus, exhibits marked seasonality in large populations, then it may disappear during the seasonal trough, even in the presence of a large number of susceptible persons. Eradication is the converse of perpetuation and can be used as a definitive approach to the control of a viral disease, as in the instance of smallpox. Therefore, the requirements for perpetuation have significant implications for practical public health goals.


id: cord-345811-f0yt2a32
title: Public Health Literacy for Lawyers
author: Parmet, Wendy E.
date: 2007-01-24
txt: ./txt/cord-345811-f0yt2a32.txt
cache: ./cache/cord-345811-f0yt2a32.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/14968671/
doi: 10.1111/j.1748-720x.2003.tb00136.x
abstract: nan
summary:
  Lochner, like most important Supreme Court cases, was about many things and many themes can be dissected the rise of the labor movement;t2 the Supreme Court majority''s antipathy to progressive labor legi~lation;~~ and the struggle between courts and legislature^.^^ Legal scholars, however, seldom discuss the public health context, although the statute at issue was presented by the State of New York as a public health measure and bakeshop workers did experience numerous diseases, including a high prevalence of infectious tubercul~sis.~~ In fact, Justice Peckhani, writing for the majority of the Supreme Court, recognized that the statute would have been constitutional if it were indeed, truly, a public health measure.26 Thus, one of the key questions implicit in Lochnerwas the meaning of public health and whether worker protection issues could be seen as a valid concern for public health.27 Examined in this manner, Lochner provides an interesting insight into the contested nature of public health and the government''s role in protecting it.


id: cord-345843-yz0buegp
author: Gushulak, BD
date: 2010-03-31
txt: ./txt/cord-345843-yz0buegp.txt
cache: ./cache/cord-345843-yz0buegp.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3134/ehtj.09.010
doi: 10.3134/ehtj.09.010
summary:
  The thesis that human population mobility is itself a major determinant of global public health is supported in this article by review of the published literature from the perspective of determinants of health (such as genetics/biology, behavior, environment, and socioeconomics), population-based disease prevalence differences, existing national and international health policies and regulations, as well as inter-regional shifts in population demographics and health outcomes. In migration health, threat and risk identification, assessment and management rarely occur ''pre-event.'' Examples of poorly studied health threats of potential societal and public health importance include domestic violence against migrant women in destination locations, 42,43 long-term impact of dietary changes 44,45 on the incidence of cardiovascular disease, 46 diabetes, 47 and certain forms of cancer in foreignborn migrants and their locally born offspring, 48 or the importation of health services or pharmaceutical products 49 from less-regulated environments, representing traditional but often unregulated or unmonitored patterns of self-care.

title:
  Migrants and emerging public health issues in a globalized world: threats, risks and challenges, an evidence-based framework

abstract:
  International population mobility is an underlying factor in the emergence of public health threats and risks that must be managed globally. These risks are often related, but not limited, to transmissible pathogens. Mobile populations can link zones of disease emergence to lowprevalence or nonendemic areas through rapid or high-volume international movements, or both. Against this background of human movement, other global processes such as economics, trade, transportation, environment and climate change, as well as civil security influence the health impacts of disease emergence. Concurrently, global information systems, together with regulatory frameworks for disease surveillance and reporting, affect organizational and public awareness of events of potential public health significance. International regulations directed at disease mitigation and control have not kept pace with the growing challenges associated with the volume, speed, diversity, and disparity of modern patterns of human movement. The thesis that human population mobility is itself a major determinant of global public health is supported in this article by review of the published literature from the perspective of determinants of health (such as genetics/biology, behavior, environment, and socioeconomics), population-based disease prevalence differences, existing national and international health policies and regulations, as well as inter-regional shifts in population demographics and health outcomes. This paper highlights some of the emerging threats and risks to public health, identifies gaps in existing frameworks to manage health issues associated with migration, and suggests changes in approach to population mobility, globalization, and public health. The proposed integrated approach includes a broad spectrum of stakeholders ranging from individual health-care providers to policy makers and international organizations that are primarily involved in global health management, or are influenced by global health events.


id: cord-346500-uwi3ezd7
title: Structure, space and size: competing drivers of variation in urban and rural measles transmission
author: Korevaar, Hannah
date: 2020-07-08
txt: ./txt/cord-346500-uwi3ezd7.txt
cache: ./cache/cord-346500-uwi3ezd7.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1098/rsif.2020.0010
doi: 10.1098/rsif.2020.0010
summary:
  The consistency of seasonality in England and Wales (hereafter E&W) as a result of the school calendar provides a unique opportunity to compare transmission rates and epidemic dynamics while isolating urban/rural status from other potentially confounding factors such as climate, variation in seasonal contact rates, population size and proximity to epidemic pacemakers. The diversity of locations in terms of geographical space and population size, as well as the temporal detail of the incidence data provide an unparalleled and uniquely apt dataset for investigating urban and rural differences in transmission. Additional comparisons of TSIR parameters such as transmission rate (β) and R 0 reveal variation with population size, but urban and rural locations remain consistent (electronic supplementary material, figure S5 ). Urban and rural areas do not differ in the number of large (final number of infections greater than the mean) outbreaks, which increases consistently with population size for both district types (electronic supplementary material, figure S4(B) ).

abstract:
  A key concern in public health is whether disparities exist between urban and rural areas. One dimension of potential variation is the transmission of infectious diseases. In addition to potential differences between urban and rural local dynamics, the question of whether urban and rural areas participate equally in national dynamics remains unanswered. Specifically, urban and rural areas may diverge in local transmission as well as spatial connectivity, and thus risk for receiving imported cases. Finally, the potential confounding relationship of spatial proximity with size and urban/rural district type has not been addressed by previous research. It is rare to have sufficient data to explore these questions thoroughly. We use exhaustive weekly case reports of measles in 954 urban and 468 rural districts of the UK (1944–1965) to compare both local disease dynamics as well as regional transmission. We employ the time-series susceptible–infected–recovered model to estimate disease transmission, epidemic severity, seasonality and import dependence. Congruent with past results, we observe a clear dependence on population size for the majority of these measures. We use a matched-pair strategy to compare proximate urban and rural districts and control for possible spatial confounders. This analytical strategy reveals a modest difference between urban and rural areas. Rural areas tend to be characterized by more frequent, smaller outbreaks compared to urban counterparts. The magnitude of the difference is slight and the results primarily reinforce the importance of population size, both in terms of local and regional transmission. In sum, urban and rural areas demonstrate remarkable epidemiological similarity in this recent UK context.


id: cord-349581-o320ogmg
title: The technological 'exposure' of populations; characterisation and future reduction
author: Robertson, Lindsay J.
date: 2020-05-25
url: https://www.sciencedirect.com/science/article/pii/S0016328720300720?v=s5
doi: 10.1016/j.futures.2020.102584
abstract:
  The nature and level of individuals' exposure to technological systems has been explored previously and is briefly restated here. This paper demonstrates how the concept of technological exposure can be extended to generic needs of individuals, and further to the needs of populations of individuals and even as far as “existential threats” to humanity. Technological categories that incur high levels of population exposure are explored, and categories are described. A theoretical basis for reducing population exposure is developed from the basic concepts of technological exposure. Technological developments that potentially enable less centralised societies having lower levels of population exposure, are considered for practicality and effectiveness as are the factors that could allow and cause transition to a less technologically centralised model. Some conclusions regarding practicality, triggers, and issues arising from a decentralised society are considered and include the key conclusion that a higher level of decentralisation and exposure reduction is both desirable and possible.


id: cord-351230-123i465d
title: Super spreader cohorts and covid-19
author: Van Esch, P.
date: 2020-05-20
txt: ./txt/cord-351230-123i465d.txt
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mime: text/plain
url: http://medrxiv.org/cgi/content/short/2020.05.15.20103184v1?rss=1
doi: 10.1101/2020.05.15.20103184
summary:
  A simple two-cohort SIR like model can explain the qualitative behaviour of the logarithmic derivative estimations of the covid-19 epidemic evolution as observed in several countries. We had to average the entries over a week because there were weekly periodic effects and the daily data was too noisy, but if one averages over 7 days, and one calculates the logarithmic derivative of the hospital entries, one finds again the same universal curve: In this paper, we try to build a model that displays a similar qualitative behaviour. In order to try to reconcile the behaviour of the logarithmic derivative which points to "herd immunity reached" and the low attack rate in the overall population, we propose to consider a small super-spreader subgroup in the population. With a simple coupled model of a small super spreader population within a general population, we can obtain the qualitative characteristics of the a priori puzzling evolution of the logarithmic derivative of proxies of the covid-19 epidemic evolution as found in several countries.

abstract:
  A simple two-cohort SIR like model can explain the qualitative behaviour of the logarithmic derivative estimations of the covid-19 epidemic evolution as observed in several countries. The model consists of a general population in which the R_0 value is slightly below 1, but in which a super-spreading small subgroup with high R_0, coupled to the general population, is contaminating a significant fraction of the population. The epidemic starts to slow down when herd immunity is reached in this subgroup. The dynamics of this system is quite robust against non-pharmaceutical measures.


id: cord-351594-8gp9mjen
author: Garwood, Tyler J.
date: 2020-03-05
txt: ./txt/cord-351594-8gp9mjen.txt
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url: https://doi.org/10.1002/ece3.6146
doi: 10.1002/ece3.6146
summary:
  title: Removal of chronic Mycoplasma ovipneumoniae carrier ewes eliminates pneumonia in a bighorn sheep population We hypothesized that persistent or recurrent pneumonia in bighorn sheep (Ovis canadensis) populations may be caused by chronic carriers of Mycoplasma ovipneumoniae (Mo). 3. We classified chronic carriers as adults that consistently tested positive for Mo carriage over a 20‐month sampling period (n = 2 in the treatment population; n = 2 in control population). We modeled daily survival rates, incorporating treatment (i.e., population identity), year (Gaillard et al., 2000) , strain type exposure (Cassirer TA B L E 1 Summary of bighorn sheep pathogen testing results and survival estimates in the treatment and control populations, We coded treatment and individual sex effects as with adults. After removal of chronic carriers, we did not detect Mo in 35 samples (26 negative and 9 indeterminate) collected from 26 individuals (9 males, 17 females) in the treatment population (Table 1 and Table S3 ).

title:
  Removal of chronic Mycoplasma ovipneumoniae carrier ewes eliminates pneumonia in a bighorn sheep population

abstract:
  1. Chronic pathogen carriage is one mechanism that allows diseases to persist in populations. We hypothesized that persistent or recurrent pneumonia in bighorn sheep (Ovis canadensis) populations may be caused by chronic carriers of Mycoplasma ovipneumoniae (Mo). Our experimental approach allowed us to address a conservation need while investigating the role of chronic carriage in disease persistence. 2. We tested our hypothesis in two bighorn sheep populations in South Dakota, USA. We identified and removed Mo chronic carriers from the Custer State Park (treatment) population. Simultaneously, we identified carriers but did not remove them from the Rapid City population (control). We predicted removal would result in decreased pneumonia, mortality, and Mo prevalence. Both population ranges had similar habitat and predator communities but were sufficiently isolated to preclude intermixing. 3. We classified chronic carriers as adults that consistently tested positive for Mo carriage over a 20‐month sampling period (n = 2 in the treatment population; n = 2 in control population). 4. We failed to detect Mo or pneumonia in the treatment population after chronic carrier removal, while both remained in the control. Mortality hazard for lambs was reduced by 72% in the treatment population relative to the control (CI = 36%, 91%). There was also a 41% reduction in adult mortality hazard attributable to the treatment, although this was not statistically significant (CI = 82% reduction, 34% increase). 5. Synthesis and Applications: These results support the hypothesis that Mo is a primary causative agent of persistent or recurrent respiratory disease in bighorn sheep populations and can be maintained by a few chronic carriers. Our findings provide direction for future research and management actions aimed at controlling pneumonia in wild sheep and may apply to other diseases.


id: cord-351880-iqr419fp
author: Fan, Changyu
date: 2020-03-04
txt: ./txt/cord-351880-iqr419fp.txt
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url: https://www.ncbi.nlm.nih.gov/pubmed/32143519/
doi: 10.3390/ijerph17051679
summary:
  Total 1999 2000 2000 2000 2000 2000 11,999 Hubei 1514 1508 1487 1465 1477 1547 8998 Henan 113 134 109 159 170 125 810 Anhui 59 58 55 53 56 46 327 Hunan 57 46 68 54 41 36 302 Jiangxi 58 40 53 57 49 34 291 Chongqing 34 29 34 33 33 35 198 Zhejiang 22 29 25 33 25 33 167 Sichuan 22 30 45 21 22 27 167 Fujian 14 17 16 15 39 19 120 Jiangsu 38 13 16 19 13 11 110 Shandong 12 18 11 13 8 12 74 Guangdong 7 8 18 18 14 8 73 Hebei 0 1 5 Tianjin 1 0 0 1 0 1 3 Shanghai 0 1 0 1 0 1 3 Inner Mongolia 1 0 0 0 1 0 2 Xizang 0 0 1 0 0 1 2 Ningxia 0 0 1 0 0 0 1 According to the current infectious features of 2019-nCoV, which are that middle-aged and elderly people have a high risk of infection, and transmission can occur between individuals, families and communities, we assessed several main variables.

title:
  Prediction of Epidemic Spread of the 2019 Novel Coronavirus Driven by Spring Festival Transportation in China: A Population-Based Study

abstract:
  After the 2019 novel coronavirus (2019-nCoV) outbreak, we estimated the distribution and scale of more than 5 million migrants residing in Wuhan after they returned to their hometown communities in Hubei Province or other provinces at the end of 2019 by using the data from the 2013–2018 China Migrants Dynamic Survey (CMDS). We found that the distribution of Wuhan’s migrants is centred in Hubei Province (approximately 75%) at a provincial level, gradually decreasing in the surrounding provinces in layers, with obvious spatial characteristics of circle layers and echelons. The scale of Wuhan’s migrants, whose origins in Hubei Province give rise to a gradient reduction from east to west within the province, and account for 66% of Wuhan’s total migrants, are from the surrounding prefectural-level cities of Wuhan. The distribution comprises 94 districts and counties in Hubei Province, and the cumulative percentage of the top 30 districts and counties exceeds 80%. Wuhan’s migrants have a large proportion of middle-aged and high-risk individuals. Their social characteristics include nuclear family migration (84%), migration with families of 3–4 members (71%), a rural household registration (85%), and working or doing business (84%) as the main reason for migration. Using a quasi-experimental analysis framework, we found that the size of Wuhan’s migrants was highly correlated with the daily number of confirmed cases. Furthermore, we compared the epidemic situation in different regions and found that the number of confirmed cases in some provinces and cities in Hubei Province may be underestimated, while the epidemic situation in some regions has increased rapidly. The results are conducive to monitoring the epidemic prevention and control in various regions.


id: cord-352664-heoj8ji8
title: Field pathogenomics reveals the emergence of a diverse wheat yellow rust population
author: Hubbard, Amelia
date: 2015-02-25
txt: ./txt/cord-352664-heoj8ji8.txt
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extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25723868/
doi: 10.1186/s13059-015-0590-8
summary:
  In this study, we developed a robust and rapid ''field pathogenomics'' strategy, using transcriptome sequencing of PST-infected wheat leaves to gain insight into the population structure of an emerging pathogen. To characterize the genotypic diversity of PST at the field level, we collected 219 samples of wheat and triticale infected with PST from 17 different counties across the UK in the spring and summer of 2013 ( Figure 1a ; Table S1 in Additional file 1). To determine the relationship between the 2013 PST field isolates and previously prevalent PST populations, the genomes of 14 UK and 7 French purified PST isolates collected between 1978 and 2011 were sequenced using an Illumina whole-genome shotgun approach Figure 2 Identification of wheat varieties using transcriptome data generated directly from PST-infected field samples. We used multivariate discriminant analysis of principal components (DAPC) with the 34,764 biallelic SNP sites to define the population structure and identify groups of genetically related PST isolates.

abstract:
  BACKGROUND: Emerging and re-emerging pathogens imperil public health and global food security. Responding to these threats requires improved surveillance and diagnostic systems. Despite their potential, genomic tools have not been readily applied to emerging or re-emerging plant pathogens such as the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici (PST). This is due largely to the obligate parasitic nature of PST, as culturing PST isolates for DNA extraction remains slow and tedious. RESULTS: To counteract the limitations associated with culturing PST, we developed and applied a field pathogenomics approach by transcriptome sequencing infected wheat leaves collected from the field in 2013. This enabled us to rapidly gain insights into this emerging pathogen population. We found that the PST population across the United Kingdom (UK) underwent a major shift in recent years. Population genetic structure analyses revealed four distinct lineages that correlated to the phenotypic groups determined through traditional pathology-based virulence assays. Furthermore, the genetic diversity between members of a single population cluster for all 2013 PST field samples was much higher than that displayed by historical UK isolates, revealing a more diverse population of PST. CONCLUSIONS: Our field pathogenomics approach uncovered a dramatic shift in the PST population in the UK, likely due to a recent introduction of a diverse set of exotic PST lineages. The methodology described herein accelerates genetic analysis of pathogen populations and circumvents the difficulties associated with obligate plant pathogens. In principle, this strategy can be widely applied to a variety of plant pathogens. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0590-8) contains supplementary material, which is available to authorized users.


id: cord-353609-no3mbg5d
title: An Ecological and Conservation Perspective on Advances in the Applied Virology of Zoonoses
author: Vandegrift, Kurt J.
date: 2011-04-15
txt: ./txt/cord-353609-no3mbg5d.txt
cache: ./cache/cord-353609-no3mbg5d.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/v3040379
doi: 10.3390/v3040379
summary:
  Conducting viral surveillance in animal reservoirs and invertebrate vectors can help explain circulation within host species; observed patterns of zoonotic transmission; and even allow for the prediction of periods of increased risk of zoonotic transmission (e.g., Rift valley fever and rainfall [25] ; West Nile virus (WNV) and American robin (Turdus turdus) migration [26] ; as well as hantavirus in mice [27, 28] ). Globalization, host ecology, host-virus dynamics, climate change, and anthropogenic landscape changes all contribute to the complexity of zoonotic viral emergence and disease, and create significant conservation and public health challenges. While the lasting efficacy of wildlife vaccination efforts has yet to be demonstrated with either endangered species or in breaking the transmission cycle of human pathogens, an increasing number of researchers are drawing attention to systems where it seems feasible [99, 103] ; demonstrating that intricate knowledge of host and virus ecology can greatly reduce the amount of vaccine coverage that is necessary to control these viruses.

abstract:
  The aim of this manuscript is to describe how modern advances in our knowledge of viruses and viral evolution can be applied to the fields of disease ecology and conservation. We review recent progress in virology and provide examples of how it is informing both empirical research in field ecology and applied conservation. We include a discussion of needed breakthroughs and ways to bridge communication gaps between the field and the lab. In an effort to foster this interdisciplinary effort, we have also included a table that lists the definitions of key terms. The importance of understanding the dynamics of zoonotic pathogens in their reservoir hosts is emphasized as a tool to both assess risk factors for spillover and to test hypotheses related to treatment and/or intervention strategies. In conclusion, we highlight the need for smart surveillance, viral discovery efforts and predictive modeling. A shift towards a predictive approach is necessary in today’s globalized society because, as the 2009 H1N1 pandemic demonstrated, identification post-emergence is often too late to prevent global spread. Integrating molecular virology and ecological techniques will allow for earlier recognition of potentially dangerous pathogens, ideally before they jump from wildlife reservoirs into human or livestock populations and cause serious public health or conservation issues.


