cord-001714-jfawhnsq	2015	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) .
cord-002774-tpqsjjet	2017	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.
cord-005189-z92vwovw	2006	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.
cord-007749-lt9is0is	2013	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.
cord-010334-7ce0xhjo	2020	(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.
cord-010903-kuwy7pbo	2020	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.
cord-012356-lmnccks8	2017	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.
cord-014922-pqy8bikp	2003	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.
cord-016310-7655ggxz	2008	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.
cord-018116-99z6ykb2	2009	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.
cord-020941-1qwbkg9o	2007	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.
cord-022141-yxttl3gh	2014	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.
cord-022506-fkddo12n	2011	Aside from informally "getting to know" cats during their initial acclimation period in a facility, a systematic � The ability to create different functional areas in the living environments for elimination, resting, and eating � The ability to hide in a secure place � The ability to rest/sleep without being disturbed � The ability to change locations within the environment, including using vertical space for perching � The ability to regulate body temperature by moving to warmer or cooler surfaces in the environment � The ability to scratch (which is necessary for claw health and stretching, as well as visual and scent marking) � The ability to play and exercise at will � 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) .
cord-030681-4brd2efp	2020	
cord-033412-acjskz00	2020	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] .
cord-034950-7gwb0o3l	2020	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.
cord-103990-qvuv289g	2019	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.
cord-151532-mpv2wegm	2020	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.
cord-176540-48mapwlq	2020	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.
cord-177001-ron8oqrn	2020	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.
cord-228049-1ttt1fgr	2020	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.
cord-257969-2tax8ajw	2020	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) .
cord-262846-1mhimfsf	2020	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.
cord-263248-8y1u0h6y	2020	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.
cord-265357-3f0xph0y	2017	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.
cord-265705-b6xuzkbb	2020	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.
cord-271687-sxl8g85p	2009	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.
cord-272319-jtr7wi6c	2020	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.
cord-274019-dao10kx9	2017	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.
cord-280048-b4dz1lnn	2019	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] ).
cord-287133-2mldz987	2014	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.
cord-296179-hobh6akq	2012	(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.
cord-297530-7zbvgvk8	2011	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.
cord-297777-lnr4w3ek	2020	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.
cord-298009-0iv9fdof	2020	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.
cord-299261-ew99nraq	2020	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.
cord-299828-fb84rtmx	2013	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.
cord-301856-71syce4n	2019	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.
cord-302056-wvf6cpib	2020	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] .
cord-303165-ikepr2p2	2014	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.
cord-303187-ny4qr2a2	2017	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.
cord-303700-rrwy3osd	2015	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.
cord-304399-7t2mu13s	2020	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.
cord-305472-w33k8pdu	2008	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.
cord-310648-oqiwnjpp	2020	
cord-312366-8qg1fn8f	2020	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.).
cord-312885-d4ku8dyz	2020	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.
cord-313869-3x2qf3yu	2019	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.
cord-314325-nquov2i0	2008	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.
cord-314488-x8mqxif9	2020	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.
cord-314992-vhjuus50	2020	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.
cord-315449-kt4m3247	2016	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] .
cord-322982-c4xhg567	2009	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.
cord-324435-qpufvt3o	2020	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).
cord-328865-ekgqdjlk	2020	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.
cord-329244-z28twpb1	2009	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.
cord-331608-ezf9r8l4	2020	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.
cord-331879-w7008uyy	2020	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].
cord-337703-637xgk6g	2020	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.
cord-341879-vubszdp2	2014	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.
cord-342181-x14iywtr	2020	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.
cord-344009-hm36pepp	2005	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.
cord-345811-f0yt2a32	2007	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.
cord-345843-yz0buegp	2010	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.
cord-346500-uwi3ezd7	2020	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) ).
cord-349581-o320ogmg	2020	
cord-351230-123i465d	2020	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.
cord-351594-8gp9mjen	2020	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 ).
cord-351880-iqr419fp	2020	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.
cord-352664-heoj8ji8	2015	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.
cord-353609-no3mbg5d	2011	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.