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    Integrating spatial analysis and questionnaire survey to better understand human-onager conflict in Southern Iran

    Study areaQatruiyeh National Park, established in 2008, is a core zone in the Bahram-e-Goor Protected Area (established in 1972) at the border of Fars and Kerman provinces in southern Iran (Fig. 1). It covers 310 km2 and is part of the Zagros Mountains. It is a semi-desert with temperate arid climate, vegetated mainly with Zygophyllum eurypterum and Artemisia sieberi20. There are seven villages in the vicinity of the protected area, where pastoralism is the main source of livelihood21.Figure 1Location of the study area. The software ArcGIS. Version 10.2. was used to generate figure. DEM map was downloaded from the WorldClim database (http://www.worldclim.org).Full size imageOne of the major threats for the Persian onager populations in this area is increasing construction of new roads and increasing road traffic. The Sirjan-Yazd (Hassan Abad-Meshkaan) asphalt road, which passes through the Bahram-e-Goor Protected Area, was recently converted into a highway and represents a substantial threat to Onagers (Fig. 1). This road has two lanes in each direction. The day-time speed limit on this road is 110 km/h and 90 km/h at night. Most vehicles on this road are heavy trucks, which pass at high speed (more than 90 km/h), with high traffic volumes at night. During winter, late autumn and summer of drought years, when fodder is scarce, onagers frequently cross the road to access gardens and agricultural fields, which causes high onager mortality due to vehicle collisions. In this research, we used spatial randomization of vehicle collisions and crossing locations to test the predictive ability of resistant kernel and factorial least-cost path predictions of movement18. We also conducted questionnaires with residents from local communities to determine the most important factors influencing human-onager conflicts in the Bahram-e-Goor Protected Area.Human-onager conflict assessmentQualitative data collectionWe administered a questionnaire through a personal interview to 200 randomly chosen farmers residing near onager populations in the Bahram-e-Goor Protected Area in Fars province. Data were collected through a questionnaire between May and August 2018 (Table S1). Ethical clearance was obtained from the DOE (under permit 32–239). All participants were given a printed descriptive summary of the research (if participants were illiterate, the document was read to them). Prior informed consent was obtained orally from all participants. In this research, we followed legal requirements of ethical issues.We calculated the sample size needed by using the family size in rural areas around Bahram-e-Goor Protected Area using the Daniel method22 (Table S1) as described below (Eq. 1):We randomly conducted 200 questionnaires in total.$$N=frac{ {Z}^{2 }P (1-P) }{{d}^{2}}$$
    (1)
    In this equation, Z is the Z statistic for a level of confidence, P is expected prevalence or proportion (if the expected prevalence is 20%, then P = 0.2), and d is precision (if the precision is 5%, then d = 0.05). In this research, we used d = 0.5 and p was selected according to family sizes in each district of rural areas22.All interviewees were adult males. We collected information on interviewees’ demographic and socioeconomic background (occupation, property, age, and income) as well as their knowledge and opinion on how to prevent onager crop-raiding.We used logistic regression to analyze the significance of sociological factors related to crop damage by onagers. Our dependent variable was “Have you had any of your crop raided by onager during the last year? (Binary response: 1 = Yes, 0 = No)”. Our independent variables included: (1) traditional solutions for reducing Persian onager damages (Response: 1 guarding dogs, 2: fencing around agricultural land, 3: use of traditional barriers (a plastic cuff with a bell on it), 4: scarecrow, 5: turn on the lights at night , 6: Bird-Scarer (Kalaghparan in Persian); (2) which of these solutions could be effective in reducing Persian onager damages (Responses included: 1: fencing around Persian onager habitat, 2: fencing around farmland, 3: give fodder and provide water for Persian onager, 4: buying fodder from local people by DoE, 4: capturing and relocating Persian onager); (3): do you agree with Persian onager hunting? (Binary response: 1 = Yes, 0= No); (4): what is the role of the Persian onager in the wild? (Response 1: distributing seed of plants, the rangelands are restored, 2: it attracts tourists in the region, 3: beauty of nature: God’s creature with a right to live (Intrinsic value), 4: none) (5): age (response: 1:  50 Years), (6): education (response: 1: Incomplete Elementary (lower than 5th grade of elementary), 2: Complete Elementary (5th grade of elementary), 3: Incomplete High school, 4: Associate Degree, 5: Bachelor of Science (BSc), 5: Master of Science (MSc) or Higher), (7) Experience of Persian onager observation in nature: Have you ever seen a Persian onager in the wild? (Response scale: 1 = Yes, frequently, 2 = Yes, several times, 3: Yes, a few times 4: No, never, 5: only seen the Asiatic wild ass carcass), (8) the presence of a Persian onager around your village damages your farms and gardens. How do you feel about this statement? (Response scale) 1: completely disagree, 2: Somewhat disagree, 3: I do not agree or disagree, 4: I agree somewhat, 5: completely agree.All statistical tests were conducted in IBM SPSS Statistics (V. 23.0). Independent variables in the logistic regression analysis were coded as showed in Table S1.Naïve Bayes classificationNaïve Bayes Classification uses a group of simple classifiers based on probabilities, which are applicable to the types of random independent variables in our study. This approach is a supervised machine learning algorithm based on the Bayes Theorem that is used to solve classification problems by following a probabilistic approach. We used the e1071 library23 in R version 3.5.324 for Naïve Bayes classification of onager crop-raiding under this scheme. We considered: Yes (local communities with experience of crop-raid damages), or No (local communities without experience of crop-raid damages during the last one year) as a dependent variable, as a function of the independent variables described in logistic regression section, except we also included farm land area (1:  5 ha) as an additional variable.We categorized data into two groups (testing and training) to determine whether the model performed correctly based on training data. Subsequently, 70% of the data were used to test and run the model along with training confirmation. The Naïve Bayes Classifier was trained to anticipate each attitude in the test data. We calculated the randomness of our results using the Mclust library25 in R version 3.5.324.Onager vehicle collisionsA 25-km section of the 99-km Hassan Abad-Meshkaan road (the area with the highest wildlife-vehicle collision reports) was monitored by motorcycling and walking daily from August to October 2017 (3 weeks). Every morning, we inspected for mammal roadkill within a 30-m buffer on each side of the road, and all carcasses of mammals were recorded using a handheld GPS (Garmin GPS Map 62S). To avoid double-counting, we removed the carcasses after recording. We also obtained collision location data during 2004–2018 from the DoE.The crossing data for onager were obtained from a variety of sources including opportunistic direct observation, environmental guard’s information, and monitoring by LED portable flashlight at night (summer and autumn seasons of 2017 and 2018).Habitat connectivity analysisHabitat suitability modelingA total of 103 presence points were obtained from DoE (2015) in the study area, including Bahram-e-Goor Protected Area, as well as nearby surroundings. To minimize spatial autocorrelation, a 1-km radius was used to eliminate points around each presence location using the SDM toolbox26. The remaining 90 presence points were used in the modeling.A habitat suitability map for onager was developed using MaxEnt software version 3.3.3k27 to create a resistance map for connectivity modeling28. We used 10,000 pseudo-absence points29. For the training data set, 75% of the presence points were randomly chosen to train and the remaining 25% were used to test the model30. We used the area under the ROC curve (AUC) to evaluate model performance. MaxEnt models were completed with 10 bootstrapped replicates.Environmental layers included in MaxEnt modeling included (1) elevation (digital elevation model [DEM]), (2) slope, (3) land cover, (4) distance from agricultural lands, (5) distance from roads and (6) distance from villages. All layers had a 30 m × 30 m resolution (Table 1).Table 1 Environmental variables used for habitat modeling of the Persian onager in the study area.Full size tableSlope was calculated from the DEM layer. Land cover for 27 vegetation classes in the study area was reclassified to 10 classes based on similarities between classes in the original landcover map and due to the importance of agricultural lands (5% of the study area) to onagers. Distance from agricultural lands, roads and villages were included as predictor variables, and were calculated with the Euclidean distance tool in the Spatial Analyst extension of ArcGIS 10.2. We checked for multi-collinearity among variables and correlation was  3 were used as a threshold to exclude variables32. VIF ranged from 1.2 to 1.8 for all variables. Therefore, all variables were retained for habitat modeling.Resistance surface for connectivity analysisTo estimate landscape resistance, we converted the habitat suitability maps to resistance maps using a negative exponential function (R = 1000(−1×HS)) where R represents the cost resistance value assigned to each pixel and HS represents the predicted habitat suitability derived from the suitability models described above33. We used 1000 as the base of our exponential decay function such that areas with  > 0.3 habitat suitability would have low-cost resistance. We rescaled the resistance values to a range between 1 and 100 by linear interpolation, such that minimum resistance (Rmin) was 1 when HS was 1, and maximum resistance (Rmax) was 100 when HS was 033.Connectivity corridor network simulationWe used the universal corridor network simulator (UNICOR)34 to predict movement core areas and corridors for Onagers. UNICOR’s key features include a driver-module framework, connectivity mapping with thresholding and buffering, and graph theory metrics. UNICOR produces two kinds of connectivity predictions: (1) resistant kernels16 and (2) factorial least-cost paths15. The factorial least-cost path analysis implanted in UNICOR simulator uses Dijkstra’s algorithm34 to solve the single-source shortest path problem from every mapped species occurrence location on a landscape to every other occurrence location34. The analysis produces predicted least-cost path routes from each source point to each destination point. The resistant kernel algorithm calculates the resistance cost weighted dispersal kernel around each source point up to a user-defined dispersal threshold, and then sums these, producing an incidence function of the rate of organism movement through every pixel in the landscape as a function of the number and density of source points, the dispersal ability of the species, and the resistance of the landscape.According to observation and reports of experts in the DoE, the maximum dispersal of threshold for movement of Onagers is about 100 km. We thus specified a dispersal threshold of 100,000 cost units for the resistant kernel analysis35. We calculated the factorial least-cost path network without dispersal the threshold35 to provide a broad-scale assessment of the regional pattern of potential linkage and to map corridors. The buffered least-cost paths were then combined through summation15 to produce maps of connectivity among all pairs of presence points.Evaluating congruence between crossing points and predicted connectivityWe used a spatial randomization testing procedure to evaluate congruence between the locations where onagers were observed crossing the road and resistant kernel values of predicted connectivity18. Spatial randomization testing of this kind is recommended in cases where there is spatial dependence among observations, and produces an unbiased estimate of the probability of the observed outcome given the data18.We compared the median value of predicted connectivity (resistant kernel) for the 104 actual onager crossing locations with the distribution of median values of 1 × 107 random samples of 104 locations along the highway within the study area. For each combination of resistance surface and connectivity modeling approach, we calculated the ranking of the median of observed values within the distribution of the medians of the 1 × 107 random samples. More

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    Major ocean currents may shape the microbiome of the topshell Phorcus sauciatus in the NE Atlantic Ocean

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    Tapping local knowledge to save a Papua New Guinea forest

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    It takes collaboration to get the full picture of a forest. Here, I’m teaming up with Sammy, a local senior-school student, to count and identify ants in a dense fragment of lowland rainforest. It’s November 2019, when I was a research technician with the New Guinea Binatang Research Centre in Madang, and we’re near the village of Boredoa on the southern coast of Papua New Guinea.I’m impressed by the locals’ knowledge of the forest and its inhabitants. It’s important to get more villagers involved in forest surveys and other conservation efforts so that they can work to protect them.Papua New Guinea — a country that makes up the eastern half of the island of New Guinea — is home to one of the world’s largest and most biodiverse rainforests, but mining and timber companies are taking a terrible toll. The areas beyond these trees have been heavily logged, and we’re checking to see how life in this remaining forest is faring, from the ants to the trees.I grew up in the northern city of Lae, a place very different from this forest. I have formal training in forestry and entomology, but, unlike Sammy and other villagers, I don’t have the experiences and insights that come from a lifetime of living on the land.Our ant survey was part of the National Forest Inventory, a project of the United Nations Programme on Reducing Emissions from Deforestation and Forest Degradation. There are many places still waiting to be studied.This forest is a hot, wet, challenging place to work. Villagers helped us to find relatively dry places to set up our tents. We had to wait for a break in the rain to set out our ant traps of tuna and fruit-flavoured drinks. In this particular sample, we identified six species, all native to the area. Introduced species such as fire ants and army ants have been taking over elsewhere in Papua New Guinea, but the local ants here have managed to hold on to their territory. For now.

    Nature 594, 466 (2021)
    doi: https://doi.org/10.1038/d41586-021-01587-7

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    Social-ecological filters drive the functional diversity of beetles in homegardens of campesinos and migrants in the southern Andes

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    Fungal culture and insect rearingThe fungus F. verticillioides was isolated from sugarcane plants and cultivated in potato dextrose (PD) medium (Difco, Sparks, NV, USA) at 25 °C with a 12 h photoperiod in climatic chambers. A. nidulans (A4 strain) was used as a control because it is not involved in red rot disease. It was cultivated in minimal medium (MM) [24] and maintained in climatic chambers at 37 °C in the dark.The D. saccharalis was provided by Prof. Dr. José R. P. Parra from the University of São Paulo, Piracicaba. The caterpillars were fed an artificial diet [25] and maintained in a room under controlled conditions (temperature 25 ± 4 °C, relative humidity 60 ± 10% and 14 h of light). Adults were kept in cages covered with white paper sheets, where the eggs were deposited, collected and sanitized with 1% copper sulfate solution daily. Newly hatched caterpillars were transferred to the artificial diet [25].Olfactory preference assayFive days before the experiment, a total of 105 fungal conidia of F. verticillioides or A. nidulans were inoculated in a Falcon tube (15 mL) containing 7 mL of MM. The negative control was sterile MM. Tubes containing fungus-colonized medium and control medium were placed at opposite ends of the Petri dish (15 cm diameter) bottom, lined with moistened filter paper. A group of ten third-instar D. saccharalis caterpillars was released in the central region of the arena. The choice was quantified in the end of the experiment when the caterpillar remained in the Falcon tube to feed. The medium in the tubes represents a food source, once the caterpillars find it, they remain in the chosen tube. The Petri dishes were closed, sealed and kept in a dark room for 5 h at 25 °C; then, the number of caterpillars inside each tube was recorded. The assay was also performed using third-instar Spodoptera frugiperda, to detect specific attractiveness, and with fifth-instar D. saccharalis, to find changes in insect behavior during different immature stages.To confirm insect attraction to fungal volatiles, VOCs collected from F. verticillioides were used to attract D. saccharalis. This assay was performed as described; however, only the control medium was added to the tubes. The hexane solvent was removed from the samples using nitrogen gas and the fungal VOCs were eluted in mineral oil. In addition to the control medium, each tube contained a piece of cotton loaded with either 50 µL of an aerated sample of F. verticillioides VOCs or solvent control (mineral oil). The dishes were placed in the dark for 7 h at 25 °C. All assays were repeated 10 times. Statistical analyses were performed using t-test (p  More

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    Cyclotide host-defense tailored for species and environments in violets from the Canary Islands

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    Role of meteorological factors in the transmission of SARS-CoV-2 in the United States

    Data collectionWe extracted hourly air temperature and SH from the North America Land Data Assimilation System project46, a near real-time dataset with a 0.125° × 0.125° grid resolution. We spatially and temporally averaged these data into daily county-level records. SH is the mass of water vapor in a unit mass of moist air (g kg−1). Daily downward UV radiation at the surface, with a wavelength of 0.20–0.44 µm, was extracted from the European Centre for Medium-Range Weather Forecasts ERA5 climate reanalysis47.Other characteristics of each county, including geographic location, population density, demographic structure of the population, socioeconomic factors, proportion of healthcare workers, intensive care unit (ICU) bed capacity, health risk factors, long-term and short-term air pollution, and climate zone were collected from multiple sources. Geographic coordinates, population density, median household income, percent of people older than 60 years, percent Black residents, percent Hispanic residents, percent owner-occupied housing, percent residents aged 25 years and over without a high school diploma, and percent healthcare practitioners or support staff were collected from the U.S. Census Bureau48. Total ICU beds in each county were derived from Kaiser Health News49. The prevalence of smoking and obesity among adults in each county was obtained from the Robert Wood Johnson Foundation’s 2020 County Health Rankings50. We extracted annual PM2.5 concentrations in the U.S. from 2014 to 2018 from the 0.01° × 0.01° grid resolution PM2.5 estimation provided by the Atmospheric Composition Analysis Group51, and calculated average PM2.5 levels during this 5-year period for each county to represent long-term PM2.5 exposure (Supplementary Fig. 5). Short-term air quality data during the study period, including daily mean PM2.5 and daily maximum 8-h O3, were obtained from the United States Environmental Protection Agency52. We categorized study counties into one of five climate zones based on the guide released by U.S. Department of Energy53 (Supplementary Fig. 6).The county-level COVID-19 case and death data were downloaded from the John Hopkins University Coronavirus Resource Center1. The U.S. county-to-county commuting data were available from the U.S. Census Bureau48. Daily numbers of inter-county visitors to points of interest (POI) were provided by SafeGraph54.Data ethicsSafeGraph utilizes data from mobile applications of which users optionally consent to provide their anonymous location data.Estimation of reproduction numberWe estimated the daily reproduction number (Rt) in all 3142 U.S. counties using a dynamic metapopulation model informed by human mobility data31,55. Rt is the mean number of new infections caused by a single infected person, given the public health measures in place, in a population in which everyone is assumed to be susceptible. In the metapopulation model, two types of movement were considered: daily work commuting and random movement. During the daytime, some commuters travel to a county other than their county of residence, where they work and mix with the populations of that county; after work, they return home and mix with individuals in their home, residential county. Apart from regular commuting, a fraction of the population in each county, assumed to be proportional to the number of inter-county commuters, travels for purposes other than work. As the population present in each county is different during daytime and night-time, we modelled the transmission dynamics of COVID-19 separately for these two time periods, each depicted by a set of ordinary differential equations (Supplementary Notes).To account for case underreporting, we explicitly simulated reported and unreported infections, for which separate transmission rates were defined. Recent studies from several countries indicate that asymptomatic cases of COVID-19, which are typically unreported, are less contagious than symptomatic cases56,57,58,59. Studies on the early transmission of SARS-CoV-2 in China18 and the U.S.60 also showed that undocumented infections are less transmissible than documented infections.In order to reflect the spatiotemporal variation of disease transmission rate and reporting, we allowed transmission rates and ascertainment rates to vary across counties and to change over time. The transmission model simulated daily confirmed cases and deaths for each county. To map infections to deaths, we used an age-stratified infection fatality rate (IFR)61 and computed the weekly IFR for each county as a weighted average using state-level age structure of confirmed cases reported by the U.S. Centers for Disease Control and Prevention. We further adjusted for reporting lags using an observational delay model informed by a U.S. line-list COVID-19 data record62.For the period prior to March 15, 2020, we used commuting data from the U.S. census survey to prescribe the inter-county movement in the transmission model48. Starting March 15, the census survey data are no longer representative due to changes in mobility behavior following the implementation of non-pharmaceutical interventions. We, therefore, used estimates of the reduction of inter-county visitors to POI (e.g., restaurants, stores, etc.) from SafeGraph54 to account for the change in inter-county movement on a county-by-county basis. Because there is no direct relationship between population-level mobility patterns and COVID-19 transmission rates63, we did not model local transmission rate as a function of inter-county mobility. Instead, the SafeGraph data were only used to inform the change of population mixing across counties.To infer key epidemiological parameters, we fitted the transmission model to county-level daily cases and deaths reported from March 15, 2020 to December 31, 2020. The estimated reproduction number was computed as follows:$${R}_{t}=beta Dleft[alpha +left(1-alpha right)mu right],$$
    (1)
    where β is the county-specific transmission rate, μ is the relative transmissibility of unreported infections, α is the county-specific ascertainment rate, and D is the average duration of infectiousness. Note (beta) and (alpha) were defined for each county separately and were allowed to vary over time. Unlike previous studies using effective reproduction number$${R}_{e}=beta Dleft[alpha +left(1-alpha right)mu right]s,$$
    (2)
    where s is the estimated local population susceptibility, we used reproduction number Rt to exclude the influence of population susceptibility on disease transmission rate.D, (mu), (Z) (the average latency period from infection to contagiousness), and a multiplicative factor adjusting random movement ((theta)) were randomly drawn from the posterior distributions inferred from case data through March 13, 202060: (D=3.56) (3.21–3.83), (mu =0.64) (0.56–0.70), (Z=3.59) (95% CI: 3.28–3.99), and (theta =0.15) (0.12–0.17). (Z) and (theta) are used in ordinary differential equations used to model transmission dynamics (Supplementary Notes).The daily transmission rate (beta) and ascertainment rate (alpha) were estimated sequentially for each county using the ensemble adjustment Kalman filter (EAKF)64. Specifically, parameters ({beta }_{i}) and ({alpha }_{i}) for county (i) were updated each day using incidence and death data. We used the estimates on day (t-1) as the prior parameters on day (t), and then updated the priors to posteriors using the EAKF and observations. The posteriors are the estimated parameter values on day (t). To ensure a smooth parameter estimation, we imposed a (pm 30 %) limit on the daily change of parameters ({beta }_{i}) and ({alpha }_{i}). Other smoothing constraints were tested and the results were similar. To avoid possible inaccurate estimation for counties with few cases, we inferred Rt in the 2669 U.S. counties with at least 400 cumulative confirmed cases as of December 31, 2020 (Supplementary Fig. 7).Statistical analysisAll statistical analyses were conducted with R software (version 3.6.1) using the mgcv and dlnm packages.Association between meteorological factors and R
    t
    Given the potential non-linear and temporally delayed effects of meteorological factors, a distributed lag non-linear model65 combined with generalized additive mixed models66 was applied to estimate the associations of daily mean temperature, daily mean SH, and daily mean UV radiation with SARS-CoV-2 Rt. To quantify the total contribution, independent effects, and relative importance of meteorological factors (i.e., temperature, SH, and UV radiation), we included all three variables in the same model. To reduce collinearity, we used cross-basis terms rather than the raw variables (Supplementary Tables 5–6). The full model can be expressed as:$$log (E({{{R}}}_{i,j,t}))= alpha +te(s({{rm{latitude}}}_{i}{,{rm{longitude}}}_{i},{rm{k}}=200),s({{rm{time}}}_{t},{rm{k}}=30))+{rm{cb}}.{rm{temperature}}+{rm{cb}}.{rm{SH}}+ {rm{cb}}.{rm{UV}}\ +{beta }_{1}({rm{population}},{rm{density}}_{i})+{beta }_{2}({rm{percent}},{rm{Black}},{rm{residents}}_{i})+{beta }_{3}({rm{percent}},{rm{Hispanic}},{rm{residents}}_{i})\ +{beta }_{4}({rm{percent}},{rm{people}},{rm{older}},{rm{than}},60,{rm{years}}_{i})+{beta }_{5}({rm{median}},{rm{household}},{rm{income}}_{i})\ +{beta }_{6}({rm{percent}},{rm{owner}}-{rm{occupied}},{rm{housing}}_{i})\ +{beta }_{7}({rm{percent}},{rm{residents}},{rm{older}},{rm{than}},25,{rm{years}},{rm{without}},{rm{a}},{rm{high}},{rm{school}},{rm{diploma}}_{i})\ +{beta }_{8}({rm{number}},{rm{of}},{rm{ICU}},{rm{beds}},{rm{per}},10,000,{rm{people}}_{i})+{beta }_{9}({rm{percent}},{rm{healthcare}},{rm{workers}}_{i})\ quad , {beta }_{10}({rm{day}},{rm{when}},100,{rm{cumulative}},{rm{cases}},{rm{per}},100,000,{rm{people}},{rm{was}},{rm{reached}}_{i})+{re}({rm{county}}_{i})+{re}({rm{state}}_{j})$$
    (3)
    where E(Ri,j,t) refers to the expected Rt in county i, state j, on day t, and α is the intercept. Given the distribution of Rt in our data close to a lognormal distribution (Supplementary Fig. 8), we used log-transformed Rt as the outcome variable, and the Gaussian family in the model. A thin plate spline with a maximum of 200 knots was used to control the coordinates of the centroid of each county; the time trend was controlled by a flexible natural cubic spline over the range of study dates with a maximum of 30 knots; due to the unique pattern of the non-linear time trend of Rt in each county (Supplementary Fig. 4), we constructed tensor product smooths (te) of the splines of geographical coordinates and time, to better control for the temporal and spatial variations (Supplementary Fig. 3).Cb.temperature, cb.SH, and cb.UV are cross-basis terms for the mean air temperature, mean SH and mean UV radiation, respectively. We modeled exposure-response associations (meteorological factors vs. percent change in Rt) using a natural cubic spline with 3 degrees of freedom (df) and modeled the lag-response association using a natural cubic spline with an intercept and 3 df with a maximum lag of 13 days. We adjusted for county-level characteristics, including population density, percent Black residents, percent Hispanic residents, percent people older than 60 years, median household income, percent owner-occupied housing, percent residents older than 25 years without a high school diploma, number of ICU beds per 10,000 people, and percent healthcare workers, given their potential relationship with SARS-CoV-2 transmission67,68,69,70. Day when 100 cumulative cases per 100,000 people was reached in each county was used to approximate local epidemic stage45 (Supplementary Fig. 9). The random effects of state and county were modeled by parametric terms penalized by a ridge penalty (re), to further control for unmeasured state- and county-level confounding. Residual plots were used to diagnose the model (Supplementary Fig. 10). In additional analyses, we included air temperature, SH, and UV radiation in separate models (Supplementary Fig. 2).Based on the estimated exposure-response curves, between the 1st and the 99th percentiles of the distribution of air temperature, SH, and UV radiation, we determined the value of exposure associated with the lowest relative risk of Rt to be the optimum temperature, the optimum SH, or the optimum UV radiation, respectively. The natural cubic spline functions of the exposure-response relationship were then re-centered with the optimum values of meteorological factors as reference values. We report the cumulative relative risk of Rt associated with daily temperature, SH, or UV radiation exposure in the previous two weeks (0– 13 lag days) as the percent changes in Rt when comparing the daily exposure with the optimum reference values (i.e., the cumulative relative risk of Rt equals one and the percent change in Rt equals zero when the temperature, SH, or UV radiation exposure is at its optimum value).Attribution of R
    t to meteorological factorsWe used the optimum value of temperature, SH, or UV radiation as the reference value for calculating the fraction of Rt attributable to each meteorological factor; i.e., the attributable fraction (AF). For these calculations, we assumed that the associations of meteorological factors with Rt were consistent across the counties. For each day in each county, based on the cumulative lagged effect (cumulative relative risk) corresponding to the temperature, SH, or UV radiation of that day, we calculated the attributable Rt in the current and next 13 days, using a previously established method71. Specifically, in a given county, the Rt attributable to a meteorological factor (xt) for a given day t was defined as the attributable absolute excess of Rt (AEx,t, the excess reproduction number on day t attributable to the deviation of temperature or SH from the optimum value) and the attributable fraction of Rt (AFx,, the fraction of Rt attributable to the deviation of the meteorological factor from its optimum value), each accumulated over the current and next 13 days. The formulas can be expressed as:$${{AF}}_{x,t}=1-{rm{exp }}left(-mathop{sum }limits_{l=0}^{13}{beta }_{{x}_{t},l}right)$$
    (4)
    $${{AE}}_{x,t}={{AF}}_{x,t}times mathop{sum }limits_{l=0}^{13}frac{{n}_{t+1}}{13+1},$$
    (5)
    where nt is the Rt on day t, and ({sum }_{l=0}^{13}{beta }_{{x}_{t},l}) is the overall cumulative log-relative risk for exposure xt on day t obtained by the exposure-response curves re-centered on the optimum values. Then, the total absolute excess of Rt attributable to temperature, SH, or UV radiation in each county was calculated by summing the absolute excesses of all days during the study period, and the attributable fraction was calculated by dividing the total absolute excess of Rt for the county by the sum of the Rt of all days during the study period for the county. The attributable fraction for the 2669 counties combined was calculated in a similar manner at the national level. We derived the 95% eCI for the attributable absolute excess and attributable fraction by 1000 Monte Carlo simulations71. The total fraction of Rt attributable to meteorological factors was the sum of the attributable fraction for temperature, SH, and UV radiation. We also calculated the attributable fractions by month in the study period.Sensitivity analysesWe conducted several sensitivity analyses to test the robustness of our results: (a) the lag dimension was redefined using a natural cubic spline and three equally placed internal knots in the log scale; (b) an alternative four df was used in the cross-basis term for meteorological factors in the exposure-response function; (c) the maximum number of knots was reduced to 25 in the flexible natural cubic spline to control time trend in the tensor product smooths; (d) all demographic and socioeconomic variables were excluded from the model; (e) adjustment for the prevalence of smoking and obesity among adults was included in the model; (f) adjustment for climate zone was included in the model; (g) additional adjustment was made for the average PM2.5 concentration in each county during 2014–201845; (h) additional adjustment was made for daily mean PM2.5, and daily maximum 8-h O3. For daily covariates with available data in only some of the counties or study period, the results of sensitivity analyses were compared to the main model re-run on the same partial dataset.Reporting summaryFurther information on research design is available in the Nature Research Reporting Summary linked to this article. More

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    Community context matters for bacteria-phage ecology and evolution

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