Estimating encounter-habitat relationships with scale-integrated resource selection functions.

Encounters between animals occur when animals are close in space and time. Encounters are important in many ecological processes including sociality, predation and disease transmission. Despite this, there is little theory regarding the spatial distribution of encounters and no formal framework to relate environmental characteristics to encounters. The probability of encounter could be estimated with resource selection functions (RSFs) by comparing locations where encounters occurred to available locations where they may have occurred, but this estimate is complicated by the hierarchical nature of habitat selection. We developed a method to relate resources to the relative probability of encounter based on a scale-integrated habitat selection framework. This framework integrates habitat selection at multiple scales to obtain an appropriate estimate of availability for encounters. Using this approach, we related encounter probabilities to landscape resources. The RSFs describe habitat associations at four scales, home ranges within the study area, areas of overlap within home ranges, locations within areas of overlap, and encounters compared to other locations, which can be combined into a single scale-integrated RSF. We apply this method to intraspecific encounter data from two species: white-tailed deer (Odocoileus virginianus) and elk (Cervus elaphus) and interspecific encounter data from a two-species system of caribou (Rangifer tarandus) and coyote (Canis latrans). Our method produced scale-integrated RSFs that represented the relative probability of encounter. The predicted spatial distribution of encounters obtained based on this scale-integrated approach produced distributions that more accurately predicted novel encounters than a naïve approach or any individual scale alone. Our results highlight the importance of accounting for the conditional nature of habitat selection in estimating the habitat associations of animal encounters as opposed to 'naïve' comparisons of encounter locations with general availability. This method has direct relevance for testing hypotheses about the relationship between habitat and social or predator-prey behaviour and generating spatial predictions of encounters. Such spatial predictions may be vital for understanding the distribution of encounters driving disease transmission, predation rates and other population and community-level processes.

SNAPSHOT USA 2021: A third coordinated national camera trap survey of the United States.

SNAPSHOT USA is a multicontributor, long-term camera trap survey designed to survey mammals across the United States. Participants are recruited through community networks and directly through a website application (https://www.snapshot-usa.org/). The growing Snapshot dataset is useful, for example, for tracking wildlife population responses to land use, land cover, and climate changes across spatial and temporal scales. Here we present the SNAPSHOT USA 2021 dataset, the third national camera trap survey across the US. Data were collected across 109 camera trap arrays and included 1711 camera sites. The total effort equaled 71,519 camera trap nights and resulted in 172,507 sequences of animal observations. Sampling effort varied among camera trap arrays, with a minimum of 126 camera trap nights, a maximum of 3355 nights, a median 546 nights, and a mean 656 ± 431 nights. This third dataset comprises 51 camera trap arrays that were surveyed during 2019, 2020, and 2021, along with 71 camera trap arrays that were surveyed in 2020 and 2021. All raw data and accompanying metadata are stored on Wildlife Insights (https://www.wildlifeinsights.org/), and are publicly available upon acceptance of the data papers. SNAPSHOT USA aims to sample multiple ecoregions in the United States with adequate representation of each ecoregion according to its relative size. Currently, the relative density of camera trap arrays varies by an order of magnitude for the various ecoregions (0.22-5.9 arrays per 100,000 km2), emphasizing the need to increase sampling effort by further recruiting and retaining contributors. There are no copyright restrictions on these data. We request that authors cite this paper when using these data, or a subset of these data, for publication. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the US Government.

Invasion by Cedrela odorata threatens long distance migration of Galapagos tortoises.

Invasive alien species are among the most pervasive threats to biodiversity. Invasive species can cause catastrophic reductions in populations of native and endemic species and the collapse of ecosystem function. A second major global conservation concern is the extirpation of large-bodied mobile animals, including long-distance migrants, which often have keystone ecological roles over extensive spatial extents. Here, we report on a potentially catastrophic synergy between these phenomena that threatens the endemic biota of the Galapagos Archipelago. We used GPS telemetry to track 140 migratory journeys by 25 Western Santa Cruz Island Galapagos tortoises. We plotted the spatial interaction between tortoise migrations and recently established non-native forest dominated by the invasive tree Cedrela odorata (Cedrela forest). We qualified (a) the proportion of migratory journeys that traversed Cedrela forest, and (b) the probability that this observed pattern occurred by chance. Tortoise migrations were overwhelmingly restricted to small corridors between Cedrela forest blocks, indicating clear avoidance of those blocks. Just eight of 140 migrations traversed extensive Cedrela stands. Tortoises avoid Cedrela forest during their migrations. Further expansion of Cedrela forest threatens long-distance migration and population viability of critically endangered Galapagos tortoises. Applied research to determine effective management solutions to mitigate Cedrela invasion is a high priority.

Assessing the Efficiency of Local Rabies Vaccination Strategies for Raccoons (Procyon lotor) in an Urban Setting.

Raccoon rabies virus (RRV) has been managed using multiple vaccination strategies, including oral rabies vaccination and trap-vaccinate-release (TVR). Identifying a rabies vaccination strategy for an area is a nontrivial task. Vaccination strategies differ in the amount of effort and monetary costs required to achieve a particular level of vaccine seroprevalence (efficiency). Simulating host movement relative to different vaccination strategies in silico can provide a useful tool for exploring the efficiency of different vaccination strategies. We refined a previously developed individual-based model of raccoon movement to evaluate vaccination strategies for urban Hamilton, Ontario, Canada. We combined different oral rabies vaccination baiting (hand baiting, helicopter, and bait stations) with TVR strategies and used GPS data to parameterize and simulate raccoon movement in Hamilton. We developed a total of 560 vaccination strategies, in consultation with the Ontario Ministry of Natural Resources and Forestry, for RRV control in Hamilton. We documented the monetary costs of each vaccination strategy and estimated the population seroprevalence. Intervention costs and seroprevalence estimates were used to calculate the efficiency of each strategy to meet targets set for the purpose of RRV control. Estimated seroprevalence across different strategies varied widely, ranging from less than 5% to more than 70%. Increasing bait densities (distributed using by hand or helicopter) led to negligible increase in seroprevalence. Helicopter baiting was the most efficient and TVR was the least efficient, but helicopter-based strategies led to lower levels of seroprevalence (6-12%) than did TVR-based strategies (17-70%). Our simulations indicated that a mixed strategy including at least some TVR may be the most efficient strategy for a local urban RRV control program when seroprevalence levels >30% may be required. Our simulations provide information regarding the efficiency of different vaccination strategies for raccoon populations, to guide local RRV control in urban settings.

COVID-19 Infection despite Previous Vaccination in Cancer Patients and Healthcare Workers: Results from a French Prospective Multicenter Cohort (PAPESCO-19).

In a multicenter prospective cohort of cancer patients (CP; n = 840) and healthcare workers (HCWs; n = 935) vaccinated against COVID-19, we noticed the following: i/after vaccination, 4.4% of HCWs and 5.8% of CP were infected; ii/no characteristic was associated with post-vaccine COVID-19 infections among HCWs; iii/CP who developed infections were younger, more frequently women (NS), more frequently had gastrointestinal, gynecological, or breast cancer and a localized cancer stage; iv/CP vaccinated while receiving chemotherapy or targeted therapy had (NS) more breakthrough infections after vaccination than those vaccinated after these treatments; the opposite was noted with radiotherapy, immunotherapy, or hormonotherapy; v/most COVID-19 infections occurred either during the Alpha wave (11/41 HCW, 20/49 CP), early after the first vaccination campaign started, or during the Omicron wave (21/41 HCW, 20/49 CP), more than 3 months after the second dose; vi/risk of infection was not associated with values of antibody titers; vii/the outcome of these COVID-19 infections after vaccination was not severe in all cases. To conclude, around 5% of our CPs or HCWs developed a COVID-19 infection despite previous vaccination. The outcome of these infections was not severe.

Behavioral responses of terrestrial mammals to COVID-19 lockdowns.

COVID-19 lockdowns in early 2020 reduced human mobility, providing an opportunity to disentangle its effects on animals from those of landscape modifications. Using GPS data, we compared movements and road avoidance of 2300 terrestrial mammals (43 species) during the lockdowns to the same period in 2019. Individual responses were variable with no change in average movements or road avoidance behavior, likely due to variable lockdown conditions. However, under strict lockdowns 10-day 95th percentile displacements increased by 73%, suggesting increased landscape permeability. Animals' 1-hour 95th percentile displacements declined by 12% and animals were 36% closer to roads in areas of high human footprint, indicating reduced avoidance during lockdowns. Overall, lockdowns rapidly altered some spatial behaviors, highlighting variable but substantial impacts of human mobility on wildlife worldwide.

Rhinodrilus priscilae and Andiorrhinus (Amazonidrilus) caxiuana (Crassiclitellata, Rcrilidae) two new species from Caxiuanã National Forest.

The amazon forest is the habitat of a high species diversity of invertebrates and unfortunately the real richness had been underestimated. Earthworms' inventories had been poor because difficult to describe new species. This study adds new records to eastern amazon of two new species belong Rhinodrilus and Andiorrhinus genera. R. priscilae n. sp. is another rare specimen of the genre having two pair of prostatoid glands. A. (Amazonidrilus) caxiuana differ of other species in size, the intestinal origin is in XXVIII and also has only one glandular mass associated to spermatheca.

An annotated checklist and distribution of earthworms from Venezuela (Megadrili: Crassiclitellata).

An earthworm checklist has produced 78 nominal taxa (species/subspecies) of earthworm reported to date in Venezuela. The list of nominal taxa was obtained through literature review and the distribution maps were plotted by ecoregion. The 78 species/subspecies are divided into 24 genera and 6 families. Native earthworm species were more widely distributed than peregrine and exotic and are more associated with the conserved areas. Exotic species had been collected mainly in the north of the country in areas with at least some disturbance history. The peregrine species P. corethrurus is also widely distributed but with a preference for disturbed areas or related to its native natural grassland condition near the Guayana's shield. This is the first accurate assessment of Venezuela's earthworm species and subspecies in the last 14 years.

Additions to earthworms (Annelida, Crassiclitellata) from Aragua and Miranda states, Venezuela.

Two new species of the earthworm genus Pontoscolex found in San Casimiro County, northern Venezuela are described. Because of some morphological variability, and to improve the previous description, we redescribe Onychochaeta windlei and Rhinodrilus fuenzalidae collected at La Cortada settlement, Miranda state. Pontoscolex (Mesoscolex) juanae sp. n. and Pontoscolex (Nulloscolex) hugoi subgen. n., sp. n have three pairs of tiny calciferous glands in 7th to 9th segments, with a simple tubular structure similar to that of the genus Onychochaeta; however, testes and funnels are enclosed in sacs in the 11th segment similar to the Pontoscolex. We also report the occurrences of Pontoscolex (Pontoscolex) corethrurus Müller, 1857, Metaphire houlleti (Perrier, 1872), Perionyx excavatus Perrier, 1872, Dichogaster bolaui (Michaelsen, 1891), and Eisenia fetida (Savigny, 1826).

Early non-invasive ventilation and high-flow nasal oxygen therapy for preventing endotracheal intubation in hypoxemic blunt chest trauma patients: the OptiTHO randomized trial.

BACKGROUND: The benefit-risk ratio of prophylactic non-invasive ventilation (NIV) and high-flow nasal oxygen therapy (HFNC-O2) during the early stage of blunt chest trauma remains controversial because of limited data. The main objective of this study was to compare the rate of endotracheal intubation between two NIV strategies in high-risk blunt chest trauma patients. METHODS: The OptiTHO trial was a randomized, open-label, multicenter trial over a two-year period. Every adult patients admitted in intensive care unit within 48 h after a high-risk blunt chest trauma (Thoracic Trauma Severity Score ≥ 8), an estimated PaO2/FiO2 ratio < 300 and no evidence of acute respiratory failure were eligible for study enrollment (Clinical Trial Registration: NCT03943914). The primary objective was to compare the rate of endotracheal intubation for delayed respiratory failure between two NIV strategies: i) a prompt association of HFNC-O2 and "early" NIV in every patient for at least 48 h with vs. ii) the standard of care associating COT and "late" NIV, indicated in patients with respiratory deterioration and/or PaO2/FiO2 ratio ≤ 200 mmHg. Secondary outcomes were the occurrence of chest trauma-related complications (pulmonary infection, delayed hemothorax or moderate-to-severe ARDS). RESULTS: Study enrollment was stopped for futility after a 2-year study period and randomization of 141 patients. Overall, 11 patients (7.8%) required endotracheal intubation for delayed respiratory failure. The rate of endotracheal intubation was not significantly lower in patients treated with the experimental strategy (7% [5/71]) when compared to the control group (8.6% [6/70]), with an adjusted OR = 0.72 (95%IC: 0.20-2.43), p = 0.60. The occurrence of pulmonary infection, delayed hemothorax or delayed ARDS was not significantly lower in patients treated by the experimental strategy (adjusted OR = 1.99 [95%IC: 0.73-5.89], p = 0.18, 0.85 [95%IC: 0.33-2.20], p = 0.74 and 2.14 [95%IC: 0.36-20.77], p = 0.41, respectively). CONCLUSION: A prompt association of HFNC-O2 with preventive NIV did not reduce the rate of endotracheal intubation or secondary respiratory complications when compared to COT and late NIV in high-risk blunt chest trauma patients with non-severe hypoxemia and no sign of acute respiratory failure. CLINICAL TRIAL REGISTRATION: NCT03943914, Registered 7 May 2019.

Microbiome resilience of Amazonian forests: Agroforest divergence to bacteria and secondary forest succession convergence to fungi.

An alarming and increasing deforestation rate threatens Amazon tropical ecosystems and subsequent degradation due to frequent fires. Agroforestry systems (AFS) may offer a sustainable alternative, reportedly mimicking the plant-soil interactions of the natural mature forest (MF). However, the role of microbial community in tropical AFS remains largely unknown. This knowledge is crucial for evaluating the sustainability of AFS and practices given the key role of microbes in the aboveground-belowground interactions. The current study, by comparing different AFS and successions of secondary and MFs, showed that AFS fostered distinct groups of bacterial community, diverging from the MFs, likely a result of management practices while secondary forests converged to the same soil microbiome found in the MF, by favoring the same groups of fungi. Model simulations reveal that AFS would require profound changes in aboveground biomass and in soil factors to reach the same microbiome found in MFs. In summary, AFS practices did not result in ecosystems mimicking natural forest plant-soil interactions but rather reshaped the ecosystem to a completely different relation between aboveground biomass, soil abiotic properties, and the soil microbiome.

COVID-19 Vaccination Campaign in Cancer Patients and Healthcare Workers-Results from a French Prospective Multicenter Cohort (PAPESCO-19).

In this prospective, real-life cohort study, we followed 523 cancer patients (CP) and 579 healthcare workers (HCW) from two cancer centers to evaluate the biological and clinical results of the COVID-19 vaccination campaign. Seventy percent of the CP and 90% of the HCW received an mRNA vaccine or the AZD1222 vaccine. Seropositivity was high after the first vaccine among HCW and poor among CP. The second dose resulted in almost 100% seropositivity in both cohorts. Antibody response was higher after the second injection than the first in both populations. Despite at least two doses, 8 CP (1.5%) and 14 HCW (2.4%) were infected, corresponding either to a weak level of antibody or a new strain of virus (particularly the Omicron variant of concern). Sixteen CP and three HCW were hospitalized but none of them died from COVID-19. To conclude, this study showed that two doses of COVID-19 vaccines were crucially necessary to attain sufficient seropositivity. However, the post-vaccination antibody level declines in individuals from the two cohorts and could not totally prevent new SARS-CoV-2 infections.

Defining an epidemiological landscape that connects movement ecology to pathogen transmission and pace-of-life.

Pathogen transmission depends on host density, mobility and contact. These components emerge from host and pathogen movements that themselves arise through interactions with the surrounding environment. The environment, the emergent host and pathogen movements, and the subsequent patterns of density, mobility and contact form an 'epidemiological landscape' connecting the environment to specific locations where transmissions occur. Conventionally, the epidemiological landscape has been described in terms of the geographical coordinates where hosts or pathogens are located. We advocate for an alternative approach that relates those locations to attributes of the local environment. Environmental descriptions can strengthen epidemiological forecasts by allowing for predictions even when local geographical data are not available. Environmental predictions are more accessible than ever thanks to new tools from movement ecology, and we introduce a 'movement-pathogen pace of life' heuristic to help identify aspects of movement that have the most influence on spatial epidemiology. By linking pathogen transmission directly to the environment, the epidemiological landscape offers an efficient path for using environmental information to inform models describing when and where transmission will occur.

Simple metrics to characterize inter-individual and temporal variation in habitat selection behaviour.

Individual variation in habitat selection and movement behaviour is receiving growing attention, but primarily with respect to characterizing behaviours in different contexts as opposed to decomposing structure in behaviour within populations. This focus may be limiting advances in understanding the diversity of individual behaviour and its influence on population organization. We propose a framework for characterizing variation in space-use behaviour with the aim of advancing interpretation of its form and function. Using outputs from integrated step-selection analyses of 20 years of telemetry data from African elephants Loxodonta Africana, we developed four metrics characterizing differentiation in resource selection behaviour within a population (specialization [magnitude of the response independent of direction], heterogeneity [inter-individual variation], consistency [temporal shift in response] and reversal [frequency of directional changes in the response]). We contrasted insight from the developed metrics relative to the mean population response using an example focused on two covariates. We then expanded this contrast by evaluating if the metrics identify structurally important information on seasonal shifts in resource selection behaviours in addition to that provided by mean selection coefficients through principal component analyses (PCAs) and a random forest classification. The simplified example highlighted that for some covariates focusing on the population average failed to capture complex individual variation in behaviours. The PCAs revealed that the developed metrics provided additional information in explaining the patterns in elephant selection beyond that offered by population average covariate values. For elephants, specialization and heterogeneity were informative, with specialization often being a better descriptor of differences in seasonal resource selection behaviour than population average responses. Summarizing these metrics spatially and temporally, we illustrate how these metrics can provide insights on overlooked aspects of animal behaviour. Our work offers a new approach in how we conceptualize variation in space-use behaviour (i.e. habitat selection and movement) by providing ways of encapsulating variation that enables diagnoses of the drivers of individual-level variability in a population. The developed metrics explicitly distil how variation in a behaviour is structured among individuals and over time which could facilitate comparative work across time, populations or strata within populations.

Accounting for animal movement improves vaccination strategies against wildlife disease in heterogeneous landscapes.

Oral baiting is used to deliver vaccines to wildlife to prevent, control, and eliminate infectious diseases. A central challenge is how to spatially distribute baits to maximize encounters by target animal populations, particularly in urban and suburban areas where wildlife such as raccoons (Procyon lotor) are abundant and baits are delivered along roads. Methods from movement ecology that quantify movement and habitat selection could help to optimize baiting strategies by more effectively targeting wildlife populations across space. We developed a spatially explicit, individual-based model of raccoon movement and oral rabies vaccine seroconversion to examine whether and when baiting strategies that match raccoon movement patterns perform better than currently used baiting strategies in an oral rabies vaccination zone in greater Burlington, Vermont, USA. Habitat selection patterns estimated from locally radio-collared raccoons were used to parameterize movement simulations. We then used our simulations to estimate raccoon population rabies seroprevalence under currently used baiting strategies (actual baiting) relative to habitat selection-based baiting strategies (habitat baiting). We conducted simulations on the Burlington landscape and artificial landscapes that varied in heterogeneity relative to Burlington in the proportion and patch size of preferred habitats. We found that the benefits of habitat baiting strongly depended on the magnitude and variability of raccoon habitat selection and the degree of landscape heterogeneity within the baiting area. Habitat baiting improved seroprevalence over actual baiting for raccoons characterized as habitat specialists but not for raccoons that displayed weak habitat selection similar to radiocollared individuals, except when baits were delivered off roads where preferred habitat coverage and complexity was more pronounced. In contrast, in artificial landscapes with either more strongly juxtaposed favored habitats and/or higher proportions of favored habitats, habitat baiting performed better than actual baiting, even when raccoons displayed weak habitat preferences and where baiting was constrained to roads. Our results suggest that habitat selection-based baiting could increase raccoon population seroprevalence in urban-suburban areas, where practical, given the heterogeneity and availability of preferred habitat types in those areas. Our novel simulation approach provides a flexible framework to test alternative baiting strategies in multiclass landscapes to optimize bait-distribution strategies.

Long-term outcome following blunt cerebrovascular injuries: occurrence of ischemic complications, treatment, and outcome.

PURPOSE: Blunt cerebrovascular injuries (BCVI) are a rare but serious complication after trauma. Among patients with BCVI, neurological status is altered in 30% of cases and the prognosis seems to be associated with ischemic complications. The aim of this study was to assess the long-term outcome of BCVI-associated ischemic events. METHODS: This retrospective cohort study (2011-2017) included all patients admitted for severe trauma with identified BCVI in two level-1 trauma centers. Patients were considered to have a poor neurological outcome with a GOS-E between 2 and 5 and a good neurological outcome with GOS-E between 6 and 8. A multivariate logistic regression identified risk factors for poor neurological outcome at 1 year. RESULTS: Of the 6,294 patients admitted in both trauma centers between 2011 and 2017, 81 patients presenting BCVI were identified (incidence of 1.3%). The median age was 35 years (24-44) with a median Injury Severity Score of 28 (17-41). 29 patients (50%) had a good neurological prognosis, while 25 patients (43%) had a poor neurological prognosis at 1 year. Ischemic stroke occurred in 11 patients (13.6%) within a median time of 2 days (2-2.5). No ischemic stroke occurred in the first year after ICU discharge in both groups. In our study, good prognosis at 1 year was not associated with ischemic complications [3 (10) vs 3 (12) p = 1]. CONCLUSION: Ischemic complications after BCVI are rare, occur within the first week and do not seem to impact independently the 1-year neurological prognosis.

Fast recovery of soil macrofauna in regenerating forests of the Amazon.

The emergence of secondary forests in deforested tropical regions represents an opportunity to mitigate biodiversity loss and climate change, but there is still debate on how fast and to which level these forests can recover biodiversity. Recent studies have shown that the recovery of plant and vertebrate species richness is relatively fast, but the pace of recovery for other groups remains unclear. Soil macroinvertebrates play critical roles on litter decomposition and seed dispersal, therefore the pace of their recovery has consequences for the entire forest ecosystem. We investigated how fast broad taxonomic groups of soil macrofauna recover in the first 30 years of forest regeneration using forests older than 50 years as reference. We surveyed the number, diversity and abundance of 19 broad taxonomic groups of soil macrofauna in 85 sites located in Brazilian Amazon, covering forests of different ages and clearing frequencies. Forest age and clearing frequency were obtained accurately from Landsat images in forests up to 30 years old. We used regression analysis to determine (a) the effects forest age and clearing frequency on macrofauna groups in secondary forests up to 30 years old; and (b) the changes in macrofauna groups between young forests (up to 10 years old), median age forests (between 10 and 30 years old) and forests older than 50 years. We found that the number and diversity of macrofauna groups recover rapidly in the first 10 years of forest regrowth, but show slower change among older forests. This rapid recovery was also observed in the abundance of several taxonomic groups and for predators and detritivores as functional groups. Forest clearing frequency had no effect on the number or the diversity of macrofauna groups, but the abundance of ants increased as forest was cleared more often. Our results for soil macrofauna align with those in plant and vertebrate studies showing that secondary forests quickly recover a large part of their biodiversity and ecological functions. Therefore, global-scale conservation strategies are needed to ensure the opportunity for secondary forests to grow. ​.

Preliminary Metabolomic Profiling of the Vitreous Humor from Hypothermia Fatalities.

The postmortem diagnosis of hypothermia fatalities is often complex due to the absence of pathognomonic lesions and biomarkers. In this study, potential novel biomarkers of hypothermia fatalities were searched in the vitreous humor of known cases of hypothermia fatalities (n = 20) compared to control cases (n = 16), using a targeted metabolomics approach allowing quantitative detection of 188 metabolites. A robust discriminant model with good predictivity was obtained with the supervised OPLS-DA multivariate analysis, showing a distinct separation between the hypothermia and control groups. This signature was characterized by the decreased concentrations of five metabolites (methionine sulfoxide, tryptophan, phenylalanine, alanine, and ornithine) and the increased concentration of 28 metabolites (21 phosphatidylcholines, 3 sphingomyelins, spermine, citrulline, acetylcarnitine, and hydroxybutyrylcarnitine) in hypothermia fatalities compared to controls. The signature shows similarities with already identified features in serum such as the altered concentrations of tryptophan, acylcarnitines, and unsaturated phosphatidylcholines, revealing a highly significant increased activity of methionine sulfoxide reductase, attested by a low methionine sulfoxide-to-methionine ratio. Our results show a preliminary metabolomics signature of hypothermia fatalities in the vitreous humor, highlighting an increased methionine sulfoxide reductase activity.