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Public health concerns about recent viral epidemics have motivated researchers to seek novel ways to understand pathogen infection in native, wildlife hosts. With its deep history of tools and perspectives for understanding the abundance and distribution of organisms, ecology can shed new light on viral infection dynamics. However, datasets allowing deep explorations of viral communities from an ecological perspective are lacking. We sampled 1086 bats from two, adjacent Puerto Rican caves and tested them for infection by herpesviruses, resulting in 3131 short, viral sequences. Using percent identity of nucleotides and a machine learning algorithm (affinity propagation), we categorized herpesviruses into 43 operational taxonomic units (OTUs) to be used in place of species in subsequent ecological analyses. Herpesvirus metacommunities demonstrated long-tailed rank frequency distributions at all analyzed levels of host organization (i.e., individual, population, and community). Although 13 herpesvirus OTUs were detected in more than one host species, OTUs generally exhibited host specificity by infecting a single core host species at a significantly higher prevalence than in all satellite species combined. We describe the natural history of herpesvirus metacommunities in Puerto Rican bats and suggest that viruses follow the general law that communities comprise few common and many rare species. To guide future efforts in the field of viral ecology, hypotheses are presented regarding mechanisms that contribute to these patterns.

Persistent organic pollutants may negatively impact cognition; however, associations between persistent organic pollutants and changes in cognition among United States Hispanic/Latino adults have not been investigated. Herein, we examined the associations between 33 persistent organic pollutants and cognitive changes among 1837 Hispanic/Latino adults. At baseline (2008–2011; Visit 1), participants provided biospecimens in which we measured levels of 5 persistent pesticides or pesticide metabolites, 4 polybrominated diphenyl ethers and 2,2’,4,4’,5,5’-hexabromobiphenyl, and 24 polychlorinated biphenyls. At Visit 1 and again at Visit 2 (2015–2018), a battery of neurocognitive tests was administered which included the Brief-Spanish English Verbal Learning Test, Word Fluency Test, and Digit Symbol Substitution Test. To estimate the adjusted associations between changes in cognition and each POP, we used linear regression for survey data. Each doubling in plasma levels of polychlorinated biphenyls 146, 178, 194, 199/206, and 209 was associated with steeper declines in global cognition (βs range:-0.053 to −0.061) with stronger associations for the Brief-Spanish English Verbal Learning Test. Persistent organic pollutants, in particular polychlorinated biphenyls, were associated with declines in cognition over 7 years and may be a concern for Hispanic/Latino adults.

Abstract Improved understanding of the genetic basis of adaptation to climate change is necessary for maintaining global biodiversity moving forward. Studies to date have largely focused on sequence variation, yet there is growing evidence that suggests that changes in genome structure may be an even more significant source of adaptive potential. The American pika (Ochotona princeps) is an alpine specialist that shows some evidence of adaptation to climate along elevational gradients, but previous work has been limited to single nucleotide polymorphism based analyses within a fraction of the species range. Here, we investigated the role of copy number variation underlying patterns of local adaptation in the American pika using genome-wide data previously collected across the entire species range. We identified 37–193 putative copy number variants (CNVs) associated with environmental variation (temperature, precipitation, solar radiation) within each of the six major American pika lineages, with patterns of divergence largely following elevational and latitudinal gradients. Genes associated (n = 158) with independent annotations across lineages, variables, and/or CNVs had functions related to mitochondrial structure/function, immune response, hypoxia, olfaction, and DNA repair. Some of these genes have been previously linked to putative high elevation and/or climate adaptation in other species, suggesting they may serve as important targets in future studies.

Abstract Background The effects of organochlorine pesticide (OCP) exposure on the development of human papillary thyroid cancer (PTC) are not well understood. A nested case-control study was conducted with data from the U.S. Department of Defense Serum Repository (DoDSR) cohort between 2000 and 2013 to assess associations of individual OCPs serum concentrations with PTC risk. Methods This study included 742 histologically confirmed PTC cases (341 females, 401 males) and 742 individually-matched controls with pre-diagnostic serum samples selected from the DoDSR. Associations between categories of lipid-corrected serum concentrations of seven OCPs and PTC risk were evaluated for classical PTC and follicular PTC using conditional logistic regression, adjusted for body mass index category and military branch to compute odds ratios (OR) and 95% confidence intervals (CIs). Effect modification by sex, birth cohort, and race was examined. Results There was no evidence of associations between most of the OCPs and PTC, overall or stratified by histological subtype. Overall, there was no evidence of an association between hexachlorobenzene (HCB) and PTC, but stratified by histological subtype HCB was associated with significantly increased risk of classical PTC (third tertile above the limit of detection (LOD) vs.

Abstract Public health concerns about recent viral epidemics have motivated researchers to seek novel ways to understand pathogen infection in native, wildlife hosts. With its deep history of tools and perspectives for understanding the abundance and distribution of organisms, ecology can shed new light on viral infection dynamics. However, datasets allowing deep explorations of viral communities from an ecological perspective are lacking. We sampled 1086 bats from two, adjacent Puerto Rican caves and tested them for infection by herpesviruses, resulting in 3131 short, viral sequences. Using percent identity of nucleotides and a machine learning algorithm (affinity propagation), we categorized herpesviruses into 43 operational taxonomic units (OTUs) to be used in place of species in subsequent ecological analyses. Herpesvirus metacommunities demonstrated long‐tailed rank frequency distributions at all analyzed levels of host organization (i.e., individual, population, and community). Although 13 herpesvirus OTUs were detected in more than one host species, OTUs generally exhibited host specificity by infecting a single core host species at a significantly higher prevalence than in all satellite species combined. We describe the natural history of herpesvirus metacommunities in Puerto Rican bats and suggest that viruses follow the general law that communities comprise few common and many rare species. To guide future efforts in the field of viral ecology, hypotheses are presented regarding mechanisms that contribute to these patterns.

Abstract Genetic tools for wildlife monitoring can provide valuable information on spatiotemporal population trends and connectivity, particularly in systems experiencing rapid environmental change. Multiplexed targeted amplicon sequencing techniques, such as genotyping‐in‐thousands by sequencing (GT‐seq), can provide cost‐effective approaches for collecting genetic data from low‐quality and quantity DNA samples, making them potentially useful for long‐term wildlife monitoring using non‐invasive and archival samples. Here, we developed a GT‐seq panel as a potential monitoring tool for the American pika (Ochotona princeps) and evaluated its performance when applied to traditional, non‐invasive, and archival samples, respectively. Specifically, we optimized a GT‐seq panel (307 single nucleotide polymorphisms (SNPs)) that included neutral, sex‐associated, and putatively adaptive SNPs using contemporary tissue samples (n = 77) from the Northern Rocky Mountains lineage of American pikas. The panel demonstrated high genotyping success (94.7%), low genotyping error (0.001%), and excellent performance identifying individuals, sex, relatedness, and population structure. We subsequently applied the GT‐seq panel to archival tissue (n = 17) and contemporary fecal pellet samples (n = 129) collected within the Canadian Rocky Mountains to evaluate its effectiveness. Although the panel demonstrated high efficacy with archival tissue samples (90.5% genotyping success, 0.0% genotyping error), this was not the case for the fecal pellet samples (79.7% genotyping success, 28.4% genotyping error) likely due to the exceptionally low quality/quantity of recovered DNA using the approaches implemented. Overall, our study reinforced GT‐seq as an effective tool using contemporary and archival tissue samples, providing future opportunities for temporal applications using historical specimens. Our results further highlight the need for additional optimization of sample and genetic data collection techniques prior to broader‐scale implementation of a non‐invasive genetic monitoring tool for American pikas.

A high proportion of horses in training, perceived as free from lameness by their owner, exhibit vertical movement asymmetries. These types of asymmetries are sensitive measures of lameness, but their specificity as indicators of orthopaedic pathology or locomotor function remains unclear. Equine athletes performing at a high level could be assumed to exhibit a higher degree of movement symmetry compared with the general horse population, but this has not been confirmed. This study investigated the prevalence of movement asymmetries in horses performing at a high level in three equestrian disciplines; show jumping, dressage and eventing, as well as the association between riders' perception of horse sidedness and said movement asymmetries. Using an inertial measurement unit-based system (Equinosis), gait analysis was performed on 123 high-performing horses. The mean difference between the two vertical minimum and between the two maximum values of each stride was recorded for the head (HDmin, HDmax) and pelvis (PDmin, PDmax). The horses were defined as asymmetric if one or multiple asymmetry parameters exceeded an absolute trial mean of: >6mm for HDmin or HDmax, and >3mm for PDmin or PDmax, with standard deviation less than the respective mean value. Based on the results, 70% of the horses were classified as asymmetric, which is similar to previous findings for young riding horses and horses competing at a lower level. More than one-third of these high-performing horses had asymmetry values of similar magnitude to those seen in clinically lame horses. No clear associations were observed between rider-perceived sidedness and the vertical movement asymmetry values, indicating that the perceived unevenness between sides is not a determinant of vertical movement asymmetry. Longitudinal studies on movement asymmetries in relation to training intensity and full clinical examinations with local or systemic analgesic testing are desired as further research to determine whether these movement asymmetries indicate a welfare problem.

Abstract Background Urban air pollution is an increasing health problem, particularly in Asia, where the combustion of fossil fuels has increased rapidly as a result of industrialization and socio-economic development. The adverse health impacts of urban air pollution are well established, but less is known about effective intervention strategies. In this demonstration study we set out to establish methods to assess whether wearing an R95 activated carbon respirator could reduce intake of polycyclic aromatic hydrocarbons (PAH) in street workers in Hanoi, Vietnam. Methods In this demonstration study we performed a cross-over study in which non-smoking participants that worked at least 4 hours per day on the street in Hanoi were randomly allocated to specific respirator wearing sequences for a duration of 2 weeks. Urines were collected after each period, i.e. twice per week, at the end of the working day to measure hydroxy PAHs (OH-PAH) using gas chromatography/high resolution mass spectrometry. The primary endpoint was the urinary concentration of 1-hydroxypyrene (1-OHP). Results Forty-four participants (54.5% male, median age 40 years) were enrolled with the majority being motorbike taxi drivers (38.6%) or street vendors (34.1%). The baseline creatinine corrected urinary level for 1-OHP was much higher than other international comparisons: 1020 ng/g creatinine (IQR: 604–1551). Wearing a R95 mask had no significant effect on 1-OHP levels: estimated multiplicative effect 1.0 (95% CI: 0.92-1.09) or other OH-PAHs, except 1-hydroxynaphthalene (1-OHN): 0.86 (95% CI: 0.11-0.96). Conclusions High levels of urine OH-PAHs were found in Hanoi street workers. No effect was seen on urine OH-PAH levels by wearing R95 particulate respirators in an area of high urban air pollution, except for 1-OHN. A lack of effect may be de to gaseous phase PAHs that were not filtered efficiently by the respirator. The high levels of urinary OH-PAHs found, urges for effective interventions. Trial registration ISRCTN74390617 (date of assignation: 04/08/2009).

Forecasting the risk of pathogen spillover from reservoir populations of wild or domestic animals is essential for the effective deployment of interventions such as wildlife vaccination or culling. Due to the sporadic nature of spillover events and limited availability of data, developing and validating robust, spatially explicit, predictions is challenging. Recent efforts have begun to make progress in this direction by capitalizing on machine learning methodologies. An important weakness of existing approaches, however, is that they generally rely on combining human and reservoir infection data during the training process and thus conflate risk attributable to the prevalence of the pathogen in the reservoir population with the risk attributed to the realized rate of spillover into the human population. Because effective planning of interventions requires that these components of risk be disentangled, we developed a multi-layer machine learning framework that separates these processes. Our approach begins by training models to predict the geographic range of the primary reservoir and the subset of this range in which the pathogen occurs. The spillover risk predicted by the product of these reservoir specific models is then fit to data on realized patterns of historical spillover into the human population. The result is a geographically specific spillover risk forecast that can be easily decomposed and used to guide effective intervention. Applying our method to Lassa virus, a zoonotic pathogen that regularly spills over into the human population across West Africa, results in a model that explains a modest but statistically significant portion of geographic variation in historical patterns of spillover. When combined with a mechanistic mathematical model of infection dynamics, our spillover risk model predicts that 897,700 humans are infected by Lassa virus each year across West Africa, with Nigeria accounting for more than half of these human infections.

Summary: Climate change is one of several drivers of recurrent outbreaks and geographical range expansion of infectious diseases in Europe. We propose a framework for the co-production of policy-relevant indicators and decision-support tools that track past, present, and future climate-induced disease risks across hazard, exposure, and vulnerability domains at the animal, human, and environmental interface. This entails the co-development of early warning and response systems and tools to assess the costs and benefits of climate change adaptation and mitigation measures across sectors, to increase health system resilience at regional and local levels and reveal novel policy entry points and opportunities. Our approach involves multi-level engagement, innovative methodologies, and novel data streams. We take advantage of intelligence generated locally and empirically to quantify effects in areas experiencing rapid urban transformation and heterogeneous climate-induced disease threats. Our goal is to reduce the knowledge-to-action gap by developing an integrated One Health—Climate Risk framework.

IntroductionPrenatal exposure to polybrominated diphenyl ethers (PBDEs) has been associated with increased symptoms of attention deficit/hyperactivity disorder (ADHD) in early to middle childhood, as well as early adolescence. However, data are limited for the long-lasting impact of exposure on outcomes assessed across the entire adolescent period and the sex-specificity of such associations.MethodsWe investigated the association between continuous natural-log-transformed cord plasma PBDE concentrations and ADHD rating scale 4th edition (ADHD-RS-IV) score from mid adolescence (approximately 11 years old) to late adolescence (approximately 17 years old). The study sample includes a subset (n = 219) of the African American and Dominican children enrolled in the Columbia Center for Children's Environmental Health Mothers and Newborns birth cohort. We used generalized estimating equations to account for the repeated measure of ADHD-RS scores. We examined interactions between exposure to PBDE and sex using cross-product terms and sex-stratified models. In addition, we used linear regression using an age-stratified sample as a sensitivity analysis.Results and DiscussionAssociations between prenatal exposure and parents’ reports of ADHD symptoms varied by sex (p-interaction

The rate at which zoonotic viruses spill over into the human population varies significantly over space and time. Remarkably, we do not yet know how much of this variation is attributable to genetic variation within viral populations. This gap in understanding arises because we lack methods of genetic analysis that can be easily applied to zoonotic viruses, where the number of available viral sequences is often limited, and opportunistic sampling introduces significant population stratification. Here, we explore the feasibility of using patterns of shared ancestry to correct for population stratification, enabling genome-wide association methods to identify genetic substitutions associated with spillover into the human population. Using a combination of phylogenetically structured simulations and Lassa virus sequences collected from humans and rodents in Sierra Leone, we demonstrate that existing methods do not fully correct for stratification, leading to elevated error rates. We also demonstrate, however, that the Type I error rate can be substantially reduced by confining the analysis to a less-stratified region of the phylogeny, even in an already-small dataset. Using this method, we detect two candidate single-nucleotide polymorphisms associated with spillover in the Lassa virus polymerase gene and provide generalized recommendations for the collection and analysis of zoonotic viruses.

Many horses, just before and during their athletic career, show vertical movement asymmetries, to the same degree as clinically lame horses. It is unknown whether these asymmetries are caused by pain or have alternative explanations, such as inherent biological variation. In the latter case, movement asymmetries would be expected to be present at a very young age. This study aimed to investigate the prevalence of movement asymmetries in foals. Motion analysis, using an inertial measurement unit-based system (Equinosis), was performed on 54 foals (31 Swedish Warmbloods, 23 Standardbreds) during straight-line trot. The foals were between 4-13 weeks old and considered sound by their owners. Differences between the vertical minimum and maximum values recorded for the head (HDmin, HDmax) and pelvis (PDmin, PDmax) between left and right stance were calculated for each stride and an average was computed for each trial. Thresholds for asymmetry were defined as absolute trial mean >6 mm for HDmin and HDmax, and >3 mm for PDmin and PDmax. These thresholds were exceeded for one or several parameters by 83% of Standardbred foals and 45% of Swedish Warmblood foals, demonstrating surprisingly high prevalence of asymmetries in young foals, although the risk of repetitive strain injuries and cumulative risk of trauma injuries was expected to be low in this age group. Standardbred foals showed similar prevalence of asymmetries to that reported previously for yearling Standardbred trotters, so relatively higher prevalence of movement asymmetries may be expected among trotters as a breed. In general, vertical head and pelvic movement asymmetries can be anticipated among foals considered sound by their owners. A better understanding of the aetiology of asymmetries is needed for correct interpretation of objective symmetry measurements in different populations of horses.

In forest management planning, the dynamic treatment unit (DTU) approach has become an increasingly relevant alternative to the traditional planning approach using fixed stands, due to improved remote sensing techniques and optimization procedures, with the potential for the higher goal fulfillment of forest activities. For the DTU approach, the traditional concept of fixed stands is disregarded, and forest data are kept in units with a high spatial resolution. Forest operations are planned by clustering cells to form treatment units for harvest operations. This paper presents a new model with an exact optimization technique for forming DTUs in forest planning. In comparison with most previous models, this model aims for increased flexibility by modelling the spatial dimension according to cell proximity rather than immediate adjacency. The model is evaluated using a case study with harvest flow constraints for a forest estate in southern Sweden, represented by 3587 cells. The parameter settings differed between cases, resulting in varying degrees of clustered DTUs, which caused relative net present value losses of up to 4.3%. The case without clustering had the lowest net present value when considering entry costs. The solution times varied between 2.2 s and 42 min 6 s and grew rapidly with increasing problem size. Key words: dynamic treatment units, mixed integer programming, optimization, remote sensing, spatial forest planning. En planification de la gestion forestiere, l'approche par unite de traitement dynamique (UTD) est devenue une alternative de plus en plus pertinente a l'approche de gestion traditionnelle fondee sur des peuplements fixes. Cela est rendu possible grace a l'amelioration des techniques de teledetection et des procedures d'optimisation et offre la possibilite d'une meilleure realisation des objectifs des activites forestieres. Avec l'approche par UTD, on ignore le concept traditionnel de peuplements fixes et les donnees forestieres sont conservees dans des unites a grande resolution spatiale. Les operations forestieres sont planifiees en regroupant les cellules pour former des unites de traitement pour les operations de recolte. Cet article presente un nouveau modele avec une technique d'optimisation exacte pour former les UTD en planification forestiere. Comparativement a la plupart des modeles precedents, ce modele vise a augmenter la flexibilite en modelisant la dimension spatiale en fonction de la proximite des cellules plutot que de leur contigu'ite. Le modele est evalue a l'aide d'une etude de cas comportant des contraintes de flux de recolte sur un domaine forestier situe dans le sud de la Suede, represente par 3587 cellules. L'ajustement des parametres differait selon le cas, ce qui se traduit par differents degres de regroupement d'UTD, causant des pertes de valeur actualisee nette relative allant jusqu'a 4,3%. Le cas qui ne comporte aucun regroupement avait la plus faible valeur actualisee nette lorsqu'on considere les couts d'entree. Le temps requis pour trouver la solution variait de 2,2 s a 42 min 6 s et augmentait rapidement avec l'augmentation de la taille du probleme. Mots-cles : unites de traitement dynamiques, programmation partiellement en nombres entiers, optimisation, teledetection, gestion forestiere spatiale., Introduction In forest management planning, the concept of stands has been of central importance for a long time (e.g., af Strom 1829). In this context, a stand is a geographically [...]

A high proportion of horses in training, perceived as free from lameness by their owner, exhibit vertical movement asymmetries. These types of asymmetries are sensitive measures of lameness, but their specificity as indicators of orthopaedic pathology or locomotor function remains unclear. Equine athletes performing at a high level could be assumed to exhibit a higher degree of movement symmetry compared with the general horse population, but this has not been confirmed. This study investigated the prevalence of movement asymmetries in horses performing at a high level in three equestrian disciplines; show jumping, dressage and eventing, as well as the association between riders' perception of horse sidedness and said movement asymmetries. Using an inertial measurement unit-based system (Equinosis), gait analysis was performed on 123 high-performing horses. The mean difference between the two vertical minimum and between the two maximum values of each stride was recorded for the head (HDmin, HDmax) and pelvis (PDmin, PDmax). The horses were defined as asymmetric if one or multiple asymmetry parameters exceeded an absolute trial mean of: >6mm for HDmin or HDmax, and >3mm for PDmin or PDmax, with standard deviation less than the respective mean value. Based on the results, 70% of the horses were classified as asymmetric, which is similar to previous findings for young riding horses and horses competing at a lower level. More than one-third of these high-performing horses had asymmetry values of similar magnitude to those seen in clinically lame horses. No clear associations were observed between rider-perceived sidedness and the vertical movement asymmetry values, indicating that the perceived unevenness between sides is not a determinant of vertical movement asymmetry. Longitudinal studies on movement asymmetries in relation to training intensity and full clinical examinations with local or systemic analgesic testing are desired as further research to determine whether these movement asymmetries indicate a welfare problem. [ABSTRACT FROM AUTHOR]

Knowledge of vertical motion patterns of the axial body segments is a prerequisite for the development of algorithms used in automated detection of lameness. To date, the focus has been on the trot. This study investigates the temporal synchronization between vertical motion of the axial body segments with limb kinematic events in walk and trot across three popular types of sport horses (19 Warmbloods, 23 Iberians, 26 Icelandics) that are known to have different stride kinematics, and it presents novel data describing vertical motion of the axial body segments in tölting and pacing Icelandic horses. Inertial measurement unit sensors recorded limb kinematics, vertical motion of the axial body at all symmetrical gaits that the horse could perform (walk, trot, tölt, pace). Limb kinematics, vertical range of motion and lowest/highest positions of the head, withers and pelvis were calculated. For all gaits except walk and pace, lowest/highest positions of the pelvis and withers were found to be closely related temporally to midstance and start of suspension of the hind/fore quarter, respectively. There were differences in pelvic/withers range of motion between all breeds where the Icelandic horses showed the smallest motion, which may explain why lameness evaluation in this breed is challenging.

Differences in movement asymmetry between surfaces and with increasing speed increase the complexity of incorporating gait analysis measurements from lunging into clinical decision making. This observational study sets out to quantify by means of quantitative gait analysis the influence of surface and speed on individual-rein movement asymmetry measurements and their averages across reins (average-rein measurements). Head, withers, and pelvic movement asymmetry was quantified in 27 horses, identified previously as presenting with considerable movement asymmetries on the straight, during trot in hand and on the lunge on two surfaces at two speeds. Mixed linear models (p < 0.05) with horse as the random factor and surface and speed category (and direction) as fixed factors analyzed the effects on 11 individual-rein and average-rein asymmetry measures. Limits of agreement quantified differences between individual-rein and average-rein measurements. A higher number of individual-rein asymmetry variables—particularly when the limb that contributed to movement asymmetry on the straight was on the inside of the circle—were affected by speed (nine variables, all p ≤ 0.047) and surface (three variables, all p ≤ 0.037) compared with average-rein asymmetry variables (two for speed, all p ≤ 0.003; two for surface, all p ≤ 0.046). Six variables were significantly different between straight-line and average-rein assessments (all p ≤ 0.031), and asymmetry values were smaller for average-rein assessments. Limits of agreement bias varied between +0.4 and +4.0 mm with standard deviations between 3.2 and 12.9 mm. Fewer average-rein variables were affected by speed highlighting the benefit of comparing left and right rein measurements. Only one asymmetry variable showed a surface difference for individual-rein and average-rein data, emphasizing the benefit of assessing surface differences on each rein individually. Variability in straight-line vs. average-rein measurements across horses and exercise conditions highlight the potential for average-rein measurements during the diagnostic process; further studies after diagnostic analgesia are needed.