Find research datasets worth reusing

opencc-zeroNov 2021View details →

Genetic polymorphisms in COMT and BDNF influence synchronization dynamics of human neuronal oscillations

Neuronal oscillations, their inter-areal synchronization, and scale-free dynamics constitute fundamental mechanisms for cognition by regulating communication in neuronal networks. These oscillatory dynamics have large inter-individual variability that is partly heritable. We hypothesized that this variability could be partially explained by genetic polymorphism in neuromodulatory genes. We recorded resting-state magnetoencephalography (MEG) from 82 healthy participants and investigated whether oscillation dynamics were influenced by genetic polymorphisms in Catechol-O-methyltransferase (COMT) Val158Met and brain-derived neurotrophic factor (BDNF) Val66Met. Both COMT and BDNF polymorphisms influenced local oscillation amplitudes and their long-range temporal correlations (LRTCs), while only BDNF polymorphism affected the strength of large-scale synchronization. Our findings demonstrate that COMT and BDNF genetic polymorphisms contribute to inter-individual variability in neuronal oscillation dynamics. Comparison of these results to computational modeling of near-critical synchronization dynamics further suggested that COMT and BDNF polymorphisms influenced local oscillations by modulating the excitation-inhibition balance according to the brain criticality framework.

opencc-zeroAug 2022View details →

Spatiotemporal influences of climate and humans on muskox range dynamics over multiple millennia

Processes leading to range contractions and population declines of Arctic megafauna during the late Pleistocene and early-Holocene are uncertain, with intense debate on the roles of human hunting, climatic change, and their synergy. Obstacles to a resolution, have included an over reliance on correlative rather than process-explicit approaches for inferring drivers of distributional and demographic change. Using process-explicit macroecological models that integrate modern and fossil occurrence records, spatiotemporal reconstructions of past climatic change, speciesspecific population ecology and the growth and spread of anatomically modern humans, we disentangle the ecological mechanisms and threats that were integral in the decline and extinction of the muskox (Ovibos moschatus) in Eurasia, and in its expansion in North America. We show that accurately reconstructing inferences of past demographic changes for muskox over the last 21,000 years requires high dispersal abilities, large maximum densities, and a small Allee effect. Climatic change was the primary driver of muskox distribution shifts and demographic changes across its previously extensive (circumpolar) range, with populations responding negatively to rapid warming events. Regional analyses reveal that the range collapse and extinction of the muskox in Europe (~ 13 thousand years ago) was caused by humans operating in synergy with climatic warming. In Canada and Greenland, climatic change and human activities combined to drive recent population sizes. The impact of past climatic change on the range and extinction dynamics of muskox during the Pleistocene-Holocene transition signals a vulnerability of this species to future increased warming. By disentangling the ecological processes that shaped the distribution of the muskox through space and time, process-explicit models have important applications for the future conservation and management of this iconic species in a warming Arctic.

zenodo40/100

Human Genetics Influences Microbiome Composition Involved in Asthma Exacerbations despite Inhaled Corticosteroid Treatment

Additional Supplement Data of the manuscript Perez-Garcia J, Espuela-Ortiz A, Hernández-Pérez JM, et al. Human Genetics Influences Microbiome Composition Involved in Asthma Exacerbations despite Inhaled Corticosteroid Treatment (in press). J Allergy Clin Immunol. 2023;S0091-6749(23)00748-0. doi:10.1016/j.jaci.2023.05.021. This Supplement Data contains the following items: <table> <tbody> <tr> <td>Additional Table 1</td> <td>List of independent mbQTLs associated with p<1x10-5 in the mbGWAS from saliva samples in Europeans (discovery).</td> </tr> <tr> <td>Additional Table 2</td> <td>List of independent mbQTLs associated with p<1x10-5 in the mbGWAS from pharyngeal samples in Europeans (discovery).</td> </tr> <tr> <td>Additional Table 3</td> <td>List of independent mbQTLs associated with p<1x10-5 in the mbGWAS from nasal samples in Europeans (discovery).</td> </tr> <tr> <td>Additional Table 4</td> <td>Summary results of enrichment analyses using the Enrichr platform.</td> </tr> <tr> <td>Additional Table 5</td> <td>Summary results of stratified enrichment analyses by biological sample type.</td> </tr> <tr> <td>Additional Table 6</td> <td>List of independent mbQTLs associated with p<1x10-5 in the mbGWAS from saliva samples in African Americans (replication phase).</td> </tr> <tr> <td>Additional Table 7</td> <td>List of independent mbQTLs associated with p<1x10-5 in the mbGWAS from saliva samples in Latinos (replication phase).</td> </tr> <tr> <td>Additional Table 8</td> <td>Summary results of replication enrichment analyses in saliva samples.</td> </tr> <tr> <td>Additional Table 9</td> <td>Summary statistics of the mbQTL analysis of Streptococcus in nasal samples.</td> </tr> <tr> <td>Additional Table 10</td> <td>Summary statistics of the mbQTL analysis of Campylobacter in pharyngeal samples.</td> </tr> <tr> <td>Additional Table 11</td> <td>Summary statistics of the mbQTL analysis of Tannerella in pharyngeal samples.</td> </tr> <tr> <td>Additional Table 12</td> <td>Summary table of the different genetic models tested for each mbQTL pair.</td> </tr> </tbody> </table>

opencc-by-4.0Jun 2023View details →

publicJan 2023View details →

Genetic polymorphisms in COMT and BDNF influence synchronization dynamics of human neuronal oscillations

Open the record for dataset details and reuse information.

publicAug 2022View details →

Spatiotemporal influences of climate and humans on muskox range dynamics over multiple millennia

Open the record for dataset details and reuse information.

edi40/100

Human influences on wildfire in Alaska from 1988 through 2005-Shapefile Outline for Interior Alaska

Data shows the outline for Interior Alaska used in my study. It's based on the Omernik-Bailey ecosytem classification and includes mostly the boreal ecozone without the Ogilvie mountains subzone.

openOpenDec 2008View details →

opencc-zeroJun 2020View details →

Data from: Influence of paleolithic range contraction, admixture and long-distance dispersal on genetic gradients of modern humans in Asia

Cavalli-Sforza and coauthors originally explored the genetic variation of modern humans throughout the world and observed an overall east-west genetic gradient in Asia. However, the specific environmental and population genetics processes causing this gradient were not formally investigated and promoted discussion in recent studies. Here we studied the influence of diverse environmental and population genetics processes on Asian genetic gradients and identified which could have produced the observed gradient. To do so, we performed extensive spatially-explicit computer simulations of genetic data under the following scenarios: (i) variable levels of admixture between Paleolithic and Neolithic populations, (ii) migration through long-distance dispersal (LDD), (iii) Paleolithic range contraction induced by the last glacial maximum (LGM) and, (iv) Neolithic range expansions from one or two geographic origins (the Fertile Crescent and the Yangzi and Yellow River Basins). Next, we estimated genetic gradients from the simulated data and we found that they were sensible to the analyzed processes, especially to the range contraction induced by LGM and to the number of Neolithic expansions. Some scenarios were compatible with the observed east-west genetic gradient, such as the Paleolithic expansion with a range contraction induced by the LGM or two Neolithic range expansions from both the east and the west. In general, LDD increased the variance of genetic gradients among simulations. We interpreted the obtained gradients as a consequence of both allele surfing caused by range expansions and isolation by distance along the vast east-west geographic axis of this continent.

opencc-by-4.0Jul 2020View details →

The influence of human disturbances on the spatio-temporal habitat selection patterns of roe deer near Trento (Italy)

This is the dataset used for the MSc. thesis of Matthijs Hinkamp for the master Earth Sciences (Environmental Management track) at the University of Amsterdam. In this thesis the Individual Movement Sequence Analysis Method (IM-SAM) was applied to analyse the influence of human disturbances on the sequential habitat use of roe deer in northern Italy. While it is known that in this area the roe deer populations are affected by anthropogenic pressures, the actual spatial and temporal implications of such pressures are unknown. The input for IM-SAM consisted of habitat sequences, which were obtained through tracking data from the Fondazione Edmund Mach, land use and land cover maps and temporal information. Based on exploratory dissimilarity trees for the real behavioural sequences, several simulation profiles were established, each with a different habitat use pattern. The results show that most roe deer prefer isolated forest areas, but alternating patterns are definitely present. Several co variables were assessed: the influence of the hunting season, increased pressure during weekends, differences between protected and unprotected areas and changes in the average NDVI. It seems that roe deer are affected by the hunting pressure in September. This month shows an increase in the prevalence of alternating profiles, which indicates that roe deer tend to change their habitat use during periods of the day when hunting takes place. It cannot be concluded that habitat use patterns are altered during the weekends and the differences between sequences in protected and unprotected areas seem to be relatively small. However, some results indicate that alternating habitat use is a strategy for some roe deer in protected areas. When looking at the NDVI values, it becomes clear that the average NDVI is higher overall for the alternating profiles, but this just underlines the general conclusions drawn about the habitat use strategies in September.

opencc-by-4.0Sep 2020View details →

The influence of human genetic variation on Epstein-Barr virus sequence diversity

This project is the first attempt to apply a "genome-to-genome" approach to investigate the impact of the host genetic pressure on the genome of a member of the Herpesviridae family. Namely, 285 pairs of human and EBV genomes were sequenced and multiple GWASes between human and EBV variations were performed. This repository contains the results of downstream analysis on the pathogen-side. The variant calling data was produced from read alignment using BWA mem using GATK HC, SNVer, VarScan2, BCFtools, freebayes and the intersection of the sets of variation from the first three. <ul> <li>The "covstats" files contains statistics about the read alignment.</li> <li>The tarball SHCS_EBV_variant_call.tar.gz contains all compressed VCF files.</li> <li>The tarball SHCS_EBV_variant_matrices_stats.tar.gz contains all matrices used as traits in the GWASes, as well as a variety of statistics.</li> </ul> The pipeline used to generate this data is publically available here: <a href="https://gitlab.com/ezlab/vir_var_calling/">https://gitlab.com/ezlab/vir_var_calling/</a>

opencc-by-4.0Nov 2020View details →

Influence of Atmospheric Parameters on Human Mortality data at Different Geographical Levels. Script and DataBase

The script and dataBase uploaded was developed to assess the association between human mortality data (segregated by age groups and sex) with meteorological and air pollutant covariates at three geographical levels: country, macro-climate regions, and county. The modeling was based on a generalized linear modeling framework, and it takes into account the common characteristic of overdispersion in human mortality data through the application of negative binomial distribution.

opencc-zeroDec 2020View details →

The extensibility of the plantar fascia influences the windlass mechanism during human running

The arch of the human foot is unique among hominins as it is compliant at ground-contact but sufficiently stiff to enable push-off. These behaviours are partly facilitated by the ligamentous plantar fascia whose role is central to two mechanisms. The ideal windlass mechanism assumes that the plantar fascia has a nearly constant length to directly couple toe dorsiflexion with a change in arch shape. However, the plantar fascia also stretches and then shortens throughout gait as the arch-spring stores and releases elastic energy. We aimed to understand how the extensible plantar fascia could behave as an ideal windlass when it has been shown to strain throughout gait, potentially compromising the one-to-one coupling between toe arc length and arch length. We measured foot bone motion and plantar fascia elongation using high-speed x-ray during running. We discovered that toe plantarflexion delays plantar fascia stretching at foot-strike, which likely modifies the distribution of the load through other arch tissues. Through a pure windlass effect in propulsion, a quasi-isometric plantar fascia's shortening is delayed to later in stance. The plantar fascia then shortens concurrently to the windlass mechanism, likely enhancing arch recoil at push-off.

opencc-zeroDec 2023View details →

Forest associated habitat variables influence human-tick encounters in the southeastern United States

Due to the increased frequency of human-tick encounters and expanding ranges of ticks in the United States, there is a critical need to identify environmental conditions associated with tick populations and their likelihood to contact human hosts. In a passive tick surveillance partnership with the United States Department of Agriculture Forest Inventory and Analysis (FIA) program, we identified environmental variables associated with tick encounters by forestry personnel. Ticks were identified to species and life stage and site-specific variables were associated with each tick using FIA forest inventory datasets and generalized linear and zero-inflated models. Of the 55 FIA variables available, we identified biotic and abiotic environmental variables associated with Amblyomma americanum (carbon in litter material and standing dead tree aboveground dry biomass), Dermacentor variabilis (live sapling belowground dry biomass, carbon in litter material, forest stand age, and elevation), and Ixodes scapularis (carbon in dead woody material and seedling species unevenness). We propose that land management decisions not only affect common flora and fauna but changes to these habitats can also alter the way ticks parasitize hosts and use vegetation to find those hosts. Testing of these results can be used with land management decisions to prevent future encounters and highlight risk areas. Foresters that inventory sites encounter ticks, which we can then use to better understand the environmental conditions conducive to increased tick abundance or habitat suitability.

opencc-zeroOct 2022View details →

High temperatures and human pressures interact to influence mortality in an African carnivore

1. The impacts of high ambient temperatures on mortality in humans and domestic animals are well understood. However much less is known about how hot weather affects mortality in wild animals. High ambient temperatures have been associated with African wild dog Lycaon pictus pup mortality, suggesting that high temperatures might also be linked to high adult mortality. 2. We analysed mortality patterns in African wild dogs radio-collared in Kenya (0°N), Botswana (20°S) and Zimbabwe (20°S), to examine whether ambient temperature was associated with adult mortality. 3. We found that high ambient temperatures were associated with increased adult wild dog mortality at the Kenya site, and there was some evidence for temperature associations with mortality at the Botswana and Zimbabwe sites. 4. At the Kenya study site, which had the highest human impact, high ambient temperatures were associated with increased risks of wild dogs being killed by people, and by domestic dog diseases. In contrast, temperature was not associated with the risk of snare-related mortality at the Zimbabwe site, which had the second-highest human impact. Causes of death varied markedly between sites. 5. Pack size was positively associated with survival at all three sites. 6. These findings suggest that while climate change may not lead to new causes of mortality, rising temperatures may exacerbate existing anthropogenic threats to this endangered species, with implications for conservation. This evidence suggests that temperature-related mortality, including interactions between temperature and other anthropogenic threats, should be investigated in a greater number of species to understand and mitigate likely impacts of climate change.

opencc-zeroDec 2022View details →

Data for: Beyond simple habituation: Anthropogenic habitats influence the escape behavior of spur-winged lapwings in response to both human and non-human threats

Habitat development may affect wildlife behavior, favoring individuals or behaviors that cope better with perceived threats (predators). Bolder behaviors in human-dominated habitats (HDH; e.g., urban and rural settlements) may represent habituation specifically to humans, or a general reduction in predator-avoidance response. However, such carry-over effects across threat types (i.e., beyond humans) and phases of the escape sequence have not been well studied to date. Here we investigated escape behaviors of a locally common wader species, the spur-winged lapwing (Vanellus spinosus). We assayed their flight initiation distance (FID) and subsequent escape behaviors in agricultural areas and in HDH. We found that lapwings in HDH were bolder, and that the difference was manifested in several phases of the predator-avoidance sequence (shorter FIDs, shorter distances fled, and a higher probability of escape by running vs. flying). When re-approached (by an observer) after landing, lapwings in HDH were also more repetitive in their FID than those in other habitats. To determine whether this apparent bolder behavior in HDH areas is merely a consequence of habituation to humans or represents a broader behavioral change, we introduced an additional threat type – a remotely-operated taxidermic jackal ("Jack-Truck"). Finding bolder responses in the HDH to the human threat alone (and not to the Jack-Truck) could have supported the habituation hypothesis. In contrast, however, we found a bolder response in the HDH to both threat types, as well as a correlation between their FIDs across different sites. These bolder behaviors suggest that HDH impose a broader behavioral change on lapwings, rather than just simple habituation. Overall, our findings demonstrate how FID trials can reveal strong behavioral carry-over effects of HDH following human and non-human threats, including effects on the subsequent phases of escaping the predator. Further, FID assays may reveal consistent behavioral types when assessed under field conditions, and offer a direct way to differentiate among the various poorly understood and non-mutually exclusive mechanisms that lead to behavioral differences among organisms in HDH. The mechanistic perspective is essential for understanding how rapid urbanization impacts wildlife behavior, populations, and the range of behaviors within them, even in species apparently resilient to such environmental changes.

opencc-zeroDec 2022View details →

Antelope space-use and behaviour indicate multi-level responses to varying anthropogenic influences in a highly human-dominated landscape

A primary means of conserving a species or a habitat in a human-dominated landscape is through promoting coexistence with humans while minimizing conflict. For this, we should understand how wildlife are impacted by direct and indirect human activities. Such information is rare from areas with high human densities. To investigate how animals respond to altered ecological conditions in human-dominated landscapes, we focussed on a wild herbivore of conservation concern in Krishnasaar Conservation Area (KrCA) in Nepal. Here, blackbuck, Antilope cervicapra, a generalist grazer, lives in refugia located in a growing human population. We studied the impacts of humans on habitat use and behaviour of blackbuck. We laid 250 x 250 m grid cells in the entire KrCA and carried out indirect sign surveys with three replications for habitat use assessment. We observed herds of blackbuck for 89 hours in different habitat types using scan sampling methods. Our habitat-use survey showed that habitats under intensive human use were hardly used by blackbuck, even when high-quality forage was available. Habitat openness was the major predictor of habitat-use inside the core area, where levels of human activities were low. We also found a positive correlation between habitat use by blackbuck and livestock. Blackbuck were substantially more vigilant when they were in forest than in grassland, again indicating an influence of risk. Overall, blackbuck appear to be sensitive to risk associated with both natural and anthropogenic factors. Our findings have direct implications for managing human-wildlife interactions in this landscape, specifically regarding strategies for livestock grazing in habitats highly used by blackbuck and concerning predictions of how changing land use will impact long-term persistence of blackbuck. Our work suggests that wild herbivores may be able to persist in landscapes with high human densities so long as there are refuges where human activities are relatively low.

opencc-by-4.0Apr 2023View details →

Dog guardians and genetic testing: Survey textbox responses & human-animal bond influences

Project was exported from Atlas.ti version 23, data analysis was completed using version 9. This subset data was derived from Wisdom PanelTM consumers in which participants provided qualitative responses and answered HAB related questions (see <a href="https://doi.org/10.3390/ani12233360">https://doi.org/10.3390/ani12233360</a>). Qualitative data were obtained via open-ended textboxes. In light of a number of participants providing meaningful data, a post-hoc analysis was added to report central themes present and provide further characterization of potential human-dog relationship influences. Please contact the author directly with any questions about the data.