Find research datasets worth reusing

opencc-zeroDec 2017View details →

Data from: Genetic diversity, infection prevalence, and possible transmission routes of Bartonella spp. in vampire bats

Bartonella spp. are globally distributed bacteria that cause endocarditis in humans and domestic animals. Recent work has suggested bats as zoonotic reservoirs of some human Bartonella infections; however, the ecological and spatiotemporal patterns of infection in bats remain largely unknown. Here we studied the genetic diversity, prevalence of infection across seasons and years, individual risk factors, and possible transmission routes of Bartonella in populations of common vampire bats (Desmodus rotundus) in Peru and Belize, for which high infection prevalence has previously been reported. Phylogenetic analysis of the gltA gene for a subset of PCR-positive blood samples revealed sequences that were related to Bartonella described from vampire bats from Mexico, other Neotropical bat species, and streblid bat flies. Sequences associated with vampire bats clustered significantly by country but commonly spanned Central and South America, implying limited spatial structure. Stable and nonzero Bartonella prevalence between years supported endemic transmission in all sites. The odds of Bartonella infection for individual bats was unrelated to the intensity of bat flies ectoparasitism, but nearly all infected bats were infested, which precluded conclusive assessment of support for vector-borne transmission. While metagenomic sequencing found no strong evidence of Bartonella DNA in pooled bat saliva and fecal samples, we detected PCR positivity in individual saliva and feces, suggesting the potential for bacterial transmission through both direct contact (i.e., biting) and environmental (i.e., fecal) exposures. Further investigating the relative contributions of direct contact, environmental, and vector-borne transmission for bat Bartonella is an important next step to predict infection dynamics within bats and the risks of human and livestock exposures.

opencc-by-4.0Oct 2016View details →

Supporting data: Prevalence of sexual dimorphism in mammalian phenotypic traits

<p>Supporting material for the manuscript <strong>“</strong><strong>Prevalence of sexual dimorphism in mammalian phenotypic traits”</strong> . This manuscript was published in Nature Communication 26th January 2017</p>

opencc-by-4.0Nov 2023View details →

Custom database for coronavirus prevalence analysis

<p>These coronavirus genomes in this dataset were obtained from the NCBI Refseq and are contained in the custom database utilised for both pan-coronavirus primer design, and homology search resulting in Figure 4c of the associated manuscript.</p>

opencc-zeroDec 2023View details →

A meta-analysis exploring associations between habitat degradation and Neotropical bat virus prevalence and seroprevalence

<p>Habitat degradation can increase zoonotic disease risks by altering infection dynamics in wildlife and increasing wildlife–human interactions. Bats are an important taxonomic group to consider these effects, because they harbour many relevant zoonotic viruses and have species- and context-dependent responses to degradation that could affect zoonotic virus dynamics. Yet our understanding of the associations between habitat degradation and bat virus prevalence and seroprevalence are limited to a small number of studies, which often differ in the bats or viruses sampled, the study region, and methodology. To develop a broad understanding of the associations between bat viruses and habitat degradation, we conducted an initial phylogenetic meta-analysis that combines published prevalence and seroprevalence ("(sero)prevalence") with remote-sensing habitat degradation data. Our dataset includes 588 unique records of (sero)prevalence across 16 studies, 64 bat species, and five virus families. We quantified the overall strength and direction of the relationship between habitat degradation and bat virus outcomes and tested how this relationship is moderated by the time between habitat degradation and bat sampling and by ecological traits of bat hosts while controlling for phylogenetic nonindependence among bat species. We found no effect of degradation on prevalence overall, although a weak effect may exist when forest loss occurs the year prior to bat sampling. In contrast, we detected a negative but weak association between degradation and seroprevalence overall that was strengthened when forest loss occurred the year prior to bat sampling. No bat traits that we investigated interacted with habitat degradation to impact virus outcomes, suggesting observed trends are independent of these traits. Biases in our initial dataset highlight opportunities for future work; prevalence was highly zero-inflated, and seroprevalence was dominated by <em>Desmodus rotundus</em> and rabies virus. These findings and subsequent analyses will improve our understanding of how global change affects host–pathogen dynamics.</p>

Sample based prevalence data complementing the European Union One Health 2022 Zoonoses Report - the United Kingdom (Northern Ireland)

<p>This dataset contains monitoring data on zoonoses and zoonotic agents under the Directive 2003/99/EC. This Directive requires Member Sates (MSs) to collect, evaluate and report data on zoonoses and zoonotic agents. MSs can also report monitoring data and information on some other pathogenic microbiological agents in foodstuffs. Relevant EU legislation: Commission Regulation (EC) No 2073/2005,Commission Regulation (EC) No 1441/2007, Commission Regulation (EU) No 1086/2011, Commission Regulation (EU) No 209/2013, Commission Regulation(EU) No 217/2014.</p>

Sample based prevalence data complementing the European Union One Health 2022 Zoonoses Report - Croatia

<p>This dataset contains monitoring data on zoonoses and zoonotic agents under the Directive 2003/99/EC. This Directive requires Member Sates (MSs) to collect, evaluate and report data on zoonoses and zoonotic agents. MSs can also report monitoring data and information on some other pathogenic microbiological agents in foodstuffs. Relevant EU legislation: Commission Regulation (EC) No 2073/2005,Commission Regulation (EC) No 1441/2007, Commission Regulation (EU) No 1086/2011, Commission Regulation (EU) No 209/2013, Commission Regulation(EU) No 217/2014.</p>

Sample based prevalence data complementing the European Union One Health 2022 Zoonoses Report - Ireland

Sample based prevalence data complementing the European Union One Health 2022 Zoonoses Report - Sweden

Sample based prevalence data complementing the European Union One Health 2022 Zoonoses Report - Norway

Sample based prevalence data complementing the European Union One Health 2022 Zoonoses Report - Luxembourg

Sample based prevalence data complementing the European Union One Health 2022 Zoonoses Report - Finland

Prevalence data complementing the European Union One Health 2022 Zoonoses Report

<p>This dataset contains monitoring data on zoonoses and zoonotic agents under the Directive 2003/99/EC. This Directive requires Member Sates (MSs) to collect, evaluate and report data on zoonoses and zoonotic agents. MSs can also report monitoring data and information on some other pathogenic microbiological agents in foodstuffs. Relevant EU legislation is: Commission Regulation (EC) No 2073/2005,Commission Regulation (EC) No 1441/2007, Commission Regulation (EU) No 1086/2011, Commission Regulation (EU) No 209/2013, Commission Regulation(EU) No 217/2014.</p>

opencc-zeroDec 2023View details →

Prevalence and characteristics of long COVID-19 in Jordan: A cross sectional survey

<p>Early in the pandemic, the spread of the emerging virus SARS-CoV-2 was causing mild illness lasting less than two weeks for most people, with a small proportion of people developing serious illness or death. However, as the pandemic progressed, many people reported suffering from symptoms for weeks or months after their initial infection. Persistence of COVID-19 symptoms beyond one month, or what is known as long COVID-19, is recognized as a risk of acute infection. Up to date, information on long COVID-19 among Jordanian patients has not been reported. Therefore, we sought to conduct this cross-sectional study utilizing a self-administered survey. The survey asks a series of questions regarding participant demographics, long COVID-19 symptoms, information about pre-existing medical history, supplements, vaccination history, and symptoms recorded after vaccination. Chi square analysis was conducted on 990 responders, and the results showed a significant correlation (P<0.05) between long COVID-19 syndrome and age, obesity, chronic illness, vitamin D intake, number of times infected by COVID-19, number of COVID-19 symptoms and whether the infection was pre or post vaccination. The long-term symptoms most enriched in those with long COVID-19 were tinnitus (73.4%), concentration problems (68.6%) and muscle and joint ache (68.3%). A binomial logistic regression analysis was done to explore the predictors of long COVID-19 and found that age 18-45, marital status, vitamin D, number of COVID-19 symptoms and signs after vaccination are positive predictors of long COVID-19, while zinc intake is a negative predictor. Although further studies on long-term persistence of symptoms are needed, the present study provides a baseline that allows us to understand the frequency and nature of long COVID-19 among Jordanians.</p>

opencc-by-4.0Feb 2024View details →

Temporal increase in ticks and pathogen prevalence in the small mammal part of the Lyme disease cycle in northern Europe

<p>Data and Scripts for our research article "Temporal increase in ticks and pathogen prevalence in the small mammal part of the enzootic Lyme disease cycle in northern Europe"</p>

opencc-by-4.0Jan 2024View details →

Prevalence of Listeria monocytogenes and other Listeria species in fish, fish products and fish processing environment: A systematic review and meta-analysis

<p>Dane wykorzytsane w publikajci "Prevalence of <em>Listeria monocytogenes</em> and other <em>Listeria</em> species in fish, fish products and fish processing environment: A systematic review and meta-analysis" . Dane obejmują wyniki surowe z baz artykułów, dane wykorzystane do wykonania metaanalizy oraz wyniki surowe uzyskane po przeprowadzaniu metaanalizy</p>

opencc-by-4.0Jul 2022View details →

Figure 1. A in Prevalence and density of Demodex mites (Acari: Demodecidae) in patients with seborrheic dermatitis

Figure 1. A. Demodex spp. (at 40x magnification), B. D. folliculorum (at 40x magnification.

Lack of shared neoantigens in prevalent mutations in cancer

<p><span>Tumors are mostly characterized by genetic instability, as result of mutations in surveillance mechanisms, such as DNA damage checkpoint, DNA repair machinery and mitotic checkpoint. Defect in one or more of these mechanisms causes additive accumulation of mutations. Some of these mutations are drivers of transformation and are positively selected during the evolution of the cancer, giving a growth advantage on the cancer cells. If such mutations would result in mutated neoantigens, these could be actionable targets for cancer vaccines and/or adoptive cell therapies. However, the results of the present analysis show, for the first time, that the most prevalent mutations identified in human cancers do not express mutated neoantigens. The hypothesis is that this is the result of the selection operated by the immune system in the very early stages of tumor development. At that stage, the tumor cells characterized by mutations giving rise to highly antigenic non-self mutated neoantigens would be efficiently targeted and eliminated. Consequently, the outgrowing tumor cells cannot be controlled by the immune system, with an ultimate growth advantage to form large tumors embedded in an immunosuppressive tumor microenvironment (TME). The outcome of such a negative selection operated by the immune system is that the development of off-the-shelf vaccines, based on shared mutated neoantigens, does not seem to be at hand.</span></p>

opencc-zeroMar 2024View details →

Data from: Effects of microclimate on disease prevalence across an urbanization gradient

<p>Increased temperatures associated with urbanization (the "urban heat island" effect) have been shown to impact a wide range of traits across diverse taxa. At the same time, climatic conditions vary at fine spatial scales within habitats due to factors including shade from shrubs, trees, and built structures. Patches of shade may function as microclimate refugia that allow species to occur in habitats where high temperatures and/or exposure to ultraviolet radiation would otherwise be prohibitive. However, the importance of shaded microhabitats for interactions between species across urbanized landscapes remains poorly understood. Weedy plants and their foliar pathogens are a tractable system for studying how multiple scales of climatic variation influence infection prevalence. Powdery mildew pathogens are particularly well suited to this work, as these fungi can be visibly diagnosed on leaf surfaces. We studied the effects of shaded microclimates on rates of powdery mildew infection on <em>Plantago</em> host species in (1) "pandemic pivot" surveys in which undergraduate students recorded shade and infection status of thousands of plants along road verges in urban and suburban residential neighborhoods, (2) monthly surveys of plant populations in 22 parks along an urbanization gradient, and (3) a manipulative field experiment directly testing effects of shade on growth and transmission of powdery mildew. Together, our field survey results show strong positive effects of shade on mildew infection in wild <em>Plantago</em> populations across urban, suburban, and rural habitats. Our experiment suggests that this relationship is causal, where microclimate conditions associated with shade promote pathogen growth. Overall, infection prevalence increased with urbanization despite a negative association between urbanization and tree cover at the landscape scale. These findings highlight the importance of taking microclimate heterogeneity into account when establishing links between macroclimate or land use context and the prevalence of disease.</p>

opencc-zeroMar 2024View details →

Data from: Variation in prevalence and intensity of macroparasites in moose and their interactions with winter tick load in eastern Canada

<p>Wild animals are infected with a large diversity and abundance of parasites that can affect their behavior, growth, body condition, and ultimately their survival. Although the adverse effects of parasites and the mechanisms involved in the interactions between a host and its parasites are generally well studied, much less is known about the additive or synergistic effects of multiple parasite species on a host. Moose populations in eastern Canada are infected by several species of endoparasites. In the last decades, the intensity of infestations by winter ticks, an ectoparasite, on moose have increased as a result of increased moose densities and favorable weather conditions that benefit winter tick survival. We aimed to document the diversity, intensity, prevalence, and distribution of different parasite species of moose in southern Quebec, Canada. We then evaluated the potential interaction between winter tick and endoparasites of moose, and we evaluated the effect of the simultaneous presence of ticks and endoparasites on moose body condition. To do so, we collected organs to identify and count endoparasite species, estimate winter tick abundance, and measure subcutaneous fat thickness from 174 hunted moose in fall 2019 in 8 regions of Quebec. Our results showed that the prevalence and intensity of winter tick and gastrointestinal parasites differed among regions, as well as the prevalence of the heart parasite <em>Taenia krabbei</em> and the intensity of lung parasite <em>Echinoccocus granulosus</em>. Moose body condition, however, was not influenced by the simultaneous presence of winter tick and endoparasites. The documentation of the interactive effects of multiple parasite species on a host is fundamental given that future environmental conditions in temperate climate will favor the reproduction, development, and survival of several parasite species, which could affect parasite diversity and abundance in the environment and modify host-parasite dynamics.</p>