Find research datasets worth reusing

Data from: Disease and climate effects on individuals drive post-reintroduction population dynamics of an endangered amphibian

The emergence of novel pathogens often has dramatic negative effects on previously unexposed host populations. Subsequent disease can drive populations and even species to extinction. After establishment in populations, pathogens can continue to affect host dynamics, influencing the success or failure of species recovery efforts. However, quantifying the effect of pathogens on host populations in the wild is challenging because individual hosts and their pathogens are difficult to observe. Here we use long-term mark-recapture data to describe the dynamics of reintroduced populations of an endangered amphibian (Rana sierrae) and evaluate the success of these recovery efforts in the presence of a recently-emerged pathogen, the amphibian chytrid fungus Batrachochytrium dendrobatidis. We find that high B. dendrobatidis infection intensities are associated with increases in frog detectability and reductions in survival. When average infection intensities are high, adults are more likely to gain infections and less likely to lose infections. We also find evidence for intensity-dependent survival, with heavily infected individuals suffering higher mortality. These results highlight the need in disease ecology for probabilistic approaches that account for uncertainty in infection intensity using imperfect observational data. Such approaches can advance the understanding of disease impacts on host population dynamics, and in the current study will improve the effectiveness of species conservation actions.

Data from: A novel approach to wildlife transcriptomics provides evidence of disease-mediated differential expression and changes to the microbiome of amphibian populations

Ranaviruses are responsible for a lethal, emerging infectious disease in amphibians and threaten their populations throughout the world. Despite this, little is known about how amphibian populations respond to ranaviral infection. In the United Kingdom, ranaviruses impact the common frog (Rana temporaria). Extensive public engagement in the study of ranaviruses in the UK has led to the formation of a unique system of field sites containing frog populations of known ranaviral disease history. Within this unique natural field system, we used RNA sequencing (RNA-Seq) to compare the gene expression profiles of R. temporaria populations with a history of ranaviral disease and those without. We have applied a RNA read filtering protocol that incorporates Bloom filters, previously used in clinical settings, to limit the potential for contamination that comes with the use of RNA-Seq in non-laboratory systems. We have identified a suite of 407 transcripts that are differentially expressed between populations of different ranaviral disease history. This suite contains genes with functions related to immunity, development, protein transport and olfactory reception amongst others. A large proportion of potential non-coding RNA transcripts present in our differentially expressed set provides first evidence of a possible role for long non-coding RNA (lncRNA) in amphibian response to viruses. Our read-filtering approach also removed significantly more bacterial reads from libraries generated from postitive disease history populations. Subsequent analysis revealed these bacterial read sets to represent distinct communities of bacterial species, which is suggestive of an interaction between ranavirus and the host microbiome in the wild.

opencc-zeroDec 2015View details →

Data from: Efficacy of a probiotic bacterium to treat bats affected by the disease white-nose syndrome

The management of infectious diseases is an important conservation concern for a growing number of wildlife species. However, effective disease control in wildlife is challenging because feasible management options are often lacking. White-nose syndrome (WNS) is an infectious disease of hibernating bats that currently threatens several North American species with extinction. Currently, no effective treatments exist for WNS. We conducted a laboratory experiment to test the efficacy of treatment with Pseudomonas fluorescens, a bacterium that naturally occurs on bats, to reduce disease severity and improve survival of little brown bats (Myotis lucifugus) exposed to Pseudogymnoacus destructans, the fungal pathogen that causes WNS. Application of the bacteria at the time of P. destructans infection reduced several measures of disease severity and increased survival, whereas bacterial treatment prior to pathogen exposure had no effect on survival and worsened disease severity. Our results suggest that probiotic treatment with Ps. fluorescens has potential for WNS disease management but the timing of application is critical and should coincide with natural exposure of bats to P. destructans. More broadly, these results add to the growing knowledge of how the natural host microbiota can influence disease outcomes.

opencc-zeroDec 2019View details →

Occupational exposure to silica and risk of heart disease: a systematic review with meta-analysis

Objective To search for evidence of the relationship between occupational silica exposure and heart disease. Design A systematic review and meta-analysis. Background Growing evidences suggest a connection between occupational silica exposure and heart disease; however, the link between them is less clear. Data sources PubMed, ScienceDirect, Springer and EMBASE were searched for articles published between 1 January 1995 and 20 June 2019. Articles that investigated the effects of occupational silica exposure on heart disease risk were considered. Study selection We included cohort studies, including prospective, retrospective and retro-prospective studies. Data extraction and synthesis We extracted data by using a piloted data collection form and conducted random-effects meta-analysis and exposure-response analyses. The meta-relative risk (meta-RR), a measure of the average ratio of heart disease rates for those with and without silica exposure, was used as an inverse variance-weighted average of relative risks from the individual studies. The Newcastle-Ottawa Quality assessment Scale about cohort studies was used for study quality assessment. Outcome measure We calculated heart disease risks of pulmonary heart disease, ischaemic heart disease and other heart diseases. Results Twenty cohort articles were included. Results suggest a significant increase of overall heart disease risk (meta-RR = 1.08, 95% CI = 1.03, 1.13). Stronger evidences of association with pulmonary heart disease were found through both categories of heart disease risk estimate (meta-RR = 1.24, 95% CI = 1.08, 1.43) and exposure-response analyses (meta-RR = 1.39, 95% CI = 1.19, 1.62). Moreover, our subgroup analyses revealed that the statistical heterogeneity among studies could be attributed mainly to the diversities of reference group, occupation and study quality score. Conclusions Silica-exposed workers have increased risk of overall heart disease, especially pulmonary heart disease. While further research is needed to better clarify the relationship between occupational silica exposure and ischaemic heart disease.

opencc-zeroJan 2020View details →

Sociality and tattoo skin disease among bottlenose dolphins in Shark Bay, Australia

Social behavior is an important driver of infection dynamics, though identifying the social interactions that foster infectious disease transmission is challenging. Here we examine how social behavior impacts disease transmission in Indo-Pacific bottlenose dolphins (Tursiops aduncus) using an easily identifiable skin disease and social network data. We analyzed tattoo skin disease (TSD) lesions based on photographs collected as part of a 34-year longitudinal study in relation to the sociality of T. aduncus using three metrics (degree, time spent socializing, and time in groups) and network structure, using the k-test. We show that calves with TSD in the second year of life associated more with TSD-positive individuals in the first year of life compared with calves that did not have TSD. Additionally, the network k-test showed that the social network links are epidemiologically relevant for transmission. However, degree, time spent in groups, and time spent socializing were not significantly different between infected and uninfected groups. Our findings indicate that association with infected individuals is predictive of an individual's risk for TSD and that the social association network can serve as a proxy for studying the epidemiology of skin diseases in bottlenose dolphins.

Data from: Tick-borne disease risk in a forest food web

Changes to the community ecology of hosts for zoonotic pathogens, particularly rodents, are likely to influence the emergence and prevalence of zoonotic diseases worldwide. However, the complex interactions between abiotic factors, pathogens, vectors, hosts, and both food resources and predators of hosts are difficult to disentangle. Here we (1) use 19 years of data from six large field plots in southeastern New York to compare the effects of hypothesized drivers of interannual variation in Lyme disease risk, including the abundance of acorns, rodents, and deer, as well as a series of climate variables; and (2) employ landscape epidemiology to explore how variation in predator community structure and forest cover influences spatial variation in the infection prevalence of ticks for the Lyme disease bacterium, Borrelia burgdorferi, and two other important tick-borne pathogens, Anaplasma phagocytophilum and Babesia microti. Acorn-driven increases in the abundance of mice were correlated with a lagged increase in the abundance of questing nymph-stage Ixodes scapularis ticks infected with Lyme disease bacteria. Abundance of white-tailed deer two years prior also correlated with increased density of infected nymphal ticks, although the effect was weak. Density of rodents in the current year was a strong negative predictor of nymph density, apparently because high current abundance of these hosts can remove nymphs from the host-seeking population. Warm, dry spring or winter weather was associated with reduced density of infected nymphs. At the landscape scale, the presence of functionally diverse predator communities or of bobcats, the only obligate carnivore, was associated with reduced infection prevalence of I. scapularis nymphs with all three zoonotic pathogens. In the case of Lyme disease, infection prevalence increased where coyotes were present but smaller predators were displaced or otherwise absent. For all pathogens, infection prevalence was lowest when forest cover within a 1km radius was high. Taken together, our results suggest that a food web perspective including bottom-up and top-down forcing is needed to understand drivers of tick-borne disease risk, a result that may also apply to other rodent-borne zoonoses. Prevention of exposure based on ecological indicators of heightened risk should help protect public health.

Data from: Symbiotic immuno-suppression: is disease susceptibility the price of bleaching resistance?

Accelerating anthropogenic climate change threatens to destroy coral reefs worldwide through the processes of bleaching and disease. These major contributors to coral mortality are both closely linked with thermal stress intensified by anthropogenic climate change. Disease outbreaks typically follow bleaching events, but a direct positive linkage between bleaching and disease has been debated. By tracking 152 individual coral ramets through the 2014 mass bleaching in a South Florida coral restoration nursery, we revealed a highly significant negative correlation between bleaching and disease in the Caribbean staghorn coral, Acropora cervicornis. To explain these results, we propose a mechanism for transient immunological protection through coral bleaching: Removal of Symbiodinium during bleaching may also temporarily eliminate suppressive symbiont modulation of host immunological function. We contextualize this hypothesis within an ecological perspective in order to generate testable predictions for future investigation.

opencc-zeroMar 2020View details →

Risk factors for cardiovascular disease (CVD) in adults with type 1 diabetes: findings from prospective real-life T1D exchange registry

Context Cardiovascular disease (CVD) is a major cause of mortality in adults with type 1 diabetes. Objective We prospectively evaluated CVD risk factors in a large, contemporary cohort of adults with type 1 diabetes living in the United States. Design Observational study of CVD and CVD risk factors over a median of 5.3 years. Setting The T1D Exchange clinic network. Patients Adults (age ≥18 years) with type 1 diabetes and without known CVD diagnosed before or at enrollment. Main Outcome Measure Associations between CVD risk factors and incident CVD were assessed by multivariable logistic regression. Results The study included 8,727 participants (53% female, 88% non-Hispanic white, median age 33 years [IQR=21, 48], type 1 diabetes duration 16 years [IQR=9, 26]). At enrollment, median HbA1c was 7.6% (66 mmol/mol) [IQR=6.9 (52), 8.6 (70)], 33% used a statin, and 37% used blood pressure medication. Over a mean follow-up of 4.6 years, 325 (3.7%) participants developed incident CVD. Ischemic heart disease was the most common CVD event. Increasing age, BMI, HbA1c, presence of hypertension and dyslipidemia, increasing duration of diabetes, and diabetic nephropathy were associated with increased risk for CVD. There were no significant gender differences in CVD risk. Conclusion HbA1c, hypertension, dyslipidemia and diabetic nephropathy are important risk factors for CVD in adults with type 1 diabetes. A longer follow-up is likely required to assess the impact of other traditional CVD risk factors on incident CVD in the current era.

opencc-zeroDec 2018View details →

Data from: Reciprocal abundance shifts of the intertidal sea stars, Evasterias troschelii and Pisaster ochraceus, following sea star wasting disease

Disease emergence occurs within the context of ecological communities, and disease driven declines in host populations can lead to complex direct and indirect ecological effects. Varying effects of a single disease among multiple susceptible hosts could benefit relatively resistant species. Beginning in 2013, an outbreak of sea star wasting disease (SSWD) led to population declines of many sea star species along the west coast of North America. Through field surveys and laboratory experiments, we investigated how and why the relative abundances of two co-occurring sea star species, Evasterias troschelii and Pisaster ochraceus, shifted during the ongoing wasting epidemic in Burrard Inlet, British Columbia, Canada. We hypothesized that Evasterias is competitively inferior to Pisaster but more resistant to SSWD. Thus, we predicted that SSWD-induced declines of Pisaster could mitigate the negative effects of SSWD on Evasterias, as the latter would experience competitive release. We document shifts in sea star abundance from 2007-2017: Pisaster abundance and mean size declined during the outbreak, while Evasterias abundance increased from relatively rare to numerically dominant within the intertidal. When exposed to symptomatic sea stars, Pisaster and Evasterias both showed signs of SSWD, but transmission and susceptibility was lower in Evasterias. Despite diet overlap documented in our field surveys, Evasterias was not outcompeted by Pisaster in laboratory trails conducted with the relatively small Pisaster available after the outbreak. Interference competition with larger Pisaster, or prey exploitation by Pisaster during summer when Evasterias is primarily subtidal, may explain the rarity of Evasterias prior to Pisaster declines. Our results suggest that indirect effects mediated by competition can mask some of the direct effects of disease outbreaks, and the combination of direct and indirect effects will determine the restructuring of a community after disturbance.

opencc-zeroDec 2015View details →

Data from: Species decline under nitrogen fertilization increases community-level competence of fungal diseases

The artificial fertilization of soils can alter the structure of natural plant communities and exacerbate pathogen emergence and transmission. Although the direct effects of fertilization on disease resistance in plants have received some research attention, its indirect effects of altered community structure on the severity of fungal disease infection remain largely uninvestigated. We designed manipulation experiments in natural assemblages of Tibetan alpine meadow vegetation along a nitrogen-fertilization gradient over 5 years to compare the relative importance of direct and indirect effects of fertilization on foliar fungal infections at the community level. We found that species with lower proneness to pathogens were more likely to be extirpated following fertilization, such that community-level competence of disease, and thus community pathogen load, increased with the intensity of fertilization. The amount of nitrogen added (direct effect) and community disease competence (indirect effect) provided the most parsimonious combination of parameters explaining the variation in disease severity. Our experiment provides a mechanistic explanation for the dilution effect in fertilized, natural assemblages in a highly specific pathogen–host system, and thus insights into the consequences of human ecosystem modifications on the dynamics of infectious diseases.

opencc-zeroJun 2021View details →

A blinded, controlled trial of objective measurement in Parkinson's disease

Medical conditions with effective therapies are usually managed with objective measurement and therapeutic targets. Parkinson's disease has effective therapies, but continuous objective measurement has only recently become available. This blinded, controlled study examined whether management of Parkinson's disease was improved when clinical assessment and therapeutic decisions were aided by objective measurement. The primary endpoint was improvement in the Movement Disorder Society-United Parkinson's Disease Rating Scale's (MDS-UPDRS) Total Score. In one arm, objective measurement assisted doctors to alter therapy over successive visits until objective measurement scores were in target. Patients in the other arm were conventionally assessed and therapies were changed until judged optimal. There were 75 subjects in the objective measurement arm and 79 in the arm with conventional assessment and treatment. There were statistically significant improvements in the moderate clinically meaningful range in the MDS-UPDRS Total, III, IV scales in the arm using objective measurement, but not in the conventionally treated arm. These findings show that global motor and non-motor disability is improved when the management of Parkinson's disease is assisted by objective measurement.

opencc-zeroFeb 2020View details →

Integrated genome-wide investigations of the housefly, a global vector of diseases reveal unique dispersal patterns and bacterial communities across farms

Background:Houseflies (Musca domesticaL.) live in intimate association with numerous microorganisms and is a vector of human pathogens. In temperate areas, houseflies willoverwinter in environments constructed by humans and recolonize surrounding areas in early summer. However, the dispersal patterns and associated bacteria across season and location are unclear.We used genotyping-by-sequencing (GBS) for the simultaneous identification and genotyping of thousands of Single Nucleotide Polymorphisms (SNPs) to establish dispersal patterns of houseflies across farms. Secondly, we used16S rRNA gene amplicon sequencing to establish the variation and association between bacterial communities and the housefly across farms. Results: Using GBS we identified 18,000 SNPs across 400 individualssampled within and between 11 dairy farms in Denmark. There was evidence for sub-structuring of Danish housefly populations and with genetic structure that differed across season and sex. Further, there was a strong isolation by distance (IBD) effect, but with large variation suggesting that other hidden geographic barriers are important. Large individual variations were observed in the community structure of the microbiome and it was found to be dependent on location, sex, and collection time. Furthermore, the relative prevalence of putative pathogens was highly dependent on location and collection time. Conclusion:We were able to identify SNPs for the determination of the spatiotemporal housefly genetic structure, and to establish the variation and association between bacterial communities and the housefly across farms using novel next‐generation sequencing (NGS)techniques. These results are important for disease prevention given the fine-scale population structure and IBD for the housefly, and that individual houseflies carry location specific bacteria including putative pathogens.

openeclipse-1.0Feb 2015View details →

Source code and datasets used to link new waves of plague outbreaks in medieval Europe to climate fluctuations affecting the reservoirs of the disease in Asia.

The zipfile contains the project directory which includes the source code and datasets used in the paper on Climate-driven introduction of the Black Death and successive plague reintroductions into Europe, as published in Proceedings of the National Academy of Sciences (PNAS). Access the paper at http://www.doi.org/pnas.1412887112 If you are not familiar with Clojure, Leiningen, and its project directory format, see http://clojure.org/getting_started for one of the IDE's to run the clojure code in, and use http://leiningen.org/ as the project / dependency manager.

opencc-by-4.0Oct 2015View details →

Mouse and Human Co-expression maps and supplementary material for: "A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels"

Co-expression maps of the human and mouse species derived from microarray data for the first release of the GeneFriend tool. The two co-expression maps  have been compared in order to discern similarities and differences between the two species. The results have been described in the manuscript titled: "A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels". The supplementary material of the manuscript have also been included in this repository.

opencc-by-4.0Aug 2016View details →

Supplementary Dataset S8 for publication "Universality in human cortical folding in health and disease"

The data sources and method of extracting the data are described in the publication "Universality in human cortical folding in health and disease". PNAS 2016 2019 update: The matlab code for extraction of relevant variables from Freesurfer subjects is now published on <a href="https://doi.org/10.5281/zenodo.3608675">Zenodo</a> and <a href="https://github.com/cnnp-lab/CorticalFoldingAnalysisTools">Github</a>.

opencc-by-4.0Feb 2017View details →

Analysis of gene expression in autoimmune and autoinflammatory diseases using GSEA

This dataset contains the results of gene set enrichment analysis (GSEA) of gene expression in the studied diseases. The archive is organized in folders according the GEO accessions for the raw data (see table 1 of the main article). If multiple diseases were studied within one GEO data series, GSEA was performed for each disease separately. Healthy subject data included in each data series were used as reference. For example "GSE3365.IBD" folder contains GSEA for Crohn's disease (CD) and ulcerative colitis (US). The "results" folder in "GSE3365.IBD" contains two subfolders "GSE3365CDvcHC" and "GSE3365UCvcHC", respectively. The results can be browsed with "index.html" files located in each subfolder.

opencc-by-4.0Feb 2017View details →

Figure 1. from: Acoustic biomarkers of Chronic Obstructive Lung Disease - Research Ideas and Outcomes 2: e9173 (11 May 2016) https://doi.org/10.3897/rio.2.e9173

Figure 1. - Poster as it was presented at the conference. Please see text for details.

opencc-by-4.0Sep 2016View details →

Dataset for Article: "Citizen Science Provides a Reliable and Scalable Tool to Track Disease-Carrying Mosquitoes"

This is the dataset used for the analysis in Citizen Science Provides a Reliable and Scalable Tool to Track Disease-Carrying Mosquitoes, by John R.B. Palmer, Aitana Oltra, Francisco Collantes, Juan Antonio Delgado, Javier Lucientes, Sarah Delacour, Mikel Bengoa, Roger Eritja, and Frederic Bartumeus. Copyright &copy; 2017 John R.B. Palmer, Aitana Oltra, Francisco Collantes, Juan Antonio Delgado, Javier Lucientes, Sarah Delacour, Mikel Bengoa, Roger Eritja, and Frederic Bartumeus. Dataset for Article: "Citizen Science Provides a Reliable and Scalable Tool to Track Disease-Carrying Mosquitoes" by John R.B. Palmer, Aitana Oltra, Francisco Collantes, Juan Antonio Delgado, Javier Lucientes, Sarah Delacour, Mikel Bengoa, Roger Eritja, and Frederic Bartumeus is licensed under a Creative Commons Attribution 4.0 International License.

opencc-by-4.0May 2024View details →

miRNA counts identified by RNA seq in the caudate nucleus of patients neuropathologically diagnosed with late-onset Alzheimer's disease (non-carriers and carriers of intermediate expansions in the HTT gene) and healthy subjects.

These data include the raw miRNA counts identified by RNA-seq in post mortem caudate nucleus samples. Samples with identifier A belong to patients with a neuropathological diagnosis of late-onset Alzheimer's disease. Group B samples belong to patients with the same neuropathological diagnosis, but carrying CAG expansions in the intermediate range (27-35 CAG) in the HTT gene. Finally, group C samples belong to healthy subjects without neuropathological diagnosis.