Find research datasets worth reusing

opencc-by-4.0Nov 2020View details →

African Swine Fever Worldwide Epidemiology Data - OIE Webscrape example - Geocoded using Google API and Manual

Example African Swine Fever dataset generated by programs described in following publication  Title: Web-scraping programmatic techniques in aggregating difficult to access OIE WAHIS animal disease outbreak information; using African Swine Fever in Europe as an example. Short running title: Methods for web-scraping OIE WAHIS data. Abstract: This study describes and makes available new methods for acquiring difficult to access, publicly available, disease surveillance data. It uses World Organisation for Animal Heath (OIE) data on African Swine Fever (ASF) outbreaks in Belarus and its neighbouring European countries to showcase the importance of adequate disease surveillance data to inform decision-making. The data acquired from these methods allow for large-scale, geospatial outbreak mapping and summary statistics of any terrestrial disease listed on the OIE World Animal Health Information System (WAHIS) database. These techniques will make important epidemiological data more accessible to the scientific community and aid in gaining further insight into the occurrence and spread of OIE listed diseases in a timely manner, fulfilling an important function of disease surveillance.

opencc-by-4.0Dec 2023View details →

Asaia spp. accelerate development of the yellow fever mosquito, Aedes aegypti, via interactions with the vertically transmitted larval microbiome

Background: Aedes aegypti mosquitoes are the primary vectors of yellow fever, dengue, chikungunya and Zika virus. Control programs primarily rely on insecticide application, which encounter challenges related to efficacy and resistance evolution. Alternative strategies, such as the sterile insect technique, highly depend on efficient mass-rearing of healthy insects prior to mass release. Based on effects seen in other mosquito species, we tested the hypothesis that acetic acid bacteria of the Asaia genus are mutualists for developing Ae. aegypti larvae. We tested for beneficial interactions across three Asaia species and whether Asaia inoculation benefited both axenic and conventionally reared larvae. To better understand the underlying mechanisms, we characterized the larval microbiome using culture-based methods and 16S rRNA gene amplicon sequencing. Results: Even though Asaia bacteria were transient members of the gut community in conventionally reared insects, two Asaia species accelerated larval development relative to controls. Despite their transient nature, the two mutualist Asaia species had lasting impacts on the larval microbiome, mostly by altering the relative abundance of the most dominant bacteria genera Klebsiella and Pseudomonas and other minor components. Axenic larvae that were inoculated with Asaia were dominated by this group, but always exhibited slower development than conventionally reared insects. Conclusions: These results reveal Asaia as a poor mutualist for Ae. aegypti, with its positive effect on the host mediated by interactions with other bacteria. A practical application of Asaia for improving mass-rearing efficiency results from the acceleration of development time to pupation by a day.

opencc-by-4.0Dec 2021View details →

Cellular and Humoral Immune Responses after Immunisation with Low Virulent African Swine Fever Virus in the Large White Inbred Babraham Line and Outbred Domestic Pigs

Raw data for manuscript. Contains temperature, clinical scores, qPCR, blood cell numbers and immune responses over time for two groups of pigs immunised with low virulent African swine fever virus and challenged with highly virulent virus. Data for each panel or figure is displayed on a separate worksheet in the file. The readme worksheet contains a brief description of each figure. The majority of data is displayed in an XY table format, with the number of days post immunisation with low virulent virus indicated.

opencc-by-4.0Apr 2024View details →

Supplementary dataset to publication: Approaching the complexity of Crimean-Congo hemorrhagic fever virus serology: a study in swine

For the detection of anti-CCHFV antibodies in swine, we established a swine-specific in-house ELISA, indirect immunofluorescence assay and a virus neutralization test. Uploaded data contains sample performance in each test. Samples used in this study include swine serum samples from Germany and Spain.

opencc-by-4.0Jul 2024View details →

Continuous phylogeography analysis of Rift Valley fever virus (RVFV) in Africa and the Arabian Peninsula

Spatiotemporal-explicit Bayesian phylogenetic trees and MCMC log files for Rift Valley fever virus large, medium and non-structural genetic sequences generated by BEAST v1.10 <ol> <li>Log files (logs.zip)</li> <li>Tree files (trees.zip)</li> </ol>

opencc-by-4.0Aug 2019View details →

Expansion of coccidioidomycosis (Valley fever) endemic regions in the United States in response to climate change: projections of disease incidence

This file contains estimations of coccidioidomycosis (Valley fever) incidence data in cases per 100,000 population per year for the contemporary time period and projections throughout the 21st century in response to RCP4.5 and RCP8.5 climate scenarios, associated with the publication: Gorris, M. E., Treseder, K. K., Zender, C. S., and Randerson, J. T. (2019). Expansion of coccidioidomycosis endemic regions in the United States in response to climate change. GeoHealth.  The data is reported for each county in the conterminous US with its associated FIPS code (Column 1), county name (Column 2), state FIPS code (Column 3), and state name (Column 4). Column 5 contains the estimation of mean annual Valley fever incidence averaged from 2000-2015. Column 6-8 contain the estimations of mean annual Valley fever incidence for the 11-year averages surrounding years 2035, 2065, and 2095 for RCP4.5 climate scenario. Likewise, Columns 9-11 contain the estimations of mean annual Valley fever incidence for the 11-year averages surrounding years 2035, 2065, and 2095 for the RCP8.5 climate scenario.  Details about how the incidence data was calculated may be read in the Methods subsection of the paper under "Modeling of current and future mean annual Valley fever incidence". The data provided here was used to create Figure 7 and Supporting Information Figure S5. Counties that have non-zero incidence are considered endemic by our climate-constrained niche model, so this data may also be used to create portions of Figures 3, 4, and S3.

opencc-by-4.0Oct 2020View details →

Reanalysis of the 2000 Rift Valley fever outbreak in Southwestern Arabia

The first documented Rift Valley hemorrhagic fever outbreak in the Arabian Peninsula occurred in northwestern Yemen and southwestern Saudi Arabia from August 2000 to September 2001. This Rift Valley fever outbreak is unique because the virus was introduced into Arabia during or after the 1997-1998 East African outbreak and before August 2000, either by wind-blown infected mosquitos or by infected animals, both from East Africa. A wet period from August 2000 into 2001 resulted in a large number of amplification vector mosquitoes, these mosquitos fed on infected animals, and the outbreak occurred. More than 1,500 people were diagnosed with the disease, at least 215 died, and widespread losses of domestic animals were reported. Using a combination of satellite data products, including 2 x 2 m digital elevation images derived from commercial satellite data, we show rainfall and potential areas of inundation or water impoundment were favorable for the 2000 outbreak. However, favorable conditions for subsequent outbreaks were present in 2007 and 2013, and very favorable conditions were also present in 2016-2018. The lack of subsequent Rift Valley fever outbreaks in this area suggests that Rift Valley fever has not been established in mosquito species in Southwest Arabia, or that strict animal import inspection and quarantine procedures, medical and veterinary surveillance, and mosquito control efforts put in place in Saudi Arabia following the 2000 outbreak have been successful. Any area with Rift Valley fever amplification vector mosquitos present is a potential outbreak area unless strict animal import inspection and quarantine procedures are in place.

opencc-by-4.0Jan 2022View details →

Twenty four hour continuous tympanic temperature recordings in healthy volunteers and patients presented with Undifferentiated fever

Twenty-four-hour continuous tympanic temperature recordings were obtained using high-accuracy tympanic probes placed at the auditory canal. Measurements were recorded at one-minute intervals over a 24-hour period, yielding 1,440 data points per subject and enabling high-resolution temporal profiling of body temperature. In Phase I, a total of 100 healthy adult volunteers were recruited to establish baseline circadian thermoregulatory patterns. These recordings were stratified by gender to examine physiological variability among individuals without fever. In Phase II, 184 adult patients presenting with undifferentiated fever of seven or more days’ duration were enrolled. Based on clinical examination and laboratory confirmation, the temperature profiles were analysed across a range of conditions, including tuberculosis, non-tubercular bacterial infections, dengue fever, malaria, leptospirosis, pyogenic sepsis, thyroiditis, malignancies, and non-infectious inflammatory diseases. This dual-phase dataset facilitated a comparative analysis between normative and pathological thermoregulatory patterns, supporting the development of classification models for diagnostic differentiation.

opencc-by-4.0Apr 2024View details →

Supplementary material from the study on survival of African swine fever virus in feed, bedding materials and mechanical vectors, and their potential role in virus transmission

Supplementary material from the experimental studies developed to analyse the survival of African swine fever virus in feed, bedding materials and mechanical vectors, and their potential role in virus transmission.

opencc-by-4.0Mar 2015View details →

Fig. 2. Kimura 2 in First record of a spotted fever group Rickettsia sp. and Theileria annulata in Hyalomma dromedarii (Acari: Ixodidae) ticks in the United Arab Emirates

Fig. 2. Kimura 2-parameter distance Neighbor Joining (NJ) tree of 12 nucleotide sequences belonging to the genus Theileria. Codes denote the accession numbers of NCBI GenBank database. * Sequence from Al-Ain, UAE. Numbers next to branches are the percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) (Felsenstein 1985).

opencc-by-4.0Aug 2017View details →

Fig. 2 in Comparison of natural and artificial odor lures for nilgai (Boselaphus tragocamelus) and white-tailed deer (Odocoileus virginianus) in South Texas: Developing treatment for cattle fever tick eradication

Fig. 2. Locations of nilgai lure transects (red bars) at the Santa Rosa Ranch near Riviera, TX. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

opencc-by-4.0Aug 2017View details →

Fig. 5 in Comparison of natural and artificial odor lures for nilgai (Boselaphus tragocamelus) and white-tailed deer (Odocoileus virginianus) in South Texas: Developing treatment for cattle fever tick eradication

Fig. 5. Nilgai cow visiting lure site (A) and (B) nilgai bull defecating at offal lure site at the East Foundation's Santa Rosa Ranch, near Riviera, TX.

Figure 6 in Indiscriminate ingestion of entomopathogenic nematodes and their symbiotic bacteria by Aedes aegypti larvae: a novel strategy to control the vector of Chikungunya, dengue and yellow fever

Figure 6. Aedes aegypti larval mortality when exposed to 1000 infective juveniles (IJs) of Heterorhabditis bacteriophora at different depths of water.

Figure 2 in Indiscriminate ingestion of entomopathogenic nematodes and their symbiotic bacteria by Aedes aegypti larvae: a novel strategy to control the vector of Chikungunya, dengue and yellow fever

Figure 2. Susceptibility of Aedes aegypti larvae to different species of EPN. Five 3rd instar larvae exposed to 1000 infective juveniles (IJs) and mortality assessed daily over 3-day period (DPI).

Figure 4 in Indiscriminate ingestion of entomopathogenic nematodes and their symbiotic bacteria by Aedes aegypti larvae: a novel strategy to control the vector of Chikungunya, dengue and yellow fever

Figure 4. Melanization of Heterorhabditis bacteriophora within Aedes aegypti larvae (3rd instar). A melanized H. bacteriophora within dead Ae. aegypti larvae (a), close up picture of melanized nematode upon larval dissection (b), nematodes representing different stages of melanization recovered from one dead Ae. aegypti larvae (c). Arrows indicate melanized nematode within Ae. aegypti larvae.

Figure 7 in Indiscriminate ingestion of entomopathogenic nematodes and their symbiotic bacteria by Aedes aegypti larvae: a novel strategy to control the vector of Chikungunya, dengue and yellow fever

Figure 7. Aedes aegypti larval mortality when exposed to supernatants and cell suspensions of Xenorhabdus nematophila (X. n.) and Photorhabdus laumondii (P. l.) in 24 well plates. Different uppercase or lower letters above error bars indicate statistical significance (Tukey's test p ≤ 0.05).

Figure 3 in Indiscriminate ingestion of entomopathogenic nematodes and their symbiotic bacteria by Aedes aegypti larvae: a novel strategy to control the vector of Chikungunya, dengue and yellow fever

Figure 3. Different stages of Heterorhabditis bacteriophora colonization of Aedes aegypti larvae (3rd instar). H. bacteriophora within larvae at 2-day post inoculation (a), H. bacteriophora emerging out of larvae upon larval dissection at 7-day post inoculation) (b), adult H. bacteriophora within larvae along with large number of infective juveniles (IJs) released from another adult H. bacteriophora (c). Black arrows indicate adult H. bacteriophora, whereas green arrows indicate newly emerged IJs.

openSep 2024View details →

Interferon-induced activation of dendritic cells and monocytes by yellow fever vaccination correlates with early antibody responses

Bulk RNA-seq analysis of sorted subpopulations isolated from PBMC of yellow fever vaccinees from before and 3, 7, 14 and 28 days after vaccination and single cell RNA-seq analysis of sorted DC and monocytes fractions isolated from PBMC of of yellow fever vaccinees from before and 3 and 7 days after vaccination.