Find research datasets worth reusing

opencc-by-4.0Jul 2020View details →

Fig. 1 in Disease reservoirs threaten the recently rediscovered Podocarpus Stubfoot Toad (Atelopus podocarpus)

Fig. 1. The Podocarpus Stubfoot Toad (Atelopus podocarpus) was rediscovered along a single stream in Yacuri National Park (Ecuador) in 2016, after having been presumed extinct in the years following the last previous sighting in 1994. Photo by Phil Jervis.

opencc-by-4.0Sep 2021View details →

Fig. 1 in Effects of relative humidity on the vector of rose rosette disease, Phyllocoptes fructiphilus (Eriophyidae), and incidence of disease symptoms

Fig. 1. Mean (± SE) number of Phyllocoptes fructiphilus under various relative humidity regimes (A) by wk and (B) for the duration of the experiment. The same letters within a wk afer infestation or bars are not significantly different (ANOVA followed by Tukey's HSD test; α = 0.05). Where no differences were observed, no letters are included.

opencc-by-4.0Sep 2021View details →

Fig. 2 in Effects of relative humidity on the vector of rose rosette disease, Phyllocoptes fructiphilus (Eriophyidae), and incidence of disease symptoms

Fig. 2. Mean (± SE) (A) proportion of rose rosette disease symptomatic terminals and (B) value of the Horsfall-Barratt scale on the severity of rose rosette disease. The same letters within a wk afer infestation are not significantly different (ANOVA followed by Tukey's HSD test; α = 0.05). Where no differences were observed, no letters are included.

opencc-by-4.0Dec 2021View details →

Fig. 1 in The raccoon dog (Nyctereutes procyonoides) as a reservoir of zoonotic diseases in Denmark

Fig. 1. Map of Denmark showing the origin of the collected raccoon dogs by county. The colour coding shows differences in the number of raccoon dogs collected. (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 2021View details →

Fig. 1 in Reptile vector-borne diseases of zoonotic concern

Fig. 1. Arthropod vectors associated to reptiles represented by a Podarcis siculus lizard and Tarentola mauritanica gecko and zoonotic pathogens they may transmit. a) Ixodes ricinus tick larva, b) Ophionyssus natricis mite, c) Sergentomyia minuta sand fly, d) Aedes albopictus mosquito. Red lines represent high importance role of transmission, orange line represents medium importance role of transmission, gray line represents mechanical vector and green line represents transmission of nonpathogenic zoonotic microorganisms. Dashed lines represent neglectable knowledge on actual role of vector. (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 2021View details →

Fig. 2 in Reptile vector-borne diseases of zoonotic concern

Fig. 2. Arthropod vectors that may feed on reptiles. a) Ixodes ricinus larva on Podarcis siculus lizard being collected with tweezers, b) Neotrombicula autumnalis larvae mites on Podarcis siculus lizard, c) female Sergentomyia minuta phlebotomine sand fly, d) Aedes albopictus mosquito.

Fig. 3 in The threat of pesticide and disease co-exposure to managed and wild bee larvae

Fig. 3. Pesticide research bias across bee genera depending on pesticide type based on Web of Science searches. The number of studies per search term is indicated for each genus with at least 10 studies across search terms; Understudied is a cumulative group including genera which contain less than 10 studies; Unexplored is a cumulative group including genera which have no published papers for any pesticide exposure category. Warmer colours are used to indicate a higher number of studies related to a genus for the corresponding pesticide search term, while colder colours indicate a lower number of studies found. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 4 in The threat of pesticide and disease co-exposure to managed and wild bee larvae

Fig. 4. Brood pathogens studies per bee genera found from Web of Science searches using search terms "brood disease", "brood pathogen", "brood virus", "larvae disease", "larvae pathogen" and "larvae virus" across bee genera. Red squares indicate that a pathogen on the x-axis has been found to infect at least one species in the bee genus corresponding to its position in the phylogeny shown on the y-axis; yellow squares indicate that the pathogen on the x-axis has been found in individuals from at least one species in the genus on the y-axis but no symptoms were reported in the studies; dark grey squares indicate that the pathogen on the x-axis has been tested for in at least one species in the genus corresponding on the yaxis, however has not been found; white squares indicate that the searches found no studies where any bee species of the genus on the y-axis were tested for in the corresponding pathogens on the x-axis. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2 in The threat of pesticide and disease co-exposure to managed and wild bee larvae

Fig. 2. Proportion of results per search term across bee genera on the Web of Science search engine (n = the total number of studies corresponding to each search term). Search terms related to brood disease (A) and pesticide exposure (B) are both compared to species diversity at the genus level. Genera with less than 5 studies in any brood disease search term (A) and less than 10 studies across any pesticide exposure search term (B) have been classified as 'Understudied' (brown) and grouped. Genera with no studies related to any brood disease search term (A) and no studies related to any pesticide exposure search term (B) have been classified as 'Unexplored' (grey) and grouped. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 1 in The threat of pesticide and disease co-exposure to managed and wild bee larvae

Fig. 1. Flowers contaminated with brood pathogens and pesticides can lead to simultaneous exposure to pesticides and brood pathogens from flowers in adult foraging bees (A). This leads to brood being co-exposed to the stressors via food provisioning (B). Pesticides may increase larval mortality from brood infections directly through compromised immunocompetence (C), and/or indirectly through manipulating microbial communities and compromising food provisions from adult bees (D) (Icons8, 2022).

Altered T-cell Reactivity to β-amyloid-related Antigens in Early Alzheimer's Disease

The code generated during this study is available at this online repository with free access. Further information and requests for resources should be directed to and will be fulfilled by the Lead Contact, Dr. Christoph Gericke (christoph.gericke@irem.uzh.ch).

Fig. 1 in Applying a modified streamlined disease risk analysis framework to a platypus conservation translocation, with special consideration for the conservation of ecto- and endoparasites

Fig. 1. An outline of how parasite conservation can be considered in translocation planning, reproduced from Carlson et al. (2020).

opencc-by-4.0Feb 2021View details →

Infectious disease dataset

This dataset contains 12090+ of unique diseases and 600 different symptoms. Each of these disease contains a different amount of symptoms while a disease have less amount of symptoms the field will be a null value. This dataset contains a total of 17 columns. Disease: The disease name Symptom_1: The first symptom of the disease Symptom_2: The second symptom of the disease Symptom_3: The third symptom of the disease Symptom_4: The fourth symptom of the disease Symptom_5: The fifth symptom of the disease Symptom_6: The sixth symptom of the disease Symptom_7: The seventh symptom of the disease Symptom_8: The eighth symptom of the disease Symptom_9: The ninth symptom of the disease Symptom_10: The tenth symptom of the disease Symptom_11: The eleventh symptom of the disease Symptom_12: The twelfth symptom of the disease Symptom_13: The thirteenth symptom of the disease Symptom_14: The fourteenth symptom of the disease Symptom_15: The fifteenth symptom of the disease Symptom_16: The sixteenth symptom of the disease Symptom_17: The seventeenth symptom of the disease

opencc-by-4.0Jul 2024View details →

Spatiotemporal dysregulation of neuron-glia related genes and pro-/anti-inflammatory miRNAs in the 5xFAD mouse model of Alzheimer's disease - Supplementary data

Supplementary Table 1.  Gene expression profile  by RT-qPCR analysis revealed no significant differences when simultaneously considering the genotype (WT/5xFAD), age (6/9 months) and brain region (HPC, hippocampus/PFC, prefrontal cortex).  Supplementary Table 2.  miRNA-target table for the Analyzed microRNAs and targets selected for this study. Obtained in the online platform https://www.mirnet.ca/ Supplementary Table 3.  Node table for the analyzed microRNAs and targets selected for this study. We only considered miRNAs and/or targets with a node degree of at least 2. Obtained in the online platform https://www.mirnet.ca/ Supplementary Table 4.  Bivariate Pearson’s correlation coefficients and respective p-values obtained between all miRNAs and genes. Supplementary Table 5.   List of microRNAs analyzed by RT-qPCR and their primer sequences. Supplementary Table 6.  List of genes and respective primer sequences used for mRNA analysis by RT-qPCR. Supplementary Table 7.  Raw data used for correlational analysis in hippocampus (HPC) and prefrontal cortex (PFC) using the cor function in RStudio software.

Analyses of metabolite profiling of Drosophila Parkinson's Disease model for identifying novel glial-based therapeutic targets

Analysis for genetic screening and metabolomics identify glial adenosine metabolism as a therapeutic target in Parkinson’s disease This project contains the analysis of metabolite abundance measurements obtained with four different liquid chromatography mass spectrometry methods of synuclein expressing or control or fly brains in a wilde type or Adk1 knockout background.   <div> <h2>Table of contents</h2> <a href="https://github.com/jravilap/Olsen_Analyses#table-of-contents"></a></div> <div> <h3>Prerequisites</h3> <a href="https://github.com/jravilap/Olsen_Analyses#prerequisites"></a></div> <ul> <li>R (version 4.3.1 or higher)</li> <li>RStudio (optional, but recommended)</li> </ul> <div> <h3>R Packages</h3> <a href="https://github.com/jravilap/Olsen_Analyses#r-packages"></a></div> The following R packages are required. You can install them using the commands below: <div> <pre>install.packages(c("readxl", "calibrate", "dplyr", "ggplot2"))</pre> <div> </div> </div> <div> <h3>Package versions</h3> <a href="https://github.com/jravilap/Olsen_Analyses#package-versions"></a></div> <ul> <li>ggplot2_3.5.1</li> <li>dplyr_1.1.4</li> <li>yaml_2.3.8</li> <li>calibrate_1.7.7</li> <li>readxl_1.4.3</li> </ul> <div> <h2>Project Structure</h2> <a href="https://github.com/jravilap/Olsen_Analyses#project-structure"></a></div> <ul> <li><code>code/</code>: Contains the R scripts for the analysis.</li> <li><code>data/</code>: Processed data files. <ul> <li><code>22_0322_alphaSyn_fly_pilot_Classes.xlsx</code>: metabolite profiling data</li> <li><code>dup_metabs_decision.csv</code>: Table defining which metabolites profiled in more than one method should be used.</li> </ul> </li> <li><code>results/</code>: Output files, including plots and tables.</li> <li><code>common_functions/</code>: Custom R functions used in the analysis.</li> <li><code>config.yml</code>: Configuration file for setting paths.</li> </ul>

Microbiota Study Crohn's Disease AG Chang

We have investigated a Crohn’s disease (CD) cohort by our multi-parameter microbiota flow cytometry approach to characterise the microbiota on single-cell level for attributes of the disease. The microbiota is isolated from stool samples and stained according to the published protocol for (a) host immunoglobulins IgA1, IgA2, IgM, IgG and (b) agglutinin binding to mannose, galactose or N-Acetyl-glucosamine surface sugar moieties. For all samples we also determined the microbiome composition by 16S rRNA (V3-V4) sequencing on the illumina MiSeq platform. We provide the raw .fcs and FASTQ files of 64 CD patients distributed into two cohorts (55) individuals in cohort 1, 19 individuals in cohort 2). Cohort 2 has two samples for two timepoints. For comparison we additionally analysed 55 healthy donors. All .fcs files were generated on BD Influx®.   The metadata is collected in the provided meta.csv. The staining parameters are summarized in provided panel.csv.

opencc-by-4.0Jun 2024View details →

DYNA: Disease-Specific Language Model for Variant Pathogenicity

For coding variant effect predictions (VEPs), our approach centers on clinical variant sets specifically related to inherited cardiomyopathies (CM) and arrhythmias (ARM). We utilize a pre-compiled dataset comprised of rare missense pathogenic and benign variants, categorized using a cohort-based approach for diseases such as cardiomyopathy and arrhythmias, as detailed in the previous report by Zhang et al. ClinVar CM and ARM datasets include all missense variants in CM and ARM, respectively, are extracted from ClinVar (Landrum et al.). In the realm of non-coding VEPs, our focus shifts to splicing-related variants, utilizing a dataset from the multiplexed assay for exon recognition by Chong et al., which highlights the significant impact of rare genetic variants on splicing disruptions. Similarly, the ClinVar Splicing dataset, compiled from ClinVar, encompasses all benign sequences and pathogenic variants pertinent to splicing.   For the ClinVar CM and ARM datasets, we translate the DNA sequences into protein sequences using the human genome assembly hg38 from https://www.ncbi.nlm.nih.gov/grc/human. We employed the GFF file, MANE.GRCh38.v1.1.ensembl\_genomic.gff.gz from https://www.ncbi.nlm.nih.gov/refseq/MANE, to annotate coding versus non-coding regions for each gene, as only coding DNA sequences are translated into proteins. Additionally, protein domains, cataloged in the Pfam database (Finn et al.), are essential for the functional characterization of proteins. These domains are identified by aligning the translated sequences to known domain structures, thereby facilitating deeper insights into protein function.

Therapeutic dosage of inflammatory bowel disease drugs

Therapeutic doses of inflammatory bowel disease drugs in adults and in pediatrics. More data specific to these drugs can be found at www.ibd-eii.com

opencc-by-4.0May 2024View details →

Figures for "A Guide to Performing Systematic reviews of Health and Disease"

These are images for "A Guide to Performing Systematic reviews of Health and Disease". Most of these images are high resolution or smart art charts which allow viewing these images in high resolution. The screenshots have been added. The book will be available for download from  <a href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fzenodo.org%2Fcommunities%2Fperforming_systematic_reviews_of_health_and_disease%2Frecords%3Fq%3D%26l%3Dlist%26p%3D1%26s%3D10%26sort%3Dnewest&data=05%7C02%7Ck.gurusamy%40ucl.ac.uk%7Cf08c366513d04e9fdcf508dcbb8156dc%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C638591411382106040%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=PPer6d%2FUumlG9P26osWIC%2BWEFQ9kfYmBXyF4MaRkeHs%3D&reserved=0">https://zenodo.org/communities/performing_systematic_reviews_of_health_and_disease/records?q=&l=list&p=1&s=10&sort=newest</a>. For other books available through UCL Press, please visit, <a href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fzenodo.org%2Fcommunities%2Fucl_press%2Frecords%3Fq%3D%26l%3Dlist%26p%3D1%26s%3D10%26sort%3Dnewest&data=05%7C02%7Ck.gurusamy%40ucl.ac.uk%7Cf08c366513d04e9fdcf508dcbb8156dc%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C638591411382093030%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=M8wiD48wVcM1gcWujtRGueCxuXkz02BnuXFIFhUlDfE%3D&reserved=0">https://zenodo.org/communities/ucl_press/records?q=&l=list&p=1&s=10&sort=newest</a>.