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opencc-by-4.0May 2017View details →

Data used in the article "Cryptic disease-induced mortality may cause host extinction in an apparently-stable host-parasite system"

These data files include all the capture-history matrices that were used in the article, including two matrices with the age of captured individuals (adults or juveniles) according to the definition presented in the main text. Infection intensity (zoospore equivalents per swab) is provided in separate files for all Rhinoderma darwinii and Eupsophus contulmoensis individuals that tested positive for Batrachochytrium dendrobatidis infection. Also, the R code used for the fully paramaterized matrix population model 1 (including figures) is provided. Other codes used to analyze our data, especifically capture-recapture models, were obtained from Kéry and Schaub 2012 (Bayesian population analysis using WinBUGS. A hierarchical perspective. Waltham, USA: Academic Press.)

opencc-by-4.0Jul 2022View details →

A hydroponics based high throughput screening system for clubroot disease pathotyping

Clubroot is a devastating disease affecting the canola industry and caused by the protist Plasmodiophora brassicae. Since the 1940s, several pathotyping systems have been developed and different classifications have been used to differentiate P. brassicae isolates based on their ability to infect different hosts. Unfortunately, none of previously developed pathotyping systems discriminate virulent and avirulent isolates of P. brassicae against the clubroot resistance profiles of commercially available canola cultivars. To try to solve this limitation we have developed a hydroponic-based bioassay using P. brassicae single spore isolates (SSIs), and four canola inbreed homozygous lines (CIH). These SSIs are representative of the virulence widely spread in the field, while these CIH are representative of the resistance commercially available to growers. Through this new phenotyping scheme, we have been able to connect P. brassicae isolates with their ability to break down clubroot resistance in canola in shorter time and economically more efficiently. This will help to tailor the selection of resistant canola varieties to use in an infested field for the longest possible time, empowering producers to make informed decisions about the best canola cultivar to use based on the P. brassicae diversity in their field

Figure 4 in Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases

Figure 4. Identification of PCR inhibitors in 18 biological samples positive for Aspergillus. Graph A: Ct values obtained from pure and diluted DNA samples (dilution rate 1/20). Graph B: Ct values obtained with 20 copies of a plasmid DNA systematically added to the same biological samples (undiluted and diluted) and a negative control sample (NC).

Figure 2 in Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases

Figure 2. Influence of proteinase K digestion (56 °C overnight) on DNA extraction. Graph A shows the Ct values obtained by quantifying THP1 cell DNA derived from direct extraction with the NucliSENS easyMAG system and extraction performed on the same quantity of cells following overnight (ON) digestion with Proteinase K. Graph B shows Leishmania quantification after extraction with the NucliSENS easyMAG system both with and without PK and quantification after extraction using a QIAamp DNA Mini kit after ON digestion with PK.

Figure 7 in Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases

Figure 7. Variation of the ratio between kinetoplastic DNA and nuclear DNA extraction with various Leishmania quantities in the presence of 103 THP1 cells.

Figure 5 in Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases

Figure 5. Yield of DNA extraction from Leishmania and THP1 cells using the NucliSENS easyMAG system.

Figure 3 in Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases

Figure 3. Results of the extraction experiments performed on yeast (Candida albicans) and filamentous fungi (Aspergillus fumigatus). A presents the kinetics of the extraction process after vortexing and glass-bead treatment. B shows the differences in DNA quantity obtained from fungal cells using the FastPrep system (with) compared to the same process without grinding.

Figure 6 in Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases

Figure 6. Influence of the quantity of human cells (THP1 cells) on Leishmania quantification at various concentrations of host cells and parasites.

opencc-by-4.0Oct 2024View details →

GINGIVAL HYPERPLASIA AND SYSTEMIC DISEASE: A COMPLEX INTERPLAY

This study investigated the association between gingival hyperplasia and various systemic diseases and medications. Data from 1055 patients were analyzed, including those with leukemia, pregnancy, diabetes, and those taking medications known to induce gingival hyperplasia (phenytoin, cyclosporine, calcium channel blockers). Results indicated a significantly higher prevalence of gingival hyperplasia in patients with leukemia (40%, 95% CI: 30-50%) and poorly controlled diabetes (25%, 95% CI: 20-30%) compared to the control group (4%, 95% CI: 2-6%). Pregnancy also showed a statistically significant increase in gingival hyperplasia, with prevalence rising from 15% in the first trimester to 25% in the third trimester. Drug-induced gingival hyperplasia was observed in a substantial proportion of patients receiving phenytoin (35%), cyclosporine (25%), and calcium channel blockers (27%). Clinical characteristics of gingival hyperplasia varied depending on the underlying etiology, with leukemia-associated hyperplasia often presenting as severe, generalized, and friable tissue. These findings highlight the importance of considering systemic factors and medication profiles when assessing and managing gingival hyperplasia. Further research is needed to elucidate the mechanisms underlying these associations and to optimize treatment strategies.

opencc-by-4.0Dec 2020View details →

"Decision support systems halve fungicide use compared to calendar-based strategies without increasing disease risk". Supplementary Data 1.

"Decision support systems halve fungicide  compared to calendar-based strategies without increasing disease risk". Supplementary Data 1.https://doi.org/10.1038/s43247-021-00291-8 | www.nature.com/commsenv Dataset includes the results of 80 independent experiments reported in 22 articles and it  has a dimension of 329 rows x 42 columns. Further information in "Description Supplementary Data 1.pdf" file.  This dataset was assembled including also the data from the publication Agronomy 2020, 10(4), 560; https://doi.org/10.3390/agronomy10040560.

openmit-licenseApr 2023View details →

PolyMed: A Medical Dataset Addressing Disease Imbalance for Robust Automatic Diagnosis Systems

We introduce the PolyMed dataset, designed to address the limitations of existing medical case data for Automatic Diagnosis Systems (ADS). ADS assists doctors by predicting diseases based on patients' basic information, such as age, gender, and symptoms. However, these systems face challenges due to imbalanced disease label data and difficulties in accessing or collecting medical data. To tackle these issues, the PolyMed dataset has been developed to improve the evaluation of ADS by incorporating medical knowledge graph data and diagnosis case data. The dataset aims to provide comprehensive evaluation, include diverse disease information, effectively utilize external knowledge, and perform tasks closer to real-world scenarios. We have also made the data collection tools publicly available to enable researchers and other interested parties to contribute additional data in a standardized format. These tools feature a range of customizable input fields that can be selectively utilized according to the user's specific requirements, ensuring consistency and professionalism in the data collection process. All train and test code of our data available in https://github.com/krchanyang/PolyMed

opencc-byJun 2023View details →

Assessment of Capacity of the primary Health System in the management of noncommunicable Diseases in Ghana

This questionnaire was used to assess the capacity of primary health system in the management of NCDs

dryad40/100

Host controls of within-host disease dynamics: insight from an invertebrate system

Open the record for dataset details and reuse information.

publicMar 2021View details →

dryad36/100

Data from: A natural gene drive system influences bovine tuberculosis susceptibility in African buffalo: possible implications for disease management

Bovine tuberculosis (BTB) is endemic to the African buffalo (Syncerus caffer) of Hluhluwe-iMfolozi Park (HiP) and Kruger National Park, South Africa. In HiP, the disease has been actively managed since 1999 through a test-and-cull procedure targeting BTB-positive buffalo. Prior studies in Kruger showed associations between microsatellite alleles, BTB and body condition. A sex chromosomal meiotic drive, a form of natural gene drive, was hypothesized to be ultimately responsible. These associations indicate high-frequency occurrence of two types of male-deleterious alleles (or multiple-allele haplotypes). One type negatively affects body condition and BTB resistance in both sexes. The other type has sexually antagonistic effects: negative in males but positive in females. Here, we investigate whether a similar gene drive system is present in HiP buffalo, using 17 autosomal microsatellites and microsatellite-derived Y-chromosomal haplotypes from 401 individuals, culled in 2002-2004. We show that the association between autosomal microsatellite alleles and BTB susceptibility detected in Kruger, is also present in HiP. Further, Y-haplotype frequency dynamics indicated that a sex chromosomal meiotic drive also occurred in HiP. BTB was associated with negative selection of male-deleterious alleles in HiP, unlike positive selection in Kruger. Birth sex ratios were female-biased. We attribute negative selection and female-biased sex ratios in HiP to the absence of a Y-chromosomal sex-ratio distorter. This distorter has been hypothesized to contribute to positive selection of male-deleterious alleles and male-biased birth sex ratios in Kruger. As previously shown in Kruger, microsatellite alleles were only associated with male-deleterious effects in individuals born after wet pre-birth years; a phenomenon attributed to epigenetic modification. We identified two additional allele types: male-specific deleterious and beneficial alleles, with no discernible effect on females. Finally, we discuss how our findings may be used for breeding disease-free buffalo and implementing BTB test-and-cull programs.

opencc-zeroAug 2020View details →

dryad36/100

Data from: The classical and alternative circulating renin-angiotensin system in normal dogs and dogs with stage B1 and B2 myxomatous mitral valve disease

The behavior of the comprehensive circulating renin‐angiotensin system (RAS) in dogs with myxomatous mitral valve disease (MMVD) before the onset of congestive heart failure remains largely unexplored. Hypothesis/Objectives: The classical and alternative RAS activity and aldosterone concentrations will be significantly higher in dogs with American College of Veterinary Internal Medicine (ACVIM) stage B2 MMVD compared to normal dogs and dogs with ACVIM stage B1 MMVD. Animals: One hundred seventeen client‐owned dogs (normal = 60; B1 = 31; B2 = 26). Methods: Prospective observational study. Angiotensin peptides (AP) and aldosterone concentrations were measured using liquid chromatography and mass spectrometry. Angiotensin converting enzymes 1 and 2 (ACE, ACE2) and renin activity surrogates were calculated from AP concentrations. Equilibrium dialysis (ED) and immediate protease inhibition (PI) methods of AP quantification were compared in 14 healthy dogs. Results: Core RAS activity and aldosterone concentrations did not differ among the 3 groups. However, the balance between the alternative and classical RAS differed, with dogs with stage B2 MMVD having significantly higher ACE2 activity surrogate (ACE2surr) when compared to normal dogs (adjusted P = .02; ratio of medians for ACE2surr [B2:normal], 1.89; 95% confidence interval [CI]: 1.4‐2.6). The ED and PI methods of AP quantification were highly correlated (AngI, r = .9, P < .0001; AngII, r = .8, P = .001). Conclusions and Clinical Importance: Circulating alternative RAS activity, specifically the surrogate measure of ACE2 activity, was increased in dogs with stage B2 MMVD as compared to normal dogs. Equilibrium dialysis results are analogous to immediate protease inhibition in dogs.

opencc-zeroApr 2024View details →

Figure 1 in Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases

Figure 1. Study design.

opencc-by-4.0Sep 2019View details →

data set related to article A Nervous System-Specific Model of Creatine Transporter Deficiency Recapitulates the Cognitive Endophenotype of the Disease: a Longitudinal Study

This record contains raw data related to article A Nervous System-Specific Model of Creatine Transporter Deficiency Recapitulates the Cognitive Endophenotype of the Disease: a Longitudinal Study

opencc-by-4.0Sep 2024View details →

Image dataset for disease quantification in barley and wheat using the Macrobot system and BluVision Macro software

This dataset contains multi-spectral high-resolution macroscopic images acquired using the Macrobot system, tailored for the automated analysis of plant disease phenotyping. The dataset includes images focused on three specific diseases:  <ul> <li>Bipolaris sorokiniana on barley, with images captured 8 days after inoculation </li> <li>Blumeria graminis f. sp. hordei resp. tritici (wheat powdery mildew) on wheat with images captured 8 days after inoculation</li> <li>Puccinia striiformis (yellow rust) on wheat, with images taken 15 days after inoculation</li> </ul> For each sample, the dataset includes individual R, G, B, UV, and backlight illumination images, along with a combined RGB preview image. The BluVision Macro software is compatible with this dataset, enabling precise quantification and analysis of disease severity on barley and wheat leaves.

opencc-by-4.0Oct 2024View details →

Systemic inflammation accelerates neurodegeneration in a rat model of Parkinson's disease overexpressing human alpha synuclein

Parkinson’s disease (PD) involves genetic and environmental risk factors. Increasing research efforts have been made to understand how they interact to impair homeostasis and elevate risk. Inflammation could be one unifying factor. In this study, wild-type (WT) and overexpressing human α-synuclein (Snca+/+) rats were intraperitoneally injected with a single dose of lipopolysaccharide (LPS) or with saline (SAL). In these animals we assessed the development of PD-like symptoms by immunohistology, high-dimensional flow cytometry, electrophysiology, and behavioral analyses. A single injection of LPS to both WT and Snca+/+ rats triggered long-lasting increased activation of pro-inflammatory microglial markers, infiltrating monocytes and T-lymphocytes. However, only LPS Snca+/+ rats displayed dopaminergic neuronal loss in the substantia nigra pars compacta (SNpc), associated with a reduction of evoked dopamine release in the striatum. No significant changes were observed in the behavioral domain.