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18,535 results for “Infections”
Fig. 12 in Highly disjunct and highly infected millipedes - a new cave-dwelling species of Chiraziulus (Diplopoda: Spirostreptida: Cambalidae) from Iran and notes on Laboulbeniales ectoparasites
Fig. 12. Chiraziulus kaiseri (Mauriès, 1983), paratypes infected with ectoparasitic fungi of the genus Rickia Cavara, order Laboulbeniales. A. Arrows indicate black dots on the body rings corresponding to the insertion of the fungi. B. Scanning electron micrograph of the collum with one fungus (arrow). Scale bars: A = 1 mm; B = 100 μm.
Fig. 5 in Highly disjunct and highly infected millipedes - a new cave-dwelling species of Chiraziulus (Diplopoda: Spirostreptida: Cambalidae) from Iran and notes on Laboulbeniales ectoparasites
Fig. 5. Chiraziulus kaiseri (Mauriès, 1983), ♂, paratypes, gonopods. Scanning electron micrographs. A. Anterior gonopods in anterior view. B. Anterior gonopods with one posterior gonopod in lateral view. C. As B, in apical view. D. As B, in posterior view. E–F. Anterior gonopod with detail of the processes on the tip of anterior gonopods. G–I. Posterior gonopod. J. Detail of the mesal sternal part. Abbreviations: C = coxal process; T = telepodite; Ta = anterior lobe of telopodite; Tb = posterior lobe of telepodite. Scale bars: A, D, I = 100 μm; B–C, E–H = 10 μm.
Fig. 11 in Highly disjunct and highly infected millipedes - a new cave-dwelling species of Chiraziulus (Diplopoda: Spirostreptida: Cambalidae) from Iran and notes on Laboulbeniales ectoparasites
Fig. 11. Cambala annulata (Say, 1821), anterior gonopod. A. Mesal view. B. Detail of the mesal sternal part. C. Apical part of coxal processes and telepodite. Scale bars: A = 100 μm; B–C = 10 μm.
Fig. 4 in Highly disjunct and highly infected millipedes - a new cave-dwelling species of Chiraziulus (Diplopoda: Spirostreptida: Cambalidae) from Iran and notes on Laboulbeniales ectoparasites
Fig. 4. Chiraziulus kaiseri (Mauriès, 1983), ♂, paratype, anterior gonopod. Scanning electron micrographs. A. Tip of flagellum. B. Flagellum insertion and loop across anterior gonopod coxite. C. Anterior gonopod showing the entire extension of the flagellum. Scale bars: A = 10 μm; B–C = 100 μm.
Data 1 for "Population- and age-specific patterns of haemosporidian assemblages and infection levels in European Bee-eaters (Merops apiaster)"
<p>Data related to the article "Population- and age-specific patterns of haemosporidian assemblages and infection levels in European Bee-eaters (<em>Merops apiaster</em>)" in the format .xlsx. The 1st sheet contains all variables for analyses done with the R script (see 10.5281/zenodo.3968360). The 2nd sheet contains explanations about the variables in sheet 1.</p>
Dataset of clinical biomarkers for prediction of the arboviral infection severity using SIMON analysis
<p>The SISA dataset was used for the identification of clinical biomarkers that can predict the severity of the arboviral infection severity using SIMON analysis, as described (<a href="https://doi.org/10.1101/2020.08.16.252767">https://doi.org/10.1101/2020.08.16.252767</a>). The dataset contains clinical data from 543 individuals hospitalized due to the arboviral infection with Dengue, chikungunya, or Zika viruses from a surveillance study in Ecuador collected from 2013 to 2017 (Suppy et al., 2020, doi: 10.1371/journal.pntd.0007969). In the SISA dataset, we have excluded columns with high level of missing values (pregnancy, <em>WomPreg</em> and complete blood count test which was not performed for all donors and includes columns: <em>PLT_count, Lymphocytes, CBC_N%, WBC_calc </em>and<em> CBC_HCT</em>). Additionally, 9 donors with missing values were removed and SIMON analysis was performed with this final dataset.</p>
Dataset - A lung-on-chip model reveals an essential role for alveolar epithelial cells in controlling bacterial growth during early M. tuberculosis infection
<p>Description of the sub-folders<br> Name, type of data, corresponding Figure in the manuscript<br> 3D view of the LoC model - .tiff image stack, Figure 1.</p> <p>Bacterial Growth Rate Data - .tiff image stacks, .csv files and MATLAB code to extract the fluorescence intensity over time, Figure 2, Figure 2 - figure supplement 2, Figure 2 - figure supplement 4, Figure 3, Figure 3 - figure supplement 2, Figure 4.</p> <p>AT Characterization - .tiff image stacks and MATLAB code to extract the number and volume of lamellar bodies from the stack of confocal images, Figure 1, Figure 1 - figure supplement 1, Figue 1 - figure supplement 2.</p> <p>AT Infection in LoC model - .tiff image stacks, Figure 2 - figure supplement 1.</p> <p>AT Infection in vivo - .tiff image stacks, Figure 1 - figure supplement 3.</p> <p>Simulations of in vivo infections - .dat files of growth rates in macrophages for the WT and ESX-1 deficient populations and MATLAB code to simulate an infection from this data, Figure 4.</p> <p> </p>
Dataset of host, habitat and vegetation parameters in relation to gastrointestinal parasite infections of small mammalian hosts in Madagascar
<p>The dataset contains information on the endoparasite infection status of 903 individuals of four small mammal species (<em>Microcebus murinus</em>, <em>M. ravelobensis</em>, <em>Eliurus myoxinus</em>, <em>Rattus rattus</em>) in relation to host-specific (sex, body condition, population density) and habitat-specific factors (degree of habitat fragmentation, fragment size, distance to the edge of the fragment, percentage of edge habitat, vegetation structure).</p>
The impact of Opisthorchis felineus infection and praziquantel treatment on the intestinal microbiome in children
<p>The presence of some species of helminths is associated with changes in host microbiota composition and diversity, which varies widely depending on the infecting helminth species and other factors. We conducted a prospective case-control study to evaluate the gut microbiota in children with Opisthorchis felineus infection (n=50) before and after anthelmintic treatment and in uninfected children (n=49) in the endemic region. A total of 99 children and adolescents aged between 7 and 18 years were enrolled to the study. Helminth infection was assessed before and at 3 months after treatment with praziquantel. A complex examination for each participant was performed in the study, including an assessment of the clinical symptoms and an intestinal microbiota survey by 16S rRNA gene sequencing of stool samples. There was no change in alpha diversity between O. felineus-infected and control groups. We found significant changes in the abundances of bacterial taxa at different taxonomic levels between the infected and uninfected individuals. Enterobacteriaceae family was more abundant in infected participants compared to uninfected children. On the genus level, O. felineus-infected participants’ microbiomes showed higher levels of Lachnospira, Escherichia-Shigella, Bacteroides, Eubacterium eligens group, Ruminiclostridium 6, Barnesiella, Oscillibacter, Faecalitalea and Anaerosporobacter and reduction of Blautia, Lachnospiraceae FCS020 and Eubacterium hallii group in comparison with the uninfected individuals. Following praziquantel therapy, there were significant differences in abundances of some microorganisms, including an increase of Faecalibacterium and decrease of Megasphaera, Roseburia. Enterobacteriaceae and Escherichia abundances were decreased up to the control group values. Our results highlight the importance of the host-parasite-microbiota interactions for the community health in the endemic regions.</p>
Post-injury immunosuppression and secondary infections are caused by an AIM2 inflammasome-driven signaling cascade
<p>RAW FCS files for the manuscript:</p> <p>"Post-injury immunosuppression and secondary infections are caused by an AIM2 inflammasome-driven signaling cascade"</p> <p> </p>
Social determinants of Covid-19 infection and death in a rural Indonesia: A rapid healthcare assessment
<p>Understanding the social determinants of Covid-19 infection and death is vital for effective Covid-19 early detection and mitigation strategies. This study aims to examine social determinants of Covid-19 infection and death in the context of rural Indonesia. We used Malang district government Covid-19 contact tracing data from 14,264 individuals, spanning the period from March 1, 2020 to July 29, 2020. The contact tracing data was merged with administrative data from 390 villages to determine whether village characteristics (i.e., the number of health workers, number of community-based healthcare interventions, access to Covid-19 referred hospitals, number of indigenous socio-cultural activities, poverty level and distance to a Covid-19 epicentre city) are associated with Covid-19 infection and death. We used multilevel logistic regression to take advantage of the nested structure of data at the village level. We found among the 14,264 samples, 551 individuals were confirmed infected with Covid-19, and 62 died of Covid-19. Individuals aged 18 and older, civil servants (non-health workers), and those having close contact with people with confirmed cases had a higher likelihood of infection with Covid-19. Greater numbers of community-based healthcare interventions and a lesser distance to a pandemic epicentre reduced the likelihood of infection with the virus. Males, older people, individuals with hypertension, individuals diagnosed with pneumonia, and those diagnosed with respiratory failure had a higher likelihood of death due to Covid-19. A greater number of community-based healthcare interventions seems to reduce the likelihood of Covid-19 infection, while better access to a Covid-19 referred hospital seems to reduce the risk of death among Covid-19 patients. The findings suggest the government to prioritise strategies to control the pandemic in rural area through empowering rural community in health education to prevent Covid-19 and in monitoring people mobility, while providing Covid-19 emergency services for rural areas for reducing mortality.</p>
Identification of co-infections in a cohort of patients diagnosed with Lyme Disease
<p>Serlogy test data used in the study: Identification of co-infections in a cohort of patients diagnosed with Lyme Disease</p>
Supplementary Data -A STUDY ON SOME STRUCTURAL FEATURES RESPONSIBLE FOR SARS-COV-2 INFECTION FATALITY
<p>A correlation between hydrodynamic properties like radius of gyration ( Rg ) vs Molecular weight of spike protein of SARS - COV-2 biopolymers .</p>
Data from: Temperature dependent effects of cutaneous bacteria on a frog's tolerance of fungal infection
<p>Defense against pathogens is one of many benefits that bacteria provide to animal hosts. A clearer understanding of how changes in the environment affect the interactions between animals and their microbial benefactors is needed in order to predict the impact and dynamics of emerging animal diseases. Due to its dramatic effects on the physiology of animals and their pathogens, temperature may be a key variable modulating the level of protection that beneficial bacteria provide to their animal hosts. Here we investigate how temperature and the makeup of the skin microbial community impact the susceptibility of amphibian hosts to infection by <em>Batrachochytrium</em> <em>dendrobatidis</em>, one of two fungal pathogens known to cause the disease chytridiomycosis. To do this, we manipulated the skin bacterial communities of susceptible hosts, northern cricket frogs (<em>Acris</em> <em>crepitans</em>), prior to exposing these animals to <em>Batrachochytrium</em> <em>dendrobatidis</em> under two different ecologically relevant temperatures. Our manipulations included one treatment where antibiotics were used to reduce the skin bacterial community, one where the bacterial community was augmented with the antifungal bacterium, <em>Stenotrophomonas</em> <em>maltophilia</em>, and one in which the frog's skin bacterial community was left intact. We predicted that frogs with reduced skin bacterial communities would be more susceptible (i.e., less resistant to and/or tolerant of <em>Bd</em> infection), and frogs with skin bacterial communities augmented with the known antifungal bacterium would be less susceptible to <em>Bd</em> infection and chytridiomycosis. However, we also predicted that this interaction would be temperature-dependent. We found a strong effect of temperature but not of skin microbial treatment on the probability and intensity of infection in <em>Bd</em>-exposed frogs. Whether temperature impacted survival, however, differed among our skin microbial treatment groups, with animals having more <em>S</em>. <em>maltophilia</em> on their skin surviving longer at 14 but not at 26 °C. Our results suggest that temperature was the predominant factor influencing <em>Bd</em>'s ability to colonize the host (i.e., resistance) but that the composition of the cutaneous bacterial community was important in modulating the host's ability to survive (i.e., tolerate) a heavy <em>Bd</em> infection.</p>
Data from: Assessing the contributions of intraspecific and environmental sources of infection in urban wildlife: Salmonella enterica and white ibis as a case study
Conversion of natural habitats into urban landscapes can expose wildlife to novel pathogens and alter pathogen transmission pathways. Because transmission is difficult to quantify for many wildlife pathogens, mathematical models paired with field observations can help select among competing transmission pathways that might operate in urban landscapes. Here we develop a mathematical model for the enteric bacteria Salmonella enterica in urban-foraging white ibis (Eudocimus albus) in south Florida as a case study to determine (i) the relative importance of contact-based versus environmental transmission among ibis and (ii) whether transmission can be supported by ibis alone or requires external sources of infection. We use biannual field prevalence data to restrict model outputs generated from a Latin hypercube sample of parameter space and select among competing transmission scenarios. We find the most support for transmission from environmental uptake rather than between-host contact and that ibis–ibis transmission alone could maintain low infection prevalence. Our analysis provides the first parameter estimates for Salmonella shedding and uptake in a wild bird and provides a key starting point for predicting how ibis response to urbanization alters their exposure to a multi-host zoonotic enteric pathogen. More broadly, our study provides an analytical roadmap to assess transmission pathways of multi-host wildlife pathogens in the face of scarce infection data.
Epidemiology, risk factors and clinical course of SARS-CoV-2 infected patients in a Swiss university hospital: an observational retrospective study
<p>This is the dataset of the study called "Epidemiology, risk factors and clinical course of SARS-CoV-2 infected patients in a Swiss university hospital: an observational retrospective study". <br> <br> <strong>Abstract: </strong></p> <p>Background<br> Coronavirus disease 2019 (COVID-19) is now a global pandemic with Europe and the USA at its epicenter. Little is known about risk factors for progression to severe disease in Europe. This study aims to describe the epidemiology of COVID-19 patients in a Swiss university hospital.</p> <p>Methods<br> This retrospective observational study included all adult patients hospitalized with a laboratory confirmed SARS-CoV-2 infection from March 1 to March 25, 2020. We extracted data from electronic health records. The primary outcome was the need to mechanical ventilation at day 14. We used multivariate logistic regression to identify risk factors for mechanical ventilation. Follow-up was of at least 14 days. <br> <br> Results<br> 200 patients were included, of whom 37 (18·5%) needed mechanical ventilation at 14 days. The median time from symptoms onset to mechanical ventilation was 9·5 days (IQR 7.00, 12.75). Multivariable regression showed increased odds of mechanical ventilation in males (3.26, 1.21-9.8; p=0.025), in patients who presented with a qSOFA score ≥2 (6.02, 2.09-18.82; p=0.001), with bilateral infiltrate (5.75, 1.91-21.06; p=0.004) or with a CRP of 40 mg/l or greater (4.73, 1.51-18.58; p=0.013). <br> <br> Conclusions<br> This study gives some insight in the epidemiology and clinical course of patients admitted in a European tertiary hospital with SARS-CoV-2 infection. Male sex, high qSOFA score, CRP of 40 mg/l or greater and a bilateral radiological infiltrate could help clinicians identify patients at high risk for mechanical ventilation.</p>
Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton
<p>Dataset for the article "Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton", Monier et al.</p> <p>Data for all phylogenetic tree reconstructions (raw and masked protein sequence alignments in fasta format, tree file in newick format) and placement file (jplace format) of two environmental sequences are available.</p> <p>Data for all assay experiments are available: ammonium and urea assays, Omnilog phenotype screening (Nitrogen substrates).</p>
Plasmodium falciparum infection in febrile Congolese children: prevalence of clinical malaria ten years after introduction of Artemisinin-combination therapies
<p>dataset used in the paper.</p>
Differential gene expression in iPSC-derived macrophages after IFNg stimulation and Salmonella infection
<p>We used likelihood ratio test implemented in DESeq2 v1.10.0 (test = “LRT”) to test if a model that allowed different mean expression in each condition explained the data better than a null model assuming the same mean expression across conditions. See the manuscript for more details: http://www.biorxiv.org/content/early/2017/05/18/102392 .</p> <p>We used the following commands in DESeq2:<br> #Run DESeq2<br> dds = DESeq2::DESeqDataSetFromMatrix(combined_expression_data_filtered$counts, design, ~condition_name) <br> dds = DESeq2::DESeq(dds, test = "LRT", reduced = ~ 1)</p> <p>#Extract differentially expressed genes in each condition<br> ifng_genes = results(dds, contrast=c("condition_name","IFNg","naive")) <br> sl1344_genes = results(dds, contrast=c("condition_name","SL1344","naive")) <br> ifng_sl1344_genes = results(dds, contrast=c("condition_name","IFNg_SL1344","naive"))</p>
Evaluation of two 4th generation point-of-care assays for the detection of Human Immunodeficiency Virus infection.
<p>Background. Fourth generation assays detect simultaneously antibodies for HIV and the p24 antigen, identifying HIV infection earlier than previous generation tests. Previous studies have shown that the Alere Determine HIV-1/2 Combo has lower than anticipated performance in detecting antibodies for HIV and the p24 antigen. Furthermore, there are currently very few studies evaluating the performance of Standard Diagnostics BIOLINE HIV Ag/Ab Combo.</p> <p>Objective: To evaluate the performance of the Alere Determine HIV-1/2 Combo and the Standard Diagnostics BIOLINE HIV Ag/Ab Combo in a panel of frozen serum samples.</p> <p>Study Design: The testing panel included 133 previously frozen serum specimens from the UCLA Clinical Microbiology & Immunoserology laboratory. Reference testing included testing for HIV antibodies by a 3<sup>rd</sup> generation enzyme immunoassay followed by HIV RNA detection. Antibody negative and RNA positive sera were also tested by a laboratory 4<sup>th</sup> generation HIV Ab/Ag enzyme immunoassay.</p> <p>Results: Reference testing yielded 97 positives for HIV infection and 36 negative samples. Sensitivity of the Alere test was 95% (88-98%), while the SD Bioline sensitivity was 91% (83-96%). Both assays showed 100% (90-100%) specificity. No indeterminate or invalid results were recorded. Among 13 samples with acute infection (HIV RNA positive, HIV antibody negative), 12 were found positive by the first assay and 8 by the second. The antigen component of the Alere assay detected 10 acute samples, while the SD Bioline assay detected only one.</p> <p>Conclusions: Both rapid assays showed very good overall performance in detecting HIV infection in frozen serum samples, but further improvements are required to improve the performance in acute infection.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.