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opencc-by-4.0Nov 2020View details →

Dataset - A lung-on-chip model reveals an essential role for alveolar epithelial cells in controlling bacterial growth during early M. tuberculosis infection

Description of the sub-folders Name, type of data, corresponding Figure in the manuscript 3D view of the LoC model - .tiff image stack, Figure 1. 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. 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. AT Infection in LoC model - .tiff image stacks, Figure 2 - figure supplement 1. AT Infection in vivo - .tiff image stacks, Figure 1 - figure supplement 3. 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.

Fig. 6 Monthly anti-F in Patterns of Fasciola hepatica infection in Danish dairy cattle: implications for on-farm control of the parasite based on different diagnostic methods

Fig. 6 Monthly anti-F. hepatica antibody levels in bulk tank milk (BTM) (solid line) and average serum antibody levels of milking cows during the study period (triangle points with dashed line, error bars showing standard error of the mean) in the four farms

Fig. 5 in Patterns of Fasciola hepatica infection in Danish dairy cattle: implications for on-farm control of the parasite based on different diagnostic methods

Fig. 5 The summary of F. hepatica diagnostic test results according to farms and age during the study period (from spring 2015 to winter 2017). Colour indicates animals that were born in the same year. Coproantigen ELISA values are log-transformed (after adding a fixed constant of 1), and the cut-off defined as 1.89 (1.061 after transformation). Faecal egg counts in 5 g faeces were also log-transformed (after adding a fixed constant of 1) for the benefit of visualisation. Any post-treatment data are excluded

Fig. 4 in Patterns of Fasciola hepatica infection in Danish dairy cattle: implications for on-farm control of the parasite based on different diagnostic methods

Fig. 4 Danish climate data for the four farms for the study period (2015–2017: red) and 30 year average (1961–1990: blue). The climate in Denmark is a mixture of oceanic and continental temperate. The mean day highest and lowest temperatures of each month are shown above, while the total monthly precipitations are shown below

Fig. 3 in Patterns of Fasciola hepatica infection in Danish dairy cattle: implications for on-farm control of the parasite based on different diagnostic methods

Fig. 3 Schematic map and Gantt chart of grazing periods (grey shaded, time of sampling; green shaded, grazing; pasture areas are indicated by capital letters), pasture characteristics (refer to the common map legend) and treatment against Fasciola hepatica on farms O1 and O2, 2015–2017

Fig. 1 in Patterns of Fasciola hepatica infection in Danish dairy cattle: implications for on-farm control of the parasite based on different diagnostic methods

Fig. 1 Map of Denmark, showing the regions and locations of the four farms that participated in the study

Fig. 2 in Patterns of Fasciola hepatica infection in Danish dairy cattle: implications for on-farm control of the parasite based on different diagnostic methods

Fig. 2 Schematic map and Gantt chart of grazing periods (grey shaded, time of sampling; green shaded, grazing; pasture areas are indicated by capital letters), pasture characteristics (refer to the common map legend) and treatment against Fasciola hepatica on farms C1 and C2, 2015–2017

Figure 5 in Cystic echinococcosis (Echinococcus granulosus sensu lato infection) in Tunisia, a One Health perspective for a future control programme

Figure 5. General patterns of transmission of Echinococcus spp. and control points in Tunisia. In red, the parasite route; in blue, the hosts involved and behaviours favouring transmission (the size of the characters indicates their presumed importance in transmission); in green, human actions that may modulate transmission.

Figure 4 in Cystic echinococcosis (Echinococcus granulosus sensu lato infection) in Tunisia, a One Health perspective for a future control programme

Figure 4. General epidemiology of the three main zoonotic diseases involving dogs in Tunisia: cystic echinococcosis (Echinococcus granulosus infection), leishmaniosis (Leishmania infantum infection) and rabies. (a) Transmission routes of Echinococcus spp., Leishmania spp. and rabies in Tunisia (domestic and peri-domestic and wild socio-ecosystems) and the disciplines involved in their control. The yellow circle limits the space of domestic and peri-domestic transmission, the green circle the space for wildlife transmission. The figure shows how different disciplines (in brown) articulate and can contribute to knowledge and control of these three zoonotic diseases involving dogs. (b) Based on the geography of Tunisia (map after [18]), we hypothesise the existence of different patterns of transmission of the three zoonotic diseases involving dogs with "north–south " and "urban–wild" gradients. The size of each circle is proportional to its importance in the transmission system. Along each gradient, the contributions of hosts and pathogens and the weights of the driving factors vary, possibly leading to different transmission patterns (numbered 1, 2, ..., n — 1, n).

opencc-by-4.0Aug 2024View details →

HIV-1 control in vivo is related to the number but not the fraction of infected cells with viral unspliced RNA

In the absence of antiretroviral therapy (ART), a subset of individuals, termed HIV controllers, have levels of plasma viremia that are orders of magnitude lower than non-controllers who are at higher risk for HIV disease progression. In addition to having fewer infected cells resulting in fewer cells with HIV RNA, it is possible that lower levels of plasma viremia in controllers is due to a lower fraction of the infected cells having HIV-1 unspliced RNA (HIV usRNA) compared with non-controllers. To directly test this possibility, we used sensitive and quantitative single cell sequencing methods to compare the fraction of infected cells that contain one or more copies of HIV usRNA in peripheral blood mononuclear cells (PBMC) obtained from controllers and non-controllers. The fraction of infected cells containing HIV usRNA did not differ between the two groups. Rather, the levels of viremia were strongly associated with the total number of infected cells that had HIV usRNA, as reported by others, with controllers having 34-fold fewer infected cells per million PBMC. These results reveal for the first time that viremic control is not associated with a lower fraction of proviruses expressing HIV usRNA, unlike what is reported for elite controllers, but is only related to having fewer infected cells overall, maybe reflecting greater immune clearance of infected cells. Our findings show that proviral silencing is not a key mechanism for viremic control and will help to refine strategies towards achieving HIV remission without ART.

ClinicalTrials.gov40/100

A Randomized Placebo-controlled Safety and Dose-finding Study for the Use of the IL-6 Inhibitor Clazakizumab in Patients With Life-threatening COVID-19 Infection

ClinicalTrials.gov study NCT04343989. IPD Sharing: YES. Countries: 1. Publications: 1.

controlledIPD-YESFeb 2026View details →

dryad36/100

Data from: Estimating transmission dynamics and serial interval of the first wave of COVID-19 infections under different control measures: A statistical analysis in Tunisia from February 29 to May 5, 2020

Background: Describing transmission dynamics of the outbreak and impact of intervention measures are critical to planning responses to future outbreaks and providing timely information to guide policy makers decision. We estimate serial interval (SI) and temporal reproduction number (Rt) of SARS-CoV-2 in Tunisia. Methods: We collected data of investigations and contact tracing between March 1, 2020 and May 5, 2020 as well as illness onset data during the period February 29-May 5, 2020 from National Observatory of New and Emerging Diseases of Tunisia. Maximum likelihood (ML) approach is used to estimate dynamics of Rt. Results: 491 of infector-infectee pairs were involved, with 14.46% reported pre-symptomatic transmission. SI follows Gamma distribution with mean 5.30 days [95% CI 4.66-5.95] and standard deviation 0.26 [95% CI 0.23-0.30]. Also, we estimated large changes in Rt in response to the combined lockdown interventions. The Rt moves from 3.18 [95% CI 2.73-3.69] to 1.77 [95% CI 1.49-2.08] with curfew prevention measure, and under the epidemic threshold (0.89 [95% CI 0.84-0.94]) by national lockdown measure. Conclusions: Overall, our findings highlight contribution of interventions to interrupt transmission of SARS-CoV-2 in Tunisia.

opencc-zeroJun 2020View details →

Figure 3 in Cystic echinococcosis (Echinococcus granulosus sensu lato infection) in Tunisia, a One Health perspective for a future control programme

Figure 3. Seized offal in a Tunisian slaughterhouse that is often thrown on the ground.

opencc-by-4.0Jul 2022View details →

Raw data to: "Vectored antibody gene delivery restores host B and T cell control of persistent viral infection"

Raw data underlying the publication by Ertuna et al. entitled "Vectored antibody gene delivery restores host B and T cell control of persistent viral infection"

dryad36/100

A randomized clinical trial to compare P. falciparum gametocytaemia and infectivity following blood-stage or mosquito bite induced controlled malaria infection

For malaria elimination efforts, it is important to better understand parasite transmission to mosquitoes and to develop models to allow early clinical evaluation of transmission-blocking interventions. We previously described a Controlled Human Malaria Infection protocol for induction of gametocytemia in malaria naïve volunteers by mosquito bite (CHMI-trans) (Reuling et al., 2018). Here, we compared gametocyte production and infectivity in the CHMI-trans model after bites of Plasmodium falciparum (Pf)- infected mosquitoes to that after intravenous administration of Pf-infected-erythrocytes. Volunteers received (sub) curative treatments with gametocyte-permissive piperaquine or sulfadoxine-pyrimethamine. Blood-stage inoculation induced considerably higher gametocyte densities compared to mosquito bitesthat was predicted by PfAP2-G transcripts indicative of gametocyte commitment, and resulted in Pf-positive mosquito infections in 9/12 volunteers versus 0/12 volunteers after mosquito bite inoculation. Current findings firmly establish the CHMI-trans with intravenous administration of asexual parasites as a model for early clinical evaluation of interventions that aim to interrupt Pf-transmission.

opencc-zeroMar 2022View details →

Figure 2 in Cystic echinococcosis (Echinococcus granulosus sensu lato infection) in Tunisia, a One Health perspective for a future control programme

Figure 2. Restaurant preparing grilled meat with non-controlled lamb meat.

Figure 1. A in Cystic echinococcosis (Echinococcus granulosus sensu lato infection) in Tunisia, a One Health perspective for a future control programme

Figure 1. A heavily infected ewe liver, called "egg basket" locally.