cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24687295
title: Control30-33h-mouse2 from Heterogeneity in killing efficacy of individual effector CD8 + T cells against Plasmodium liver stages

description: Vaccination strategies in mice inducing high numbers of memory CD8 + T cells specific to a single epitope are able to provide sterilizing protection against infection with Plasmodium sporozoites. We have recently found that Plasmodium-specific CD8 + T cells cluster around sporozoite-infected hepatocytes but whether such clusters are important in elimination of the parasite remains incompletely understood. Here, we used our previously generated data in which we employed intravital microscopy to longitudinally image 32 green fluorescent protein (GFP)-expressing <i>Plasmodium yoelii</i> parasites in livers of mice that had received activated Plasmodium-specific CD8 + T cells after sporozoite infection. We found significant heterogeneity in the dynamics of the normalized GFP signal from the parasites (termed ‘vitality index’ or VI) that was weakly correlated with the number of T cells near the parasite. We also found that a simple model assuming mass-action, additive killing by T cells well describes the VI dynamics for most parasites and predicts a highly variable killing efficacy by individual T cells. Given our estimated median <i>per capita</i> kill rate of <i>k</i> = 0.031/h we predict that a single T cell is typically incapable of killing a parasite within the 48 h lifespan of the liver stage in mice. Stochastic simulations of T cell clustering and killing of the liver stage also suggested that: (i) three or more T cells per infected hepatocyte are required to ensure sterilizing protection; (ii) both variability in killing efficacy of individual T cells and resistance to killing by individual parasites may contribute to the observed variability in VI decline, and (iii) the stable VI of some clustered parasites cannot be explained by measurement noise. Taken together, our analysis for the first time provides estimates of efficiency at which individual CD8 + T cells eliminate intracellular parasitic infection <i>in vivo</i>.
DOI: 10.6084/m9.figshare.24687295.v1
title: Control30-33h-mouse2 from Heterogeneity in killing efficacy of individual effector CD8 + T cells against Plasmodium liver stages

description: Vaccination strategies in mice inducing high numbers of memory CD8 + T cells specific to a single epitope are able to provide sterilizing protection against infection with Plasmodium sporozoites. We have recently found that Plasmodium-specific CD8 + T cells cluster around sporozoite-infected hepatocytes but whether such clusters are important in elimination of the parasite remains incompletely understood. Here, we used our previously generated data in which we employed intravital microscopy to longitudinally image 32 green fluorescent protein (GFP)-expressing <i>Plasmodium yoelii</i> parasites in livers of mice that had received activated Plasmodium-specific CD8 + T cells after sporozoite infection. We found significant heterogeneity in the dynamics of the normalized GFP signal from the parasites (termed ‘vitality index’ or VI) that was weakly correlated with the number of T cells near the parasite. We also found that a simple model assuming mass-action, additive killing by T cells well describes the VI dynamics for most parasites and predicts a highly variable killing efficacy by individual T cells. Given our estimated median <i>per capita</i> kill rate of <i>k</i> = 0.031/h we predict that a single T cell is typically incapable of killing a parasite within the 48 h lifespan of the liver stage in mice. Stochastic simulations of T cell clustering and killing of the liver stage also suggested that: (i) three or more T cells per infected hepatocyte are required to ensure sterilizing protection; (ii) both variability in killing efficacy of individual T cells and resistance to killing by individual parasites may contribute to the observed variability in VI decline, and (iii) the stable VI of some clustered parasites cannot be explained by measurement noise. Taken together, our analysis for the first time provides estimates of efficiency at which individual CD8 + T cells eliminate intracellular parasitic infection <i>in vivo</i>.
DOI: 10.6084/m9.figshare.24552331
title: Supplementary analyses and additional figures and tables from Heterogeneity in killing efficacy of individual effector CD8 + T cells against Plasmodium liver stages

description: Vaccination strategies in mice inducing high numbers of memory CD8 + T cells specific to a single epitope are able to provide sterilizing protection against infection with Plasmodium sporozoites. We have recently found that Plasmodium-specific CD8 + T cells cluster around sporozoite-infected hepatocytes but whether such clusters are important in elimination of the parasite remains incompletely understood. Here, we used our previously generated data in which we employed intravital microscopy to longitudinally image 32 green fluorescent protein (GFP)-expressing <i>Plasmodium yoelii</i> parasites in livers of mice that had received activated Plasmodium-specific CD8 + T cells after sporozoite infection. We found significant heterogeneity in the dynamics of the normalized GFP signal from the parasites (termed ‘vitality index’ or VI) that was weakly correlated with the number of T cells near the parasite. We also found that a simple model assuming mass-action, additive killing by T cells well describes the VI dynamics for most parasites and predicts a highly variable killing efficacy by individual T cells. Given our estimated median <i>per capita</i> kill rate of <i>k</i> = 0.031/h we predict that a single T cell is typically incapable of killing a parasite within the 48 h lifespan of the liver stage in mice. Stochastic simulations of T cell clustering and killing of the liver stage also suggested that: (i) three or more T cells per infected hepatocyte are required to ensure sterilizing protection; (ii) both variability in killing efficacy of individual T cells and resistance to killing by individual parasites may contribute to the observed variability in VI decline, and (iii) the stable VI of some clustered parasites cannot be explained by measurement noise. Taken together, our analysis for the first time provides estimates of efficiency at which individual CD8 + T cells eliminate intracellular parasitic infection <i>in vivo</i>.
DOI: 10.6084/m9.figshare.24552331.v1
title: Supplementary analyses and additional figures and tables from Heterogeneity in killing efficacy of individual effector CD8 + T cells against Plasmodium liver stages

description: Vaccination strategies in mice inducing high numbers of memory CD8 + T cells specific to a single epitope are able to provide sterilizing protection against infection with Plasmodium sporozoites. We have recently found that Plasmodium-specific CD8 + T cells cluster around sporozoite-infected hepatocytes but whether such clusters are important in elimination of the parasite remains incompletely understood. Here, we used our previously generated data in which we employed intravital microscopy to longitudinally image 32 green fluorescent protein (GFP)-expressing <i>Plasmodium yoelii</i> parasites in livers of mice that had received activated Plasmodium-specific CD8 + T cells after sporozoite infection. We found significant heterogeneity in the dynamics of the normalized GFP signal from the parasites (termed ‘vitality index’ or VI) that was weakly correlated with the number of T cells near the parasite. We also found that a simple model assuming mass-action, additive killing by T cells well describes the VI dynamics for most parasites and predicts a highly variable killing efficacy by individual T cells. Given our estimated median <i>per capita</i> kill rate of <i>k</i> = 0.031/h we predict that a single T cell is typically incapable of killing a parasite within the 48 h lifespan of the liver stage in mice. Stochastic simulations of T cell clustering and killing of the liver stage also suggested that: (i) three or more T cells per infected hepatocyte are required to ensure sterilizing protection; (ii) both variability in killing efficacy of individual T cells and resistance to killing by individual parasites may contribute to the observed variability in VI decline, and (iii) the stable VI of some clustered parasites cannot be explained by measurement noise. Taken together, our analysis for the first time provides estimates of efficiency at which individual CD8 + T cells eliminate intracellular parasitic infection <i>in vivo</i>.
DOI: 10.6084/m9.figshare.24687298
title: fit-VIdynamics-mass-action-DDRmodel-Tcellnumbers-32parasites from Heterogeneity in killing efficacy of individual effector CD8 + T cells against Plasmodium liver stages

description: Vaccination strategies in mice inducing high numbers of memory CD8 + T cells specific to a single epitope are able to provide sterilizing protection against infection with Plasmodium sporozoites. We have recently found that Plasmodium-specific CD8 + T cells cluster around sporozoite-infected hepatocytes but whether such clusters are important in elimination of the parasite remains incompletely understood. Here, we used our previously generated data in which we employed intravital microscopy to longitudinally image 32 green fluorescent protein (GFP)-expressing <i>Plasmodium yoelii</i> parasites in livers of mice that had received activated Plasmodium-specific CD8 + T cells after sporozoite infection. We found significant heterogeneity in the dynamics of the normalized GFP signal from the parasites (termed ‘vitality index’ or VI) that was weakly correlated with the number of T cells near the parasite. We also found that a simple model assuming mass-action, additive killing by T cells well describes the VI dynamics for most parasites and predicts a highly variable killing efficacy by individual T cells. Given our estimated median <i>per capita</i> kill rate of <i>k</i> = 0.031/h we predict that a single T cell is typically incapable of killing a parasite within the 48 h lifespan of the liver stage in mice. Stochastic simulations of T cell clustering and killing of the liver stage also suggested that: (i) three or more T cells per infected hepatocyte are required to ensure sterilizing protection; (ii) both variability in killing efficacy of individual T cells and resistance to killing by individual parasites may contribute to the observed variability in VI decline, and (iii) the stable VI of some clustered parasites cannot be explained by measurement noise. Taken together, our analysis for the first time provides estimates of efficiency at which individual CD8 + T cells eliminate intracellular parasitic infection <i>in vivo</i>.
DOI: 10.6084/m9.figshare.24687298.v1
title: fit-VIdynamics-mass-action-DDRmodel-Tcellnumbers-32parasites from Heterogeneity in killing efficacy of individual effector CD8 + T cells against Plasmodium liver stages

description: Vaccination strategies in mice inducing high numbers of memory CD8 + T cells specific to a single epitope are able to provide sterilizing protection against infection with Plasmodium sporozoites. We have recently found that Plasmodium-specific CD8 + T cells cluster around sporozoite-infected hepatocytes but whether such clusters are important in elimination of the parasite remains incompletely understood. Here, we used our previously generated data in which we employed intravital microscopy to longitudinally image 32 green fluorescent protein (GFP)-expressing <i>Plasmodium yoelii</i> parasites in livers of mice that had received activated Plasmodium-specific CD8 + T cells after sporozoite infection. We found significant heterogeneity in the dynamics of the normalized GFP signal from the parasites (termed ‘vitality index’ or VI) that was weakly correlated with the number of T cells near the parasite. We also found that a simple model assuming mass-action, additive killing by T cells well describes the VI dynamics for most parasites and predicts a highly variable killing efficacy by individual T cells. Given our estimated median <i>per capita</i> kill rate of <i>k</i> = 0.031/h we predict that a single T cell is typically incapable of killing a parasite within the 48 h lifespan of the liver stage in mice. Stochastic simulations of T cell clustering and killing of the liver stage also suggested that: (i) three or more T cells per infected hepatocyte are required to ensure sterilizing protection; (ii) both variability in killing efficacy of individual T cells and resistance to killing by individual parasites may contribute to the observed variability in VI decline, and (iii) the stable VI of some clustered parasites cannot be explained by measurement noise. Taken together, our analysis for the first time provides estimates of efficiency at which individual CD8 + T cells eliminate intracellular parasitic infection <i>in vivo</i>.
DOI: 10.6084/m9.figshare.24687301
title: control-data-mouse1 from Heterogeneity in killing efficacy of individual effector CD8 + T cells against Plasmodium liver stages

description: Vaccination strategies in mice inducing high numbers of memory CD8 + T cells specific to a single epitope are able to provide sterilizing protection against infection with Plasmodium sporozoites. We have recently found that Plasmodium-specific CD8 + T cells cluster around sporozoite-infected hepatocytes but whether such clusters are important in elimination of the parasite remains incompletely understood. Here, we used our previously generated data in which we employed intravital microscopy to longitudinally image 32 green fluorescent protein (GFP)-expressing <i>Plasmodium yoelii</i> parasites in livers of mice that had received activated Plasmodium-specific CD8 + T cells after sporozoite infection. We found significant heterogeneity in the dynamics of the normalized GFP signal from the parasites (termed ‘vitality index’ or VI) that was weakly correlated with the number of T cells near the parasite. We also found that a simple model assuming mass-action, additive killing by T cells well describes the VI dynamics for most parasites and predicts a highly variable killing efficacy by individual T cells. Given our estimated median <i>per capita</i> kill rate of <i>k</i> = 0.031/h we predict that a single T cell is typically incapable of killing a parasite within the 48 h lifespan of the liver stage in mice. Stochastic simulations of T cell clustering and killing of the liver stage also suggested that: (i) three or more T cells per infected hepatocyte are required to ensure sterilizing protection; (ii) both variability in killing efficacy of individual T cells and resistance to killing by individual parasites may contribute to the observed variability in VI decline, and (iii) the stable VI of some clustered parasites cannot be explained by measurement noise. Taken together, our analysis for the first time provides estimates of efficiency at which individual CD8 + T cells eliminate intracellular parasitic infection <i>in vivo</i>.
DOI: 10.6084/m9.figshare.24687301.v1
title: control-data-mouse1 from Heterogeneity in killing efficacy of individual effector CD8 + T cells against Plasmodium liver stages

description: Vaccination strategies in mice inducing high numbers of memory CD8 + T cells specific to a single epitope are able to provide sterilizing protection against infection with Plasmodium sporozoites. We have recently found that Plasmodium-specific CD8 + T cells cluster around sporozoite-infected hepatocytes but whether such clusters are important in elimination of the parasite remains incompletely understood. Here, we used our previously generated data in which we employed intravital microscopy to longitudinally image 32 green fluorescent protein (GFP)-expressing <i>Plasmodium yoelii</i> parasites in livers of mice that had received activated Plasmodium-specific CD8 + T cells after sporozoite infection. We found significant heterogeneity in the dynamics of the normalized GFP signal from the parasites (termed ‘vitality index’ or VI) that was weakly correlated with the number of T cells near the parasite. We also found that a simple model assuming mass-action, additive killing by T cells well describes the VI dynamics for most parasites and predicts a highly variable killing efficacy by individual T cells. Given our estimated median <i>per capita</i> kill rate of <i>k</i> = 0.031/h we predict that a single T cell is typically incapable of killing a parasite within the 48 h lifespan of the liver stage in mice. Stochastic simulations of T cell clustering and killing of the liver stage also suggested that: (i) three or more T cells per infected hepatocyte are required to ensure sterilizing protection; (ii) both variability in killing efficacy of individual T cells and resistance to killing by individual parasites may contribute to the observed variability in VI decline, and (iii) the stable VI of some clustered parasites cannot be explained by measurement noise. Taken together, our analysis for the first time provides estimates of efficiency at which individual CD8 + T cells eliminate intracellular parasitic infection <i>in vivo</i>.
DOI: 10.6084/m9.figshare.24686820
title: Dengue Serotype and Genotype 2019 Dhaka outbreak

description: Background: Acute arboviral infections like dengue have a significant negative socioeconomic and health impact on many tropical and subtropical areas of the world. 3.9 billion Individuals are at risk of contracting the dengue virus, with Asia bearing the brunt of that load. Bangladesh, like other south-east Asian countries faced a massive outbreak of dengue in 2019. The purpose of this study was to describe the clinical and laboratory variations among severe dengue cases and to conduct a serotype survey and forecast future changes in the clinical or serological profile of this virus. Methods: This cross sectional study was done in three tertiary care centers in Dhaka, Bangladesh during the worst outbreak of dengue in this hyperendemic region spanning from 1st August to 31st December, 2019. The study enrolled 1978 participants who were grouped into group B and C according to national guidelines. Thus, the clinical and laboratory difference between these two groups are described. Furthermore, 81 samples were serotyped using Qiagen One step RT-PCR kit (Cat. No: 210212). In addition sequencing (ABI sequencing platform) of partial C-prM gene of five DENV-3 isolates were done and analyzed (BLAST tool of NCBI) for phylogenetics (MEGA6 software package Results: Among the 1978 enrolled participants group B and C patients were 1580 (80%) and 398 (20%) respectively. The median (IQR) age of the patients were 26(11 to 41). Maximum proportion of the enrolled were male (72.2%) (p=0.0002). Median (IQR) of the cohort was 26(11 to 41). Only 5.56% were secondary infections. Group C patients more commonly presented with vomiting (p 0.133), diarrhea (p&lt;0.0001) and abdominal pain (p 0.0203). Most common co- morbidities were hypertension (90; 4.55%) and DM (70; 3.54%). The major mode of bleeding was melaena (12%). Only 13 (0.66%) patients succumbed to death, 12 of them belonged to group B. Hemoglobin and hematocrit was lower in group C cases (p 0.004 and 0.006 respectively). Aspartate transaminase was higher in the same group (p 0.0016). Fluid requirement was higher in group C (p&lt;0.0001) and platelet requirement was more in group B (0.0070). Only 12 (0.7%) required ICU. Only one patient got antibiotics and none were managed by steroids. Out of 81 samples 79% patients were serotyped as DENV-3, followed by DENV 2,3 (13.6% ) and DENV-2 (7.4%). Following phylogenetic analysis DENV-3 and DENV2 were deemed to be of genotype I and cosmopolitan variety. Conclusions: This study presents the first instance of heterogeneous co-infection with several serotypes since 2000 in Bangladesh. It also gives an overview of serotype prevalence, management evaluation and clinical results that promises to navigate future control planning.
DOI: 10.7284/119012
title: GNSS (Global Navigation Satellite System) data collected during research cruise BH14-16 using a Northstar 941X instrument system onboard the platform RV Blue Heron

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/147077
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise BH21-10 using a Hawaii UHDAS instrument system onboard the platform RV Blue Heron

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/147079
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise BH21-10 using a SeaBird SBE-911+ instrument system onboard the platform RV Blue Heron

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/147081
title: GNSS (Global Navigation Satellite System) data collected during research cruise BH21-10 using a Furuno GP-90 instrument system onboard the platform RV Blue Heron

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/147076
title: INS (Inertial Navigation System) data collected during research cruise BH21-10 using a Applanix POS/MV-320 V2 instrument system onboard the platform RV Blue Heron

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/147080
title: Meteorological Station data collected during research cruise BH21-10 using a RMYoung 26700 instrument system onboard the platform RV Blue Heron

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/147078
title: pCO2 (Partial Pressure of Carbon Dioxide) data collected during research cruise BH21-10 using a SUNBURST SuperCO2 instrument system onboard the platform RV Blue Heron

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/151820
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise BH22-08 using a Hawaii UHDAS instrument system onboard the platform RV Blue Heron

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/151822
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise BH22-08 using a SeaBird SBE-911+ instrument system onboard the platform RV Blue Heron

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/151823
title: GNSS (Global Navigation Satellite System) data collected during research cruise BH22-08 using a Furuno GP-90 instrument system onboard the platform RV Blue Heron

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/151818
title: INS (Inertial Navigation System) data collected during research cruise BH22-08 using a Applanix POS/MV-320 V2 instrument system onboard the platform RV Blue Heron

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/151824
title: Meteorological Station data collected during research cruise BH22-08 using a RMYoung 26700 instrument system onboard the platform RV Blue Heron

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/151821
title: pCO2 (Partial Pressure of Carbon Dioxide) data collected during research cruise BH22-08 using a SUNBURST SuperCO2 instrument system onboard the platform RV Blue Heron

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/151819
title: TSG (Thermosalinograph) data collected during research cruise BH22-08 using a SeaBird SBE-21 instrument system onboard the platform RV Blue Heron

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/151827
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise BH22-09 using a Hawaii UHDAS instrument system onboard the platform RV Blue Heron

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/151829
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise BH22-09 using a SeaBird SBE-911+ instrument system onboard the platform RV Blue Heron

description: Original (unprocessed) data collected during a Field_expedition