cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10076567
title: Patellar Tendon Load Progression during Rehabilitation Exercises: Implications for the Treatment of Patellar Tendon Injuries

description: Purpose 
To evaluate patellar tendon loading profiles (loading index, based on loading peak, loading impulse, and loading rate) of rehabilitation exercises to develop clinical guidelines to incrementally increase the rate and magnitude of patellar tendon loading during rehabilitation.
Methods 
Twenty healthy adults (10 females/10 males, 25.9 ± 5.7 years) performed 35 rehabilitation exercises, including different variations of squats, lunge, jumps, hops, landings, running, and sports specific tasks. Kinematic and kinetic data were collected and a patellar tendon loading index was determined for each exercise using a weighted sum of loading peak, loading rate, and cumulative loading impulse. Then, the exercises were ranked, according to the loading index, into tier 1 (loading index≤0.33), tier 2 (0.33 < loading index<0.66), and tier 3 (loading index≥0.66).
Results 
The single-leg decline squat showed the highest loading index (0.747). Other tier 3 exercises included single-leg forward hop (0.666), single-leg countermovement jump (0.711), and running cut (0.725). The Spanish squat was categorized as a tier 2 exercise (0.563), as was running (0.612), double-leg countermovement jump (0.610), single-leg drop vertical jump (0.599), single-leg full squat (0.580), double-leg drop vertical jump (0.563), lunge (0.471), double-leg full squat (0.428), single-leg 60° squat (0.411), and the Bulgarian squat (0.406). Tier 1 exercises included 20 cm step up (0.187), 20 cm step down (0.288), 30 cm step up (0.321), and double-leg 60° squat (0.224).
Conclusions 
Three patellar tendon loading tiers were established based on a combination of loading peak, loading impulse, and loading rate. Clinicians may use these loading tiers as a guide to progressively increase patellar tendon loading during the rehabilitation of patients with patellar tendon disorders and after anterior cruciate ligament reconstruction using the bone patellar tendon bone graft.
DOI: 10.34740/kaggle/dsv/6903526
title: US counties COVID 19 dataset
DOI: 10.25378/janelia.24512767
title: FIB-SEM subvolumes and region selection information for <b>Motion of VAPB molecules reveals ER-mitochondria contact site subdomains</b>

description: These are the regions in the context of the FIB-SEM volume that were selected for the paper and the data from other regions that were visually inspected for biological consistancy.From the paper:Obara + Nixon-Abell et al. 2023, https://www.biorxiv.org/content/10.1101/2022.09.03.505525v1<b>Motion of VAPB molecules reveals ER-mitochondria contact site subdomains</b>To coordinate cellular physiology, eukaryotic cells rely on the rapid exchange of molecules at specialized organelle-organelle contact sites. Endoplasmic reticulum-mitochondrial contact sites (ERMCSs) are particularly vital communication hubs, playing key roles in the exchange of signaling molecules, lipids, and metabolites. ERMCSs are maintained by interactions between complementary tethering molecules on the surface of each organelle. However, due to the extreme sensitivity of these membrane interfaces to experimental perturbation, a clear understanding of their nanoscale organization and regulation is still lacking. Here, we combine 3D electron microscopy with high-speed molecular tracking of a model organelle tether, VAPB, to map the structure and diffusion landscape of ERMCSs. We uncovered dynamic subdomains within VAPB contact sites that correlate with ER membrane curvature and undergo rapid remodeling. We show that VAPB molecules enter and leave ERMCSs within seconds, despite the contact site itself remaining stable over much longer time scales. This metastability allows ERMCSs to remodel with changes in the physiological environment to accommodate metabolic needs of the cell. An amyotrophic lateral sclerosis (ALS)-associated mutation in VAPB perturbs these subdomains, likely impairing their remodeling capacity and resulting in impaired inter-organelle communication. These results establish high speed single molecule imaging as a new tool for mapping the structure of contact site interfaces and reveal that the diffusion landscape of VAPB at contact sites is a crucial component of ERMCS homeostasis.
DOI: 10.25378/janelia.24512767.v1
title: FIB-SEM subvolumes and region selection information for <b>Motion of VAPB molecules reveals ER-mitochondria contact site subdomains</b>

description: These are the regions in the context of the FIB-SEM volume that were selected for the paper and the data from other regions that were visually inspected for biological consistancy.From the paper:Obara + Nixon-Abell et al. 2023, https://www.biorxiv.org/content/10.1101/2022.09.03.505525v1<b>Motion of VAPB molecules reveals ER-mitochondria contact site subdomains</b>To coordinate cellular physiology, eukaryotic cells rely on the rapid exchange of molecules at specialized organelle-organelle contact sites. Endoplasmic reticulum-mitochondrial contact sites (ERMCSs) are particularly vital communication hubs, playing key roles in the exchange of signaling molecules, lipids, and metabolites. ERMCSs are maintained by interactions between complementary tethering molecules on the surface of each organelle. However, due to the extreme sensitivity of these membrane interfaces to experimental perturbation, a clear understanding of their nanoscale organization and regulation is still lacking. Here, we combine 3D electron microscopy with high-speed molecular tracking of a model organelle tether, VAPB, to map the structure and diffusion landscape of ERMCSs. We uncovered dynamic subdomains within VAPB contact sites that correlate with ER membrane curvature and undergo rapid remodeling. We show that VAPB molecules enter and leave ERMCSs within seconds, despite the contact site itself remaining stable over much longer time scales. This metastability allows ERMCSs to remodel with changes in the physiological environment to accommodate metabolic needs of the cell. An amyotrophic lateral sclerosis (ALS)-associated mutation in VAPB perturbs these subdomains, likely impairing their remodeling capacity and resulting in impaired inter-organelle communication. These results establish high speed single molecule imaging as a new tool for mapping the structure of contact site interfaces and reveal that the diffusion landscape of VAPB at contact sites is a crucial component of ERMCS homeostasis.
DOI: 10.25378/janelia.24512989
title: Organelle structure correlative imaging for sptPALM for <b>Motion of VAPB molecules reveals ER-mitochondria contact site subdomains</b>

description: Post-processing imaging data for generation of sptPALM trajectories and associated images of underlying organelles.For the paper:Obara + Nixon-Abell et al. 2023, https://www.biorxiv.org/content/10.1101/2022.09.03.505525v1<b>Motion of VAPB molecules reveals ER-mitochondria contact site subdomains</b>To coordinate cellular physiology, eukaryotic cells rely on the rapid exchange of molecules at specialized organelle-organelle contact sites. Endoplasmic reticulum-mitochondrial contact sites (ERMCSs) are particularly vital communication hubs, playing key roles in the exchange of signaling molecules, lipids, and metabolites. ERMCSs are maintained by interactions between complementary tethering molecules on the surface of each organelle. However, due to the extreme sensitivity of these membrane interfaces to experimental perturbation, a clear understanding of their nanoscale organization and regulation is still lacking. Here, we combine 3D electron microscopy with high-speed molecular tracking of a model organelle tether, VAPB, to map the structure and diffusion landscape of ERMCSs. We uncovered dynamic subdomains within VAPB contact sites that correlate with ER membrane curvature and undergo rapid remodeling. We show that VAPB molecules enter and leave ERMCSs within seconds, despite the contact site itself remaining stable over much longer time scales. This metastability allows ERMCSs to remodel with changes in the physiological environment to accommodate metabolic needs of the cell. An amyotrophic lateral sclerosis (ALS)-associated mutation in VAPB perturbs these subdomains, likely impairing their remodeling capacity and resulting in impaired inter-organelle communication. These results establish high speed single molecule imaging as a new tool for mapping the structure of contact site interfaces and reveal that the diffusion landscape of VAPB at contact sites is a crucial component of ERMCS homeostasis.
DOI: 10.25378/janelia.24512989.v1
title: Organelle structure correlative imaging for sptPALM for <b>Motion of VAPB molecules reveals ER-mitochondria contact site subdomains</b>

description: Post-processing imaging data for generation of sptPALM trajectories and associated images of underlying organelles.For the paper:Obara + Nixon-Abell et al. 2023, https://www.biorxiv.org/content/10.1101/2022.09.03.505525v1<b>Motion of VAPB molecules reveals ER-mitochondria contact site subdomains</b>To coordinate cellular physiology, eukaryotic cells rely on the rapid exchange of molecules at specialized organelle-organelle contact sites. Endoplasmic reticulum-mitochondrial contact sites (ERMCSs) are particularly vital communication hubs, playing key roles in the exchange of signaling molecules, lipids, and metabolites. ERMCSs are maintained by interactions between complementary tethering molecules on the surface of each organelle. However, due to the extreme sensitivity of these membrane interfaces to experimental perturbation, a clear understanding of their nanoscale organization and regulation is still lacking. Here, we combine 3D electron microscopy with high-speed molecular tracking of a model organelle tether, VAPB, to map the structure and diffusion landscape of ERMCSs. We uncovered dynamic subdomains within VAPB contact sites that correlate with ER membrane curvature and undergo rapid remodeling. We show that VAPB molecules enter and leave ERMCSs within seconds, despite the contact site itself remaining stable over much longer time scales. This metastability allows ERMCSs to remodel with changes in the physiological environment to accommodate metabolic needs of the cell. An amyotrophic lateral sclerosis (ALS)-associated mutation in VAPB perturbs these subdomains, likely impairing their remodeling capacity and resulting in impaired inter-organelle communication. These results establish high speed single molecule imaging as a new tool for mapping the structure of contact site interfaces and reveal that the diffusion landscape of VAPB at contact sites is a crucial component of ERMCS homeostasis.
DOI: 10.25378/janelia.24512728
title: Raw Airyscan Images for PTPIP51 experiments for <b>Motion of VAPB molecules reveals ER-mitochondria contact site subdomains</b>

description: Airyscan images of cells overexpressing PTPIP51 in a variety of tagged and labeled conditions. Expansion of ERMCSs are visible as mitochondria wrapped with ER.Obara + Nixon-Abell et al. 2023, https://www.biorxiv.org/content/10.1101/2022.09.03.505525v1<b>Motion of VAPB molecules reveals ER-mitochondria contact site subdomains</b>To coordinate cellular physiology, eukaryotic cells rely on the rapid exchange of molecules at specialized organelle-organelle contact sites. Endoplasmic reticulum-mitochondrial contact sites (ERMCSs) are particularly vital communication hubs, playing key roles in the exchange of signaling molecules, lipids, and metabolites. ERMCSs are maintained by interactions between complementary tethering molecules on the surface of each organelle. However, due to the extreme sensitivity of these membrane interfaces to experimental perturbation, a clear understanding of their nanoscale organization and regulation is still lacking. Here, we combine 3D electron microscopy with high-speed molecular tracking of a model organelle tether, VAPB, to map the structure and diffusion landscape of ERMCSs. We uncovered dynamic subdomains within VAPB contact sites that correlate with ER membrane curvature and undergo rapid remodeling. We show that VAPB molecules enter and leave ERMCSs within seconds, despite the contact site itself remaining stable over much longer time scales. This metastability allows ERMCSs to remodel with changes in the physiological environment to accommodate metabolic needs of the cell. An amyotrophic lateral sclerosis (ALS)-associated mutation in VAPB perturbs these subdomains, likely impairing their remodeling capacity and resulting in impaired inter-organelle communication. These results establish high speed single molecule imaging as a new tool for mapping the structure of contact site interfaces and reveal that the diffusion landscape of VAPB at contact sites is a crucial component of ERMCS homeostasis.
DOI: 10.25378/janelia.24512728.v1
title: Raw Airyscan Images for PTPIP51 experiments for <b>Motion of VAPB molecules reveals ER-mitochondria contact site subdomains</b>

description: Airyscan images of cells overexpressing PTPIP51 in a variety of tagged and labeled conditions. Expansion of ERMCSs are visible as mitochondria wrapped with ER.Obara + Nixon-Abell et al. 2023, https://www.biorxiv.org/content/10.1101/2022.09.03.505525v1<b>Motion of VAPB molecules reveals ER-mitochondria contact site subdomains</b>To coordinate cellular physiology, eukaryotic cells rely on the rapid exchange of molecules at specialized organelle-organelle contact sites. Endoplasmic reticulum-mitochondrial contact sites (ERMCSs) are particularly vital communication hubs, playing key roles in the exchange of signaling molecules, lipids, and metabolites. ERMCSs are maintained by interactions between complementary tethering molecules on the surface of each organelle. However, due to the extreme sensitivity of these membrane interfaces to experimental perturbation, a clear understanding of their nanoscale organization and regulation is still lacking. Here, we combine 3D electron microscopy with high-speed molecular tracking of a model organelle tether, VAPB, to map the structure and diffusion landscape of ERMCSs. We uncovered dynamic subdomains within VAPB contact sites that correlate with ER membrane curvature and undergo rapid remodeling. We show that VAPB molecules enter and leave ERMCSs within seconds, despite the contact site itself remaining stable over much longer time scales. This metastability allows ERMCSs to remodel with changes in the physiological environment to accommodate metabolic needs of the cell. An amyotrophic lateral sclerosis (ALS)-associated mutation in VAPB perturbs these subdomains, likely impairing their remodeling capacity and resulting in impaired inter-organelle communication. These results establish high speed single molecule imaging as a new tool for mapping the structure of contact site interfaces and reveal that the diffusion landscape of VAPB at contact sites is a crucial component of ERMCS homeostasis.
DOI: 10.25378/janelia.24502930
title: Analyzed FIB-SEM data for <b>Motion of VAPB molecules reveals ER-mitochondria contact site subdomains</b>

description: Analysis for FIB-SEM data used in the paper:Obara + Nixon-Abell et al. 2023, https://www.biorxiv.org/content/10.1101/2022.09.03.505525v1<b>Motion of VAPB molecules reveals ER-mitochondria contact site subdomains</b>To coordinate cellular physiology, eukaryotic cells rely on the rapid exchange of molecules at specialized organelle-organelle contact sites. Endoplasmic reticulum-mitochondrial contact sites (ERMCSs) are particularly vital communication hubs, playing key roles in the exchange of signaling molecules, lipids, and metabolites. ERMCSs are maintained by interactions between complementary tethering molecules on the surface of each organelle. However, due to the extreme sensitivity of these membrane interfaces to experimental perturbation, a clear understanding of their nanoscale organization and regulation is still lacking. Here, we combine 3D electron microscopy with high-speed molecular tracking of a model organelle tether, VAPB, to map the structure and diffusion landscape of ERMCSs. We uncovered dynamic subdomains within VAPB contact sites that correlate with ER membrane curvature and undergo rapid remodeling. We show that VAPB molecules enter and leave ERMCSs within seconds, despite the contact site itself remaining stable over much longer time scales. This metastability allows ERMCSs to remodel with changes in the physiological environment to accommodate metabolic needs of the cell. An amyotrophic lateral sclerosis (ALS)-associated mutation in VAPB perturbs these subdomains, likely impairing their remodeling capacity and resulting in impaired inter-organelle communication. These results establish high speed single molecule imaging as a new tool for mapping the structure of contact site interfaces and reveal that the diffusion landscape of VAPB at contact sites is a crucial component of ERMCS homeostasis.
DOI: 10.25378/janelia.24502930.v1
title: Analyzed FIB-SEM data for <b>Motion of VAPB molecules reveals ER-mitochondria contact site subdomains</b>

description: Analysis for FIB-SEM data used in the paper:Obara + Nixon-Abell et al. 2023, https://www.biorxiv.org/content/10.1101/2022.09.03.505525v1<b>Motion of VAPB molecules reveals ER-mitochondria contact site subdomains</b>To coordinate cellular physiology, eukaryotic cells rely on the rapid exchange of molecules at specialized organelle-organelle contact sites. Endoplasmic reticulum-mitochondrial contact sites (ERMCSs) are particularly vital communication hubs, playing key roles in the exchange of signaling molecules, lipids, and metabolites. ERMCSs are maintained by interactions between complementary tethering molecules on the surface of each organelle. However, due to the extreme sensitivity of these membrane interfaces to experimental perturbation, a clear understanding of their nanoscale organization and regulation is still lacking. Here, we combine 3D electron microscopy with high-speed molecular tracking of a model organelle tether, VAPB, to map the structure and diffusion landscape of ERMCSs. We uncovered dynamic subdomains within VAPB contact sites that correlate with ER membrane curvature and undergo rapid remodeling. We show that VAPB molecules enter and leave ERMCSs within seconds, despite the contact site itself remaining stable over much longer time scales. This metastability allows ERMCSs to remodel with changes in the physiological environment to accommodate metabolic needs of the cell. An amyotrophic lateral sclerosis (ALS)-associated mutation in VAPB perturbs these subdomains, likely impairing their remodeling capacity and resulting in impaired inter-organelle communication. These results establish high speed single molecule imaging as a new tool for mapping the structure of contact site interfaces and reveal that the diffusion landscape of VAPB at contact sites is a crucial component of ERMCS homeostasis.
DOI: 10.25378/janelia.24502906
title: Raw sptPALM imaging files for <b>Motion of VAPB molecules reveals ER-mitochondria contact site subdomains</b>

description: Raw imaging files for sptPALM analysis for the paper:Obara + Nixon-Abell et al. 2023, https://www.biorxiv.org/content/10.1101/2022.09.03.505525v1<b>Motion of VAPB molecules reveals ER-mitochondria contact site subdomains</b>To coordinate cellular physiology, eukaryotic cells rely on the rapid exchange of molecules at specialized organelle-organelle contact sites. Endoplasmic reticulum-mitochondrial contact sites (ERMCSs) are particularly vital communication hubs, playing key roles in the exchange of signaling molecules, lipids, and metabolites. ERMCSs are maintained by interactions between complementary tethering molecules on the surface of each organelle. However, due to the extreme sensitivity of these membrane interfaces to experimental perturbation, a clear understanding of their nanoscale organization and regulation is still lacking. Here, we combine 3D electron microscopy with high-speed molecular tracking of a model organelle tether, VAPB, to map the structure and diffusion landscape of ERMCSs. We uncovered dynamic subdomains within VAPB contact sites that correlate with ER membrane curvature and undergo rapid remodeling. We show that VAPB molecules enter and leave ERMCSs within seconds, despite the contact site itself remaining stable over much longer time scales. This metastability allows ERMCSs to remodel with changes in the physiological environment to accommodate metabolic needs of the cell. An amyotrophic lateral sclerosis (ALS)-associated mutation in VAPB perturbs these subdomains, likely impairing their remodeling capacity and resulting in impaired inter-organelle communication. These results establish high speed single molecule imaging as a new tool for mapping the structure of contact site interfaces and reveal that the diffusion landscape of VAPB at contact sites is a crucial component of ERMCS homeostasis.
DOI: 10.25378/janelia.24502906.v1
title: Raw sptPALM imaging files for <b>Motion of VAPB molecules reveals ER-mitochondria contact site subdomains</b>

description: Raw imaging files for sptPALM analysis for the paper:Obara + Nixon-Abell et al. 2023, https://www.biorxiv.org/content/10.1101/2022.09.03.505525v1<b>Motion of VAPB molecules reveals ER-mitochondria contact site subdomains</b>To coordinate cellular physiology, eukaryotic cells rely on the rapid exchange of molecules at specialized organelle-organelle contact sites. Endoplasmic reticulum-mitochondrial contact sites (ERMCSs) are particularly vital communication hubs, playing key roles in the exchange of signaling molecules, lipids, and metabolites. ERMCSs are maintained by interactions between complementary tethering molecules on the surface of each organelle. However, due to the extreme sensitivity of these membrane interfaces to experimental perturbation, a clear understanding of their nanoscale organization and regulation is still lacking. Here, we combine 3D electron microscopy with high-speed molecular tracking of a model organelle tether, VAPB, to map the structure and diffusion landscape of ERMCSs. We uncovered dynamic subdomains within VAPB contact sites that correlate with ER membrane curvature and undergo rapid remodeling. We show that VAPB molecules enter and leave ERMCSs within seconds, despite the contact site itself remaining stable over much longer time scales. This metastability allows ERMCSs to remodel with changes in the physiological environment to accommodate metabolic needs of the cell. An amyotrophic lateral sclerosis (ALS)-associated mutation in VAPB perturbs these subdomains, likely impairing their remodeling capacity and resulting in impaired inter-organelle communication. These results establish high speed single molecule imaging as a new tool for mapping the structure of contact site interfaces and reveal that the diffusion landscape of VAPB at contact sites is a crucial component of ERMCS homeostasis.