cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7548537
title: The Robot Tracking Benchmark (RTB)

description: The Robot Tracking Benchmark (RTB) is a synthetic dataset that facilitates the quantitative evaluation of 3D tracking algorithms for multi-body objects. It was created using the procedural rendering pipeline BlenderProc. The dataset contains photo-realistic sequences with HDRi lighting and physically-based materials. Perfect ground truth annotations for camera and robot trajectories are provided in the BOP format. Many physical effects, such as motion blur, rolling shutter, and camera shaking, are accurately modeled to reflect real-world conditions. For each frame, four depth qualities exist to simulate sensors with different characteristics. While the first quality provides perfect ground truth, the second considers measurements with the distance-dependent noise characteristics of the Azure Kinect time-of-flight sensor. Finally, for the third and fourth quality, two stereo RGB images with and without a pattern from a simulated dot projector were rendered. Depth images were then reconstructed using Semi-Global Matching (SGM). The benchmark features six robotic systems with different kinematics, ranging from simple open-chain and tree topologies to structures with complex closed kinematics. For each robotic system, three difficulty levels are provided: easy, medium, and hard. In all sequences, the kinematic system is in motion. While for easy sequences the camera is mostly static with respect to the robot, medium and hard sequences feature faster and shakier motions for both the robot and camera. Consequently, motion blur increases, which also reduces the quality of stereo matching. Finally, for each object, difficulty level, and depth image quality, 10 sequences with 150 frames are rendered. In total, this results in 108.000 frames that feature different kinematic structures, motion patterns, depth measurements, scenes, and lighting conditions. In summary, the Robot Tracking Benchmark allows to extensively measure, compare, and ablate the performance of multi-body tracking algorithms, which is essential for further progress in the field.
DOI: 10.5281/zenodo.7548536
title: The Robot Tracking Benchmark (RTB)

description: The Robot Tracking Benchmark (RTB) is a synthetic dataset that facilitates the quantitative evaluation of 3D tracking algorithms for multi-body objects. It was created using the procedural rendering pipeline BlenderProc. The dataset contains photo-realistic sequences with HDRi lighting and physically-based materials. Perfect ground truth annotations for camera and robot trajectories are provided in the BOP format. Many physical effects, such as motion blur, rolling shutter, and camera shaking, are accurately modeled to reflect real-world conditions. For each frame, four depth qualities exist to simulate sensors with different characteristics. While the first quality provides perfect ground truth, the second considers measurements with the distance-dependent noise characteristics of the Azure Kinect time-of-flight sensor. Finally, for the third and fourth quality, two stereo RGB images with and without a pattern from a simulated dot projector were rendered. Depth images were then reconstructed using Semi-Global Matching (SGM). The benchmark features six robotic systems with different kinematics, ranging from simple open-chain and tree topologies to structures with complex closed kinematics. For each robotic system, three difficulty levels are provided: easy, medium, and hard. In all sequences, the kinematic system is in motion. While for easy sequences the camera is mostly static with respect to the robot, medium and hard sequences feature faster and shakier motions for both the robot and camera. Consequently, motion blur increases, which also reduces the quality of stereo matching. Finally, for each object, difficulty level, and depth image quality, 10 sequences with 150 frames are rendered. In total, this results in 108.000 frames that feature different kinematic structures, motion patterns, depth measurements, scenes, and lighting conditions. In summary, the Robot Tracking Benchmark allows to extensively measure, compare, and ablate the performance of multi-body tracking algorithms, which is essential for further progress in the field.
DOI: 10.5281/zenodo.7554534
title: MODES DATA - vertical structure functions

description: MODES DATA - vertical structure functions (VSF)
DOI: 10.5281/zenodo.7554535
title: MODES DATA - vertical structure functions

description: MODES DATA - vertical structure functions (VSF)
DOI: 10.5281/zenodo.7554592
title: Dataset and codebook for the article by Gaume J, Bertholet N, McCambridge J, et al. Effect of a Novel Brief Motivational Intervention for Alcohol-Intoxicated Young Adults in the Emergency Department: A Randomized Clinical Trial. JAMA Netw Open. 2022;5(10):e2237563. doi: 10.1001/jamanetworkopen.2022.37563

description: Dataset and codebook for the article Gaume J, Bertholet N, McCambridge J, et al. <strong>Effect of a Novel Brief Motivational Intervention for Alcohol-Intoxicated Young Adults in the Emergency Department: A Randomized Clinical Trial</strong>. JAMA Netw Open. 2022;5(10):e2237563. doi: 10.1001/jamanetworkopen.2022.37563 The dataset contains all data needed to reproduce the results in the above cited article. Variable description and labels can be found in the codebook. Please refer to the published article and supplemental online content for further information about the data and the study procedures.
DOI: 10.23728/b2share.014c9b9dc0374b1fb647e0e071a4fd27
title: Atmospheric deposition in Pallanza, Lake Maggiore watershed, 1980-2018

description: Monthly bulk deposition of SO4, NO3, NH4, P-PO4, major cations (Ca, Mg, Na, K) in kg ha-1 at the sampling station of Pallanza, in Lake Maggiore watershed. Data are volume weighted monthly average values calculated from weekly data
DOI: 10.5281/zenodo.7554591
title: Dataset and codebook for the article by Gaume J, Bertholet N, McCambridge J, et al. Effect of a Novel Brief Motivational Intervention for Alcohol-Intoxicated Young Adults in the Emergency Department: A Randomized Clinical Trial. JAMA Netw Open. 2022;5(10):e2237563. doi: 10.1001/jamanetworkopen.2022.37563

description: Dataset and codebook for the article Gaume J, Bertholet N, McCambridge J, et al. <strong>Effect of a Novel Brief Motivational Intervention for Alcohol-Intoxicated Young Adults in the Emergency Department: A Randomized Clinical Trial</strong>. JAMA Netw Open. 2022;5(10):e2237563. doi: 10.1001/jamanetworkopen.2022.37563 The dataset contains all data needed to reproduce the results in the above cited article. Variable description and labels can be found in the codebook. Please refer to the published article and supplemental online content for further information about the data and the study procedures.
DOI: 10.5281/zenodo.7554646
title: Steady states of Λ-type three-level systems excited by quantum light with various photon statistics in lossy cavities

description: Dataset of the publication "Steady states of Λ-type three-level systems excited by quantum light with various photon statistics in lossy cavities" H. Rose, O. V. Tikhonova, T. Meier, and P. R. Sharapova, New J. Phys.<strong> 24</strong>, 063020 (2022). ( https://doi.org/10.1088/1367-2630/ac74d8 ). The zip file includes the data on which the plots shown in figures 2,4,5,6,7, B1, and B2 are based.
description: The joint grant by the Deutsche Forschungsgemeinschaft (DFG) and the Russian Science Foundation (RSF) (projects SH 1228/2-1, ME 1916/7-1, No. 19-42-04105) is gratefully acknowledged. We thank the PC^2 (Paderborn Center for Parallel Computing) for a computing time grant.
DOI: 10.5281/zenodo.7554645
title: Steady states of Λ-type three-level systems excited by quantum light with various photon statistics in lossy cavities

description: Dataset of the publication "Steady states of Λ-type three-level systems excited by quantum light with various photon statistics in lossy cavities" H. Rose, O. V. Tikhonova, T. Meier, and P. R. Sharapova, New J. Phys.<strong> 24</strong>, 063020 (2022). ( https://doi.org/10.1088/1367-2630/ac74d8 ). The zip file includes the data on which the plots shown in figures 2,4,5,6,7, B1, and B2 are based.
description: The joint grant by the Deutsche Forschungsgemeinschaft (DFG) and the Russian Science Foundation (RSF) (projects SH 1228/2-1, ME 1916/7-1, No. 19-42-04105) is gratefully acknowledged. We thank the PC^2 (Paderborn Center for Parallel Computing) for a computing time grant.
DOI: 10.5281/zenodo.7554287
title: Dataset related to: Therapeutic Small Interfering RNA Targeting Complement C3 in a Mouse Model of C3 Glomerulopathy

description: The files contain all the dataset included in the manuscript divided by figures. Abstract Alternative pathway complement dysregulation with abnormal glomerular C3 deposits and glomerular damage is a key mechanism of pathology in C3 glomerulopathy (C3G). No disease-specific treatments are currently available for C3G. Therapeutics inhibiting complement are emerging as a potential strategy for the treatment of C3G. In this study, we investigated the effects of N-acetylgalactosamine (GalNAc) conjugated small interfering RNA (siRNA) targeting the C3 component of complement that inhibits liver C3 expression in the C3G model of mice with heterozygous deficiency of factor H (Cfh+/- mice). We showed a duration of action for GalNAc-conjugated C3 siRNA in reducing the liver C3 gene expression in Cfh+/- mice that were dosed s.c. once a month for up to 7 mo. C3 siRNA limited fluid-phase alternative pathway activation, reducing circulating C3 fragmentation and activation of factor B. Treatment with GalNAc-conjugated C3 siRNA reduced glomerular C3d deposits in Cfh+/- mice to levels similar to those of wild-type mice. Ultrastructural analysis further revealed the efficacy of the C3 siRNA in slowing the formation of mesangial and subendothelial electron-dense deposits. The present data indicate that RNA interference mediated C3 silencing in the liver may be a relevant therapeutic strategy for treating patients with C3G associated with the haploinsufficiency of complement factor H.
description: This work was supported by Silence Therapeutics GmbH.
description: {"references": ["Zanchi C, Locatelli M, Cerullo D, Aumiller V, Corna D, Rottoli D, Eisermann M, Donadelli R, Mousavi M, Noris M, Remuzzi G, Benigni A, Zoja C. Therapeutic Small Interfering RNA Targeting Complement C3 in a Mouse Model of C3 Glomerulopathy. J Immunol. 2022 Apr 1;208(7):1772-1781"]}
DOI: 10.5281/zenodo.7554288
title: Dataset related to: Therapeutic Small Interfering RNA Targeting Complement C3 in a Mouse Model of C3 Glomerulopathy

description: The files contain all the dataset included in the manuscript divided by figures. Abstract Alternative pathway complement dysregulation with abnormal glomerular C3 deposits and glomerular damage is a key mechanism of pathology in C3 glomerulopathy (C3G). No disease-specific treatments are currently available for C3G. Therapeutics inhibiting complement are emerging as a potential strategy for the treatment of C3G. In this study, we investigated the effects of N-acetylgalactosamine (GalNAc) conjugated small interfering RNA (siRNA) targeting the C3 component of complement that inhibits liver C3 expression in the C3G model of mice with heterozygous deficiency of factor H (Cfh+/- mice). We showed a duration of action for GalNAc-conjugated C3 siRNA in reducing the liver C3 gene expression in Cfh+/- mice that were dosed s.c. once a month for up to 7 mo. C3 siRNA limited fluid-phase alternative pathway activation, reducing circulating C3 fragmentation and activation of factor B. Treatment with GalNAc-conjugated C3 siRNA reduced glomerular C3d deposits in Cfh+/- mice to levels similar to those of wild-type mice. Ultrastructural analysis further revealed the efficacy of the C3 siRNA in slowing the formation of mesangial and subendothelial electron-dense deposits. The present data indicate that RNA interference mediated C3 silencing in the liver may be a relevant therapeutic strategy for treating patients with C3G associated with the haploinsufficiency of complement factor H.
description: This work was supported by Silence Therapeutics GmbH.
description: {"references": ["Zanchi C, Locatelli M, Cerullo D, Aumiller V, Corna D, Rottoli D, Eisermann M, Donadelli R, Mousavi M, Noris M, Remuzzi G, Benigni A, Zoja C. Therapeutic Small Interfering RNA Targeting Complement C3 in a Mouse Model of C3 Glomerulopathy. J Immunol. 2022 Apr 1;208(7):1772-1781"]}
DOI: 10.5517/ccdc.csd.cc144d8y
title: CCDC 1046909: Experimental Crystal Structure Determination

description: Related Article: Christopher M. Lemon, David C. Powers, Michael Huynh, Andrew G. Maher, Austin A. Phillips, Brian P. Tripet, Daniel G. Nocera|2022|Inorg.Chem.|62|3|doi:10.1021/acs.inorgchem.2c02285
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc27vmvl
title: CCDC 2081180: Experimental Crystal Structure Determination

description: Related Article: Bo Li, Jianping Zhu, Xia Zheng, Wenqing Ti, Yue Huang, Hequan Yao|2022|J.Org.Chem.|88|548|doi:10.1021/acs.joc.2c02557
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc295pw2
title: CCDC 2120644: Experimental Crystal Structure Determination

description: Related Article: Qing An, Yang-Yang Xing, Ruihua Pu, Menghui Jia, Yuegang Chen, Anhua Hu, Shuo-Qing Zhang, Na Yu, Jianbo Du, Yanxia Zhang, Jinquan Chen, Weimin Liu, Xin Hong, Zhiwei Zuo|2022|J.Am.Chem.Soc.|145|359|doi:10.1021/jacs.2c10126
description: Related Article: yuegang chen|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc29f99c
title: CCDC 2127942: Experimental Crystal Structure Determination

description: Related Article: Yunus Güçlü, Hakan Erer, Hakan Demiral, Yunus Zorlu, Cigdem Altintas, Seda Keskin, Fatih Semerci|2023|J.Solid State Chem.|319|123778|doi:10.1016/j.jssc.2022.123778
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc29f9bd
title: CCDC 2127943: Experimental Crystal Structure Determination

description: Related Article: Yunus Güçlü, Hakan Erer, Hakan Demiral, Yunus Zorlu, Cigdem Altintas, Seda Keskin, Fatih Semerci|2023|J.Solid State Chem.|319|123778|doi:10.1016/j.jssc.2022.123778
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc29f9cf
title: CCDC 2127944: Experimental Crystal Structure Determination

description: Related Article: Yunus Güçlü, Hakan Erer, Hakan Demiral, Yunus Zorlu, Cigdem Altintas, Seda Keskin, Fatih Semerci|2023|J.Solid State Chem.|319|123778|doi:10.1016/j.jssc.2022.123778
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.7554032
title: Dataset related to: Empagliflozin protects glomerular endothelial cell architecture in experimental diabetes through the VEGF-A/caveolin-1/PV-1 signaling pathway

description: The files contain all the dataset included in the manuscript divided by figures. Abstract<br> In addition to having blood glucose-lowering effects, inhibitors of sodium glucose cotransporter 2 (SGLT2) afford renoprotection in diabetes. We sought to investigate which components of the glomerular filtration barrier could be involved in the antiproteinuric and renoprotective effects of SGLT2 inhibition in diabetes. BTBR (black and tan, brachyuric) <em>ob/ob</em> mice that develop a type 2 diabetic nephropathy received a standard diet with or without empagliflozin for 10 weeks, starting at 8 weeks of age, when animals had developed albuminuria. Empagliflozin caused marked decreases in blood glucose levels and albuminuria but did not correct glomerular hyperfiltration. The protective effect of empagliflozin against albuminuria was not due to a reduction in podocyte damage as empagliflozin did not affect the larger podocyte filtration slit pore size nor the defective expression of nephrin and nestin. Empagliflozin<br> did not reduce the thickening of the glomerular basement membrane. In BTBR <em>ob/ob</em> mice, the most profound abnormality seen using electron microscopy was in the endothelial aspect of the glomerular capillary, with significant loss of endothelial fenestrations. Remarkably, empagliflozin ameliorated the subverted microvascular endothelial ultrastructure. Caveolae and bridging diaphragms between adjacent endothelial fenestrae were seen in diabetic mice and associated with increased expression of caveolin-1 and the appearance of PV-1. These endothelial abnormalities were limited by the SGLT2 inhibitor. Although no expression of SGLT2 was found in glomerular endothelial cells, SGLT2 was expressed in the podocytes of diabetic mice. VEGF-A, which is a known stimulus for endothelial caveolin-1 and PV-1, was increased in podocytes of BTBR <em>ob/ob</em> mice and normalized by SGLT2 inhibitor treatment.<br> Thus, empagliflozin’s protective effect on the glomerular endothelium of diabetic mice could be due to a limitation of the paracrine signaling of podocyte-derived VEGF-A that resulted in a reduction of the abnormal endothelial caveolin-1 and PV-1, with the consequent preservation of glomerular endothelial function and permeability.
description: This work was supported in part by Boehringer Ingelheim Italia, Milan, Italy
description: {"references": ["Locatelli M, Zoja C, Conti S, Cerullo D, Corna D, Rottoli D, Zanchi C, Tomasoni S, Remuzzi G, Benigni A. Empagliflozin protects glomerular endothelial cell architecture in experimental diabetes through the VEGF-A/caveolin-1/PV-1 signaling pathway. J Pathol. 2022 Apr;256(4):468-479"]}
DOI: 10.5281/zenodo.7554031
title: Dataset related to: Empagliflozin protects glomerular endothelial cell architecture in experimental diabetes through the VEGF-A/caveolin-1/PV-1 signaling pathway

description: The files contain all the dataset included in the manuscript divided by figures. Abstract<br> In addition to having blood glucose-lowering effects, inhibitors of sodium glucose cotransporter 2 (SGLT2) afford renoprotection in diabetes. We sought to investigate which components of the glomerular filtration barrier could be involved in the antiproteinuric and renoprotective effects of SGLT2 inhibition in diabetes. BTBR (black and tan, brachyuric) <em>ob/ob</em> mice that develop a type 2 diabetic nephropathy received a standard diet with or without empagliflozin for 10 weeks, starting at 8 weeks of age, when animals had developed albuminuria. Empagliflozin caused marked decreases in blood glucose levels and albuminuria but did not correct glomerular hyperfiltration. The protective effect of empagliflozin against albuminuria was not due to a reduction in podocyte damage as empagliflozin did not affect the larger podocyte filtration slit pore size nor the defective expression of nephrin and nestin. Empagliflozin<br> did not reduce the thickening of the glomerular basement membrane. In BTBR <em>ob/ob</em> mice, the most profound abnormality seen using electron microscopy was in the endothelial aspect of the glomerular capillary, with significant loss of endothelial fenestrations. Remarkably, empagliflozin ameliorated the subverted microvascular endothelial ultrastructure. Caveolae and bridging diaphragms between adjacent endothelial fenestrae were seen in diabetic mice and associated with increased expression of caveolin-1 and the appearance of PV-1. These endothelial abnormalities were limited by the SGLT2 inhibitor. Although no expression of SGLT2 was found in glomerular endothelial cells, SGLT2 was expressed in the podocytes of diabetic mice. VEGF-A, which is a known stimulus for endothelial caveolin-1 and PV-1, was increased in podocytes of BTBR <em>ob/ob</em> mice and normalized by SGLT2 inhibitor treatment.<br> Thus, empagliflozin’s protective effect on the glomerular endothelium of diabetic mice could be due to a limitation of the paracrine signaling of podocyte-derived VEGF-A that resulted in a reduction of the abnormal endothelial caveolin-1 and PV-1, with the consequent preservation of glomerular endothelial function and permeability.
description: This work was supported in part by Boehringer Ingelheim Italia, Milan, Italy
description: {"references": ["Locatelli M, Zoja C, Conti S, Cerullo D, Corna D, Rottoli D, Zanchi C, Tomasoni S, Remuzzi G, Benigni A. Empagliflozin protects glomerular endothelial cell architecture in experimental diabetes through the VEGF-A/caveolin-1/PV-1 signaling pathway. J Pathol. 2022 Apr;256(4):468-479"]}
DOI: 10.6084/m9.figshare.21926154.v1
title: Supporting data for 'Thermodynamic origins of two-component multiphase condensates of proteins' (2023)

description: This file is part of the supporting data for the manuscript 'Thermodynamic origins of two-component multiphase condensates of proteins', and contains the data used to plot the figures and the full sequence populations from the four main genetic-algorithm runs presented in the main text. An example LAMMPS input script (with pair parameters for the Mpipi coarse-grained model) used in this work and an example input configuration for a multilayered system that can be used as the initial system in a coevolution run, as well as a multilayered system containing the WT A1 LCD in the centre and its predicted partner protein are also included. <br> The structure and contents of this file are outlined in the README file in the root directory.