cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/qsgr9-hj161
title: H. pylori 26695 / AGS

description: Grid box YWC054
description: <strong>Tilt Series Date:</strong> 2013-11-25</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 210.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> H.pylori prepared by Lee Rettberg</p>
<strong>Purification / Growth Conditions / Treatment:</strong> H.pylori cells grown in BLBB + 10% heat inactivated fetal bovine serum at 37 degrees in microaerobic chamber with GasPak EZ Campy Sachets for 2 days, OD600=0.4AGS cells cultivated on QF Au finder grid for 2 day in DMEM + 10% FBS. Infect by pylori for 6 hr.</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 37 C, 3µl BSA treated gold (1 ml gold resuspent in 30 ul). Manual blot by Whatman 40 filter paper. Ethane/propane mix.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-11-25-35/rawdata/</p>20131125_YWC054_10035.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-11-25-35/rawdata/20131125_YWC054_10035.mrc"
        > <i class="download icon"></i> Download </a></p>

        20131125_YWC054_10035_full.rec,  Reconstruction (Pixel Size 1.92 nm), 712.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-11-25-35/3dimage_35137/20131125_YWC054_10035_full.rec"
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DOI: 10.22002/kemqa-e0518
title: H. pylori 26695 / AGS

description: Grid box YWC054
description: <strong>Tilt Series Date:</strong> 2013-11-25</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 210.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> H.pylori prepared by Lee Rettberg</p>
<strong>Purification / Growth Conditions / Treatment:</strong> H.pylori cells grown in BLBB + 10% heat inactivated fetal bovine serum at 37 degrees in microaerobic chamber with GasPak EZ Campy Sachets for 2 days, OD600=0.4AGS cells cultivated on QF Au finder grid for 2 day in DMEM + 10% FBS. Infect by pylori for 6 hr.</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 37 C, 3µl BSA treated gold (1 ml gold resuspent in 30 ul). Manual blot by Whatman 40 filter paper. Ethane/propane mix.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-11-25-62/rawdata/</p>20131125_YWC054_10061.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-11-25-62/rawdata/20131125_YWC054_10061.mrc"
        > <i class="download icon"></i> Download </a></p>

        20131125_YWC054_10061_part121_4.rec,  Reconstruction (Pixel Size 1.92 nm), 712.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.57760/sciencedb.29418
title: Tracking control of industrial manipulator based on adaptive RBF neural network with local model approximation
title: Tracking control of industrial manipulator based on adaptive RBF neural network with local model approximation

description: This algorithm eliminates the need for an exact plant mathematical model, enabling real-time learning and compensation of system nonlinearities and uncertainties. An adaptive control law adjusts neural network parameters online to achieve high-precision tracking control of robot manipulators. Particle Swarm Optimization (PSO) is employed to optimize the RBF basis width parameters. Validation was performed using the ABB IRB1600 industrial robot, modeled and simulated in MATLAB Simscape.
description: This algorithm eliminates the need for an exact plant mathematical model, enabling real-time learning and compensation of system nonlinearities and uncertainties. An adaptive control law adjusts neural network parameters online to achieve high-precision tracking control of robot manipulators. Particle Swarm Optimization (PSO) is employed to optimize the RBF basis width parameters. Validation was performed using the ABB IRB1600 industrial robot, modeled and simulated in MATLAB Simscape.
DOI: 10.57760/sciencedb.29412
title: Structural analysis of ASCH domain-containing proteins and their implications for nucleotide processing
title: Structural analysis of ASCH domain-containing proteins and their implications for nucleotide processing

description: ASC-1 homology (ASCH) domain family proteins are believed to play essential roles in RNA metabolism, but detailed structural and functional information is limited. Research has shown that the E. coli enzyme YqfB, which contains an ASCH domain, has amidohydrolase activity, converting N4-acetylcytidine (ac4C) RNA nucleoside into cytidine. Here, we present the crystal structures of EcYqfB both in its unbound state and bound to a substrate. Our analysis reveals how the substrate interacts with the enzyme, offering insights into its catalytic mechanism. In vivo experiments further show that deleting EcYqfB does not change overall ac4C levels across various RNA types, indicating that EcYqfB specifically functions in ac4C nucleoside metabolism. We also determined the structures of two homologous proteins: mouse EOLA1 and the human TRIP4-ASCH domain, highlighting differences in their substrate preferences. These findings offer important insights for future research into the structure and function of the ASCH domain protein family.
description: ASC-1 homology (ASCH) domain family proteins are believed to play essential roles in RNA metabolism, but detailed structural and functional information is limited. Research has shown that the E. coli enzyme YqfB, which contains an ASCH domain, has amidohydrolase activity, converting N4-acetylcytidine (ac4C) RNA nucleoside into cytidine. Here, we present the crystal structures of EcYqfB both in its unbound state and bound to a substrate. Our analysis reveals how the substrate interacts with the enzyme, offering insights into its catalytic mechanism. In vivo experiments further show that deleting EcYqfB does not change overall ac4C levels across various RNA types, indicating that EcYqfB specifically functions in ac4C nucleoside metabolism. We also determined the structures of two homologous proteins: mouse EOLA1 and the human TRIP4-ASCH domain, highlighting differences in their substrate preferences. These findings offer important insights for future research into the structure and function of the ASCH domain protein family.
DOI: 10.22002/26cr7-7kp56
title: Myxococcus xanthus pilM-YFP

description: strain SA4088grid box YWC101
description: <strong>Tilt Series Date:</strong> 2014-05-16</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Myxococcus xanthus</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1.0°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -8.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain form Lotte Sogaard-Andersen</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown 48 hr in shaking CTT medium at 30 degrees without antibiotics. OD600=0.9</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated 10 nm gold. -4 offset, 4 sec blot time, no drain. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
  ycw2014-05-16-20_slicer7055.jpg: Unknown appendage ycw2014-05-16-20_slicer7060.jpg: Unknown filament ycw2014-05-16-20_slicer7062.jpg: Unknown curved flat vesicle
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2014-05-16-20/3dimage_42773/</p>20140516_Janelia_YWC096_10010_full.rec,  Reconstruction (Pixel Size 1.32 nm), 688.9 MB  
        
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        20140516_Janelia_YWC096_10010.mrc,  Tilt Series (Pixel Size 0.33 nm), 3.6 GB  
        
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DOI: 10.57760/sciencedb.29407
title: Ga2O3 Vertical SBD With Suspended Field Plate Assisted Shallow Mesa Termination for Multi-kilovolt and Ampere-class Applications
title: Ga2O3 Vertical SBD With Suspended Field Plate Assisted Shallow Mesa Termination for Multi-kilovolt and Ampere-class Applications

description: In this work, a vertical Ga2O3 Schottky barrier diode with suspended field plate assisted shallow mesa termination (SFPM-SBD) is proposed and fabricated. The suspended field plate is achieved by using Cl2 in the ICP etching process to facilitate isotropic etching of Ga2O3. Compared with shallow mesa SBD, the introduction of SFPM can further optimize the electric field distribution. Consequently, a high breakdown voltage (BV) of over 3.5 kV and a low specific on-resistance of 5.77 mΩ∙cm2 are achieved, resulting in a power figure of merit &gt;2.12 GW/cm2. Furthermore, the large-area device with 3×3 mm2 is fabricated, achieving a BV exceeding 1.5 kV and a high forward current of 12 A at 2 V. The simplified fabrication process of the SFPM-SBD, combined with its outstanding performance, makes it a promising candidate for multi-kilovolt and ampere-class applications.
description: In this work, a vertical Ga2O3 Schottky barrier diode with suspended field plate assisted shallow mesa termination (SFPM-SBD) is proposed and fabricated. The suspended field plate is achieved by using Cl2 in the ICP etching process to facilitate isotropic etching of Ga2O3. Compared with shallow mesa SBD, the introduction of SFPM can further optimize the electric field distribution. Consequently, a high breakdown voltage (BV) of over 3.5 kV and a low specific on-resistance of 5.77 mΩ∙cm2 are achieved, resulting in a power figure of merit &gt;2.12 GW/cm2. Furthermore, the large-area device with 3×3 mm2 is fabricated, achieving a BV exceeding 1.5 kV and a high forward current of 12 A at 2 V. The simplified fabrication process of the SFPM-SBD, combined with its outstanding performance, makes it a promising candidate for multi-kilovolt and ampere-class applications.
DOI: 10.57760/sciencedb.29338
title: Federated Learning for Compliance-Preserving Cyberattack Detection in Same Institution Internet of Medical Things (IoMT) Network
title: Federated Learning for Compliance-Preserving Cyberattack Detection in Same Institution Internet of Medical Things (IoMT) Network

description: The study proposes a novel federated learning (FL) framework specifically designed for compliance-preserving cyber attack detection within a single healthcare institution's IoMT network. This framework enables collaborative threat detection across various internal departments or units (acting as federated clients) without requiring the direct sharing of raw patient medical data. Our approach implements and compares four state-of-the-art federated learning algorithms: FedAvg, FedProx, FedNova, and SCAFFOLD, across five different neural network architectures, including standard deep neural networks (DNN). The experiment methodology addresses realistic IoMT deployment scenarios within a healthcare institution, simulating heterogeneous data distributions from patient beds equipped with a total of 36 IoMT devices. This repository support the findings of the study, contains:  Dataset: icu-dataset/ (Attack.csv, patient/environment monitoring.csv)  Analysis notebook: FL-privacy-icu-iot.ipynb
description: The study proposes a novel federated learning (FL) framework specifically designed for compliance-preserving cyber attack detection within a single healthcare institution's IoMT network. This framework enables collaborative threat detection across various internal departments or units (acting as federated clients) without requiring the direct sharing of raw patient medical data. Our approach implements and compares four state-of-the-art federated learning algorithms: FedAvg, FedProx, FedNova, and SCAFFOLD, across five different neural network architectures, including standard deep neural networks (DNN). The experiment methodology addresses realistic IoMT deployment scenarios within a healthcare institution, simulating heterogeneous data distributions from patient beds equipped with a total of 36 IoMT devices. This repository support the findings of the study, contains:  Dataset: icu-dataset/ (Attack.csv, patient/environment monitoring.csv)  Analysis notebook: FL-privacy-icu-iot.ipynb
DOI: 10.22002/byv8c-f6q29
title: Rhodobacter1 558 lysed/PVP

description: Rhodobacter1 558 lysed/PVP
description: <strong>Tilt Series Date:</strong> 2013-10-04</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Rhodobacter sphaeroides</p>
<strong>Strain:</strong> ATCC 17023</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -10.0 μm,  magnification: 34000x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Judy Armitage</p>
<strong>Purification / Growth Conditions / Treatment:</strong> -     grew 5mL cultures of 1558 (with kanamycin and IPTG) to log phase (OD600 between 0.12-0.15)-     spun down 10' at 5000 xg-     resuspended pellets in 2mL appropriate Buffer 1-     Added 200µL fresh lysozme (50 mg/mL in 10mM Tris-HCl, pH 8.0)-     Incubated 15' at RT-     Added 11.2µL 1M MgCl2, 1.3µL 1M CaCl2, 2.2µL DNase I-     Incubated 30' at 37C-     Spun down 10' at 5000 xgBuffer 1:10% Polyvinylpyrrolidone (PVP)1 g sucroseQ.S. 5mL 25mM Tris-HCl, pH 7.0</p>
description: Files available via S3 at ttps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-10-04-9/rawdata/</p>Rhodopvp0009.mrc,  Tilt Series (Pixel Size 0.32 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-10-04-9/rawdata/Rhodopvp0009.mrc"
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        Rhodopvp0009_full.rec,  Reconstruction (Pixel Size 0.64 nm), 2.9 GB  
        
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DOI: 10.57760/sciencedb.26843
title: Aboveground biomass mapping in semi-arid forests based on Multi-features Deep Learning Framework (MFF-TTSM model)
title: Aboveground biomass mapping in semi-arid forests based on Multi-features Deep Learning Framework (MFF-TTSM model)

description: We have provided the data and codes for our research here.We have provided all the variables of Sentinel 1, including polarization metrics and texture features, which can be queried in a file named "data_S1". All variables of Sentinel 2, including band, vegetation index, biophysical features and seasonal features, can be queried in files named "data_band", "data_VI", "data_bio" and "data_jijie". The GEDI data of the study area from 2019 to 2023 that we obtained can also be queried in this database.The measured data is also provided and it is stored in the "measured_data" file.In addition, we have provided all the codes for implementing this research, including the codes for all the models used in this study, as well as the codes for processing Sentinel 1 data, Sentinel 2 data, and GEDI data to obtain the feature data required for this study.These codes are stored in the file "code".
description: We have provided the data and codes for our research here.We have provided all the variables of Sentinel 1, including polarization metrics and texture features, which can be queried in a file named "data_S1". All variables of Sentinel 2, including band, vegetation index, biophysical features and seasonal features, can be queried in files named "data_band", "data_VI", "data_bio" and "data_jijie". The GEDI data of the study area from 2019 to 2023 that we obtained can also be queried in this database.The measured data is also provided and it is stored in the "measured_data" file.In addition, we have provided all the codes for implementing this research, including the codes for all the models used in this study, as well as the codes for processing Sentinel 1 data, Sentinel 2 data, and GEDI data to obtain the feature data required for this study.These codes are stored in the file "code".
DOI: 10.22002/jstb5-dpc11
title: Myxococcus xanthus delta-tsaP

description: Grid box YWC121
description: <strong>Tilt Series Date:</strong> 2014-10-22</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Myxococcus xanthus</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain form Lotte Sogaard-Andersen</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown 2 days in 200 rpm shaking CTT medium at 30 degrees without antibiotics. OD600=0.8</p>
<strong>Sample Preparation:</strong> Vitrobot (MK vi) settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. Blot force 6, blot time 2.5 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2014-10-22-62/rawdata/</p>20141022_YWC121_40032.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
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        20141022_YWC121_40032_part121_2.rec,  Reconstruction (Pixel Size 1.56 nm), 712.7 MB  
        
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DOI: 10.22002/pv1mb-gx775
title: Vibrio cholerae MKW1383

description: In the mixture with Bdellovibrio.Something wrong with the dosage setting.
description: <strong>Tilt Series Date:</strong> 2013-09-10</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> 2740-80</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1.0°, constant angular increment, dosage: 80.0 eV/Å²,  defocus: -8.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Cells prepared by Lee Rettberg</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown in S17-1 prey solution at 30 degrees, OD600=0.2, filtered by 0.22 um filter, mixed with overnight Vibrio cholarea MKW1383 for 90 min before freezing</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 3µl sample, 10 nm BSA treated gold. -3 offset, 4 sec blot time, no drain. Ethane/propane mix. Quantifoil Cu Finder grid</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-09-10-17/rawdata/</p>20130909_Janelia_Bdellovibrio_Vibrio_10017.mrc,  Tilt Series (Pixel Size 0.42 nm), 3.6 GB  
        
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        20130909_Janelia_Bdellovibrio_Vibrio_10017_part131_22.rec,  Reconstruction (Pixel Size 1.68 nm), 688.9 MB  
        
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