cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.3xm9bz
title: Occurrence Download

description: A dataset containing 2010765 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Emberiza citrinella Linnaeus, 1758",
 "HasCoordinate is true",
 "Year is greater than or equal to 2011",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 2010765 records from 2722 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0077901-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.7594929
title: Himawari-8/AHI hourly clear-sky land surface temperature and emissivity dataset (2017.9-2017.12)

description: This is the clear-sky LST and LSE dataset (0.02°, hourly) derived by the iTES algorithm (Zhou and Cheng, 2020) from the Himawari-8 AHI thermal infrared data. A broadband emissivity (BBE, 8-13.5μm) dataset was also produced using the derived AHI narrowband LSEs (Cheng et al. 2013). The in-situ validation results show that the bias and RMSE of the retrieved AHI LST are 0.19 and 2.93 K in the daytime, and −0.43 and 1.95 K in the nighttime, respectively. The bias and RMSE of the retrieved LSE are less than 0.005 and 0.014, respectively, compared with the latest MYD21 LSE. The time period of this dataset is 2016-2021, covering the AHI 0.02° nominal fixed grid (60°N∼60°S, 80°E∼160°W). This is the LST&E dataset in 2017.09-2017.12 <strong>Dataset Characteristics:</strong> Spatial Coverage: East Asia and Western Pacific regions (60°N∼60°S, 80°E-140°E) Temporal Coverage: 2017.09-2017.12 Spatial Resolution: 0.02 ° Temporal Resolution: one hour Projection: GCS_WGS_1984 Data Format: NetCDF <strong>Citation </strong>(Please cite these papers when using the data)<strong>:</strong> Zhou, S., & Cheng, J. (2020). An Improved Temperature and Emissivity Separation Algorithm for the Advanced Himawari Imager. <em>IEEE Transactions on Geoscience and Remote Sensing, 58</em>, 7105-7124 Cheng, J., et al. (2013). Estimating the Optimal Broadband Emissivity Spectral Range for Calculating Surface Longwave Net Radiation. <em>IEEE Geoscience and Remote Sensing Letters, 10</em>, 401-40 If you have any questions, please contact Prof. Jie Cheng (Jie_Cheng@bnu.edu.cn).
DOI: 10.5281/zenodo.7594928
title: Himawari-8/AHI hourly clear-sky land surface temperature and emissivity dataset (2017.9-2017.12)

description: This is the clear-sky LST and LSE dataset (0.02°, hourly) derived by the iTES algorithm (Zhou and Cheng, 2020) from the Himawari-8 AHI thermal infrared data. A broadband emissivity (BBE, 8-13.5μm) dataset was also produced using the derived AHI narrowband LSEs (Cheng et al. 2013). The in-situ validation results show that the bias and RMSE of the retrieved AHI LST are 0.19 and 2.93 K in the daytime, and −0.43 and 1.95 K in the nighttime, respectively. The bias and RMSE of the retrieved LSE are less than 0.005 and 0.014, respectively, compared with the latest MYD21 LSE. The time period of this dataset is 2016-2021, covering the AHI 0.02° nominal fixed grid (60°N∼60°S, 80°E∼160°W). This is the LST&E dataset in 2017.09-2017.12 <strong>Dataset Characteristics:</strong> Spatial Coverage: East Asia and Western Pacific regions (60°N∼60°S, 80°E-140°E) Temporal Coverage: 2017.09-2017.12 Spatial Resolution: 0.02 ° Temporal Resolution: one hour Projection: GCS_WGS_1984 Data Format: NetCDF <strong>Citation </strong>(Please cite these papers when using the data)<strong>:</strong> Zhou, S., & Cheng, J. (2020). An Improved Temperature and Emissivity Separation Algorithm for the Advanced Himawari Imager. <em>IEEE Transactions on Geoscience and Remote Sensing, 58</em>, 7105-7124 Cheng, J., et al. (2013). Estimating the Optimal Broadband Emissivity Spectral Range for Calculating Surface Longwave Net Radiation. <em>IEEE Geoscience and Remote Sensing Letters, 10</em>, 401-40 If you have any questions, please contact Prof. Jie Cheng (Jie_Cheng@bnu.edu.cn).
DOI: 10.5281/zenodo.7598381
title: Himawari-8/AHI hourly clear-sky land surface temperature and emissivity dataset (2018.1-2018.4)

description: This is the clear-sky LST and LSE dataset (0.02°, hourly) derived by the iTES algorithm (Zhou and Cheng, 2020) from the Himawari-8 AHI thermal infrared data. A broadband emissivity (BBE, 8-13.5μm) dataset was also produced using the derived AHI narrowband LSEs (Cheng et al. 2013). The in-situ validation results show that the bias and RMSE of the retrieved AHI LST are 0.19 and 2.93 K in the daytime, and −0.43 and 1.95 K in the nighttime, respectively. The bias and RMSE of the retrieved LSE are less than 0.005 and 0.014, respectively, compared with the latest MYD21 LSE. The time period of this dataset is 2016-2021, covering the AHI 0.02° nominal fixed grid (60°N∼60°S, 80°E∼160°W). This is the LST&E dataset in 2018.01-2018.04 <strong>Dataset Characteristics:</strong> Spatial Coverage: East Asia and Western Pacific regions (60°N∼60°S, 80°E-140°E) Temporal Coverage: 2018.01-2018.04 Spatial Resolution: 0.02 ° Temporal Resolution: one hour Projection: GCS_WGS_1984 Data Format: NetCDF <strong>Citation </strong>(Please cite these papers when using the data)<strong>:</strong> Zhou, S., & Cheng, J. (2020). An Improved Temperature and Emissivity Separation Algorithm for the Advanced Himawari Imager. <em>IEEE Transactions on Geoscience and Remote Sensing, 58</em>, 7105-7124 Cheng, J., et al. (2013). Estimating the Optimal Broadband Emissivity Spectral Range for Calculating Surface Longwave Net Radiation. <em>IEEE Geoscience and Remote Sensing Letters, 10</em>, 401-40 If you have any questions, please contact Prof. Jie Cheng (Jie_Cheng@bnu.edu.cn).
DOI: 10.5281/zenodo.7598380
title: Himawari-8/AHI hourly clear-sky land surface temperature and emissivity dataset (2018.1-2018.4)

description: This is the clear-sky LST and LSE dataset (0.02°, hourly) derived by the iTES algorithm (Zhou and Cheng, 2020) from the Himawari-8 AHI thermal infrared data. A broadband emissivity (BBE, 8-13.5μm) dataset was also produced using the derived AHI narrowband LSEs (Cheng et al. 2013). The in-situ validation results show that the bias and RMSE of the retrieved AHI LST are 0.19 and 2.93 K in the daytime, and −0.43 and 1.95 K in the nighttime, respectively. The bias and RMSE of the retrieved LSE are less than 0.005 and 0.014, respectively, compared with the latest MYD21 LSE. The time period of this dataset is 2016-2021, covering the AHI 0.02° nominal fixed grid (60°N∼60°S, 80°E∼160°W). This is the LST&E dataset in 2018.01-2018.04 <strong>Dataset Characteristics:</strong> Spatial Coverage: East Asia and Western Pacific regions (60°N∼60°S, 80°E-140°E) Temporal Coverage: 2018.01-2018.04 Spatial Resolution: 0.02 ° Temporal Resolution: one hour Projection: GCS_WGS_1984 Data Format: NetCDF <strong>Citation </strong>(Please cite these papers when using the data)<strong>:</strong> Zhou, S., & Cheng, J. (2020). An Improved Temperature and Emissivity Separation Algorithm for the Advanced Himawari Imager. <em>IEEE Transactions on Geoscience and Remote Sensing, 58</em>, 7105-7124 Cheng, J., et al. (2013). Estimating the Optimal Broadband Emissivity Spectral Range for Calculating Surface Longwave Net Radiation. <em>IEEE Geoscience and Remote Sensing Letters, 10</em>, 401-40 If you have any questions, please contact Prof. Jie Cheng (Jie_Cheng@bnu.edu.cn).
DOI: 10.34740/kaggle/dsv/4949364
title: LUFlow Network Intrusion Detection Data Set
DOI: 10.5517/ccdc.csd.cc2bc8hh
title: CCDC 2155786: Experimental Crystal Structure Determination

description: Related Article: Neng Wang, Hang Wang, Lin-Xi Wan, Xiao-Huan Li, Xian-Li Zhou, Jia-Hong Li, Steven De Jonghe, Dominique Schols, Jin-Bu Xu, Feng Gao|2023|Org.Lett.|25|597|doi:10.1021/acs.orglett.2c04116
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.cc2bc8kk
title: CCDC 2155788: Experimental Crystal Structure Determination

description: Related Article: Neng Wang, Hang Wang, Lin-Xi Wan, Xiao-Huan Li, Xian-Li Zhou, Jia-Hong Li, Steven De Jonghe, Dominique Schols, Jin-Bu Xu, Feng Gao|2023|Org.Lett.|25|597|doi:10.1021/acs.orglett.2c04116
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.cc2c2gtr
title: CCDC 2177124: Experimental Crystal Structure Determination

description: Related Article: Tian-Tian Zhao, Hao-Ni Qin, Peng-Fei Xu|2023|Org.Lett.|25|636|doi:10.1021/acs.orglett.2c04210
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: 10.15151/esrf-es-1026511616
title: Southern Germany cryo-EM BAG: Structural analysis of protein machineries using single particle cryo-EM

description: In the past, many macromolecular complexes could not be structurally characterized at atomic resolution as they were unsuitable for crystallization and X-ray crystallography and as electron microscopy could not provide high resolution data. This changed rapidly in the last decade, as tremendous progress was achieved in the single particle cryo electron microscopy (cryo-EM) field. Meanwhile, cryo-EM became the method of choice to determine the structure of such complexes, opening a new era of structural biology. In this BAG we will, using cryo-EM, determine the structures of complicated protein machineries including large multi-subunit complexes, protein-nucleic acid complexes and membrane protein complexes. Our projects will contribute to improve the understanding of the molecular basis of energy conversion and cellular respiration, nitrate and ammonium metabolism, ribosome and ribosome-associated functions, DNA damage repair and maintenance.
DOI: 10.17632/h7ft3337g4.1
title: Mesoporous silica nanoparticles incorporated with zinc oxide as a novel antifungal agent against toxigenic fungi strains

description: MSNs–ZnO were synthesized and characterized as antifungal agents against F. graminearum and A. flavus. The MSNs were used as the carriers of ZnO release to prolong the duration of the antifungal effects on toxigenic strains. These compounds promoted morphological alteration in the fungi structure, leading to strong antifungal and antimycotoxin effects.
DOI: 10.17632/nf3vs87fyd.1
title: Malarial parasite infection varies annually, seasonally, spatially and between the sexes in song sparrows

description: Raw data
DOI: 10.17632/5cmncz59nx.1
title: Data for: Selecting the Optimal Antenna for Microwave Fracturing of Igneous Rocks

description: The datasets are for the manuscript: Selecting the Optimal Antenna for Microwave Fracturing of Igneous Rocks. They contian the antenna dimenson and the corresponding microwave power density (Table S1 and S2), the rock mineralogies (Table S3) and the heating and damage of the rock specimens when using the four different microwave antennas (Table S4).
DOI: 10.17632/f77brpmvhc.1
title: CircPRKAA1 activates a Ku80/Ku70/SREBP-1 axis driving de novo fatty acid synthesis in cancer cells

description: Many metabolism-related genes undergo alternative splicing to generate circular RNAs although their functions remain poorly understood. Here we report that circPRKAA1, a circRNA derived from the α1 subunit of AMPK, fulfils a fundamental role in maintaining lipid homeostasis. CircPRKAA1 expression facilitates fatty acid synthesis and promotes lipid storage through two coordinated functions. First, circPRKAA1 promotes a tetrameric complex between the Ku80/Ku70 heterodimer and the mature form of sterol regulatory element-binding protein-1 (mSREBP-1) to enhance the stability of mSREBP-1. Secondly, circPRKAA1 selectively binds to the promoters of the ACC1, ACLY, SCD1 and FASN genes to recruit mSREBP-1, upregulating their transcription and increasing fatty acid synthesis to promote cancer growth. Moreover, circPRKAA1 biogenesis is negatively regulated by AMPK activity with lower AMPK activation in hepatocellular carcinoma tissues frequently associated with elevated circPRKAA1 expression. Together, this work identifies circPRKAA1 as an integral element of AMPK-regulated reprogramming of lipid metabolism in cancer cells.
This dataset contains the raw data of our study.
DOI: 10.5281/zenodo.7606973
title: mapping

description: dasfa ea gaegae gaegaeg
DOI: 10.5281/zenodo.7606979
title: Scyphozoan species abundance and water parameters in the Klang Strait during June 2010-December 2011

description: This is the raw (unprocessed) datasets for scyphozoan jellyfish abundance (catch per unit effort: no. of individual/net) and environmental water parameters (salinity, temperature, pH, DO, turbidity, current speed) collected during the monthly sampling routine (June 2010-December 2011) and 24-hour sampling series conducted during the dry period of the southwest monsoon (June-July 2011) and wet period of the northeast monsoon (November-December 2011) at the Klang Strait, Malaysia. Jellyfish samples were collected during daylight flood tide occasion of the full moon on a monthly basis for 19 months (June 2010-December 2011). Sampling times were fixed at approximately six hours during the flood tide. To investigate the effect of rainfall (dry/wet period), moon phases, diel cycle and tide cycle on scyphozoan abundance, two additional sampling series were conducted on the driest period (June – July, SWM) and wettest period (November – December, NEM) of the year based on past data (Malaysian Meteorological Department). At each dry and wet period, jellyfish were collected at approximately 6-hourly sampling intervals over a 24-hour cycle every week for a month. The samplings thus covered all daily tides in the tide cycle (two flood tides and two ebb tides), day and night (diel cycle), and four consecutive moon phases (1<sup>st </sup>quarter moon, full moon, 3<sup>rd</sup> quarter moon, new moon). The number of bag nets (as replicates) set during samplings were highly dependent on weather condition and ranged from 8 to 20 nets per sampling occasion. All jellyfish from the bag nets were instantly examined and photographed in the field for identification using the keys and descriptions of Rizman-Idid et al. (2016), Jarms and Morandini (2019), and Syazwan et al. (2020b). Physical water parameters were obtained monthly at the surface layer (0.5 - 1.0 m depth from the surface) of the water column during day time (monthly sampling series), and at approximately two-hourly intervals over 24 hours (24-hour sampling series). Legends: SWM = southwest monsoon; IN = inter-monsoon; NEM = northeast monsoon; D = dry period; W = wet period; 1Q = 1<sup>st</sup> quarter moon; FM = full moon; 3Q = 3<sup>rd</sup> quarter moon; NM = new moon; D = day; N = night; F = flood tide; E = ebb tide
DOI: 10.5281/zenodo.7606978
title: Scyphozoan species abundance and water parameters in the Klang Strait during June 2010-December 2011

description: This is the raw (unprocessed) datasets for scyphozoan jellyfish abundance (catch per unit effort: no. of individual/net) and environmental water parameters (salinity, temperature, pH, DO, turbidity, current speed) collected during the monthly sampling routine (June 2010-December 2011) and 24-hour sampling series conducted during the dry period of the southwest monsoon (June-July 2011) and wet period of the northeast monsoon (November-December 2011) at the Klang Strait, Malaysia. Jellyfish samples were collected during daylight flood tide occasion of the full moon on a monthly basis for 19 months (June 2010-December 2011). Sampling times were fixed at approximately six hours during the flood tide. To investigate the effect of rainfall (dry/wet period), moon phases, diel cycle and tide cycle on scyphozoan abundance, two additional sampling series were conducted on the driest period (June – July, SWM) and wettest period (November – December, NEM) of the year based on past data (Malaysian Meteorological Department). At each dry and wet period, jellyfish were collected at approximately 6-hourly sampling intervals over a 24-hour cycle every week for a month. The samplings thus covered all daily tides in the tide cycle (two flood tides and two ebb tides), day and night (diel cycle), and four consecutive moon phases (1<sup>st </sup>quarter moon, full moon, 3<sup>rd</sup> quarter moon, new moon). The number of bag nets (as replicates) set during samplings were highly dependent on weather condition and ranged from 8 to 20 nets per sampling occasion. All jellyfish from the bag nets were instantly examined and photographed in the field for identification using the keys and descriptions of Rizman-Idid et al. (2016), Jarms and Morandini (2019), and Syazwan et al. (2020b). Physical water parameters were obtained monthly at the surface layer (0.5 - 1.0 m depth from the surface) of the water column during day time (monthly sampling series), and at approximately two-hourly intervals over 24 hours (24-hour sampling series). Legends: SWM = southwest monsoon; IN = inter-monsoon; NEM = northeast monsoon; D = dry period; W = wet period; 1Q = 1<sup>st</sup> quarter moon; FM = full moon; 3Q = 3<sup>rd</sup> quarter moon; NM = new moon; D = day; N = night; F = flood tide; E = ebb tide
DOI: 10.5281/zenodo.3994326
title: Pure POPC Membrane with 450mM CaCl2 simulations using Drude Polarizable Force Field and OpenMM

description: 500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 52 CaCl2, and 6400 SWM4 water molecules. The simulation have been performed using OpenMM 7.4.1 Frames are saved in every 10 ps. Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset. wrapped.dcd has a frame saving frequency of 100 ps. <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were centered with VMD command "pbc wrap -center origin -centersel lipid -compound residue -all", concatenated and saved in xtc format with MDAnalysis.</strong>
DOI: 10.5281/zenodo.7424729
title: MD Simulation data for a pure DOPC bilayer (1000 mM CaCl2) with AMOEBA force field + OpenMM

description: MD simulation data for the DOPC bilayer + 1000 mM CaCl2 with the AMOEBA-based force field developed by Li (https://doi.org/10.1080/00268976.2018.1436201). The simulation contains 72 DOPC lipids, 36 CaCl2 ions, and 2880 water molecules. The trajectory is 218,41 ns long (21841 frames with 10 ps saving frequency). <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the previously uploaded trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "unwrapped_all_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 12 sub-trajectories, each of which starts from the last frame of the previous one. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong>
DOI: 10.5281/zenodo.7424654
title: MD Simulation data for a pure DOPC bilayer (450 mM CaCl2) with AMOEBA force field + OpenMM

description: MD simulation data for the DOPC bilayer + 450 mM CaCl2 with the AMOEBA-based force field developed by Li (https://doi.org/10.1080/00268976.2018.1436201). The simulation contains 72 DOPC lipids, 16 CaCl2 ions, and 2880 water molecules. The trajectory is 218,41 ns long (21841 frames with 10 ps saving frequency). <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the previously uploaded trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "unwrapped_all_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 12 sub-trajectories, each of which starts from the last frame of the previous one. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong>
DOI: 10.5281/zenodo.7418855
title: MD Simulation data for a pure DOPC bilayer (450 mM NaCl) with AMOEBA force field + OpenMM

description: MD simulation data for the DOPC bilayer + 450 mM NaCl with the AMOEBA-based force field developed by Li (https://doi.org/10.1080/00268976.2018.1436201). The simulation contains 72 DOPC lipids, 17 NaCl ions, and 2880 water molecules. The trajectory is 218,41 ns long (21841 frames with 10 ps saving frequency). <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the previously uploaded trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "unwrapped_all_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 12 sub-trajectories, each of which starts from the last frame of the previous one. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong>