cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14312582
title: Figure 1C datasource file.xlsx

description: HIV-1 Vpr mediated degradation of CCDC137 requires neddylation. CCDC137 band quantification results in the presence or absence of neddylation inhibitor MLN4924.
DOI: 10.6084/m9.figshare.14188853.v2
title: NWRS Acquisition Portfolio Optimization for MBCF

description: The NWRS Acquisition Portfolio Optimization for MBCF is an Excel-based model, supplement for the "Multicriteria decisions and portfolio analysis: Land acquisition for biological and social objectives" in Ecological Applications. The model illustrates a constrained optimization based on multiple criteria and a defined annual budget for the MBCF. The file includes the mutlicriteria optimization, a Pareto Efficiency Frontier analysis, and a weight sensitivity analysis.
DOI: 10.6084/m9.figshare.14312591
title: Figure 1B datasource file.xlsx

description: HIV-1 Vpr medicated degradation of CCDC137 requires DCAF1. Endogenous CCDC137 protein band quantification in the presence or absence of DCAF1 siRNA.
DOI: 10.6084/m9.figshare.14312591.v1
title: Figure 1B datasource file.xlsx

description: HIV-1 Vpr medicated degradation of CCDC137 requires DCAF1. Endogenous CCDC137 protein band quantification in the presence or absence of DCAF1 siRNA.
DOI: 10.6073/pasta/89e07484a91d8b503ae19d772555fbb4
title: Ammonium desorption of hyporheic sediments from Von Guerard Stream, McMurdo Dry Valleys, Antarctica (January 2019)

description: This data package provides analytic results for a laboratory assay on sediment samples collected in January 2019 from a transect (“P2”) across Von Guerard Stream (as described by Heindel et al. 2021), located in Taylor Valley, McMurdo Dry Valleys, Antarctica. We used excess sample from that study in a laboratory desorption assay to assess conductivity dependent desorption of ammonium. The assay was performed by mixing samples with potassium chloride treatment solutions that replicate the range of specific conductivities observed in Von Guerard Stream, shaking and centrifuging slurries, and analyzing filtered supernatant.
DOI: 10.5281/zenodo.4637926
title: Datasets used in the dyngen manuscript

description: These datasets are generated by [dyngen](https://dyngen.dynverse.org) to evaluate Trajectory Alignment, RNA velocity and Cell-Specific Network Inference methods. To reproduce the findings of the manuscript, clone the [dyngen_manuscript](https://github.com/dynverse/dyngen_manuscript) repository and extract these files in the `temporary_files` folder.
DOI: 10.5281/zenodo.4637925
title: Datasets used in the dyngen manuscript

description: These datasets are generated by [dyngen](https://dyngen.dynverse.org) to evaluate Trajectory Alignment, RNA velocity and Cell-Specific Network Inference methods. To reproduce the findings of the manuscript, clone the [dyngen_manuscript](https://github.com/dynverse/dyngen_manuscript) repository and extract these files in the `temporary_files` folder.
DOI: 10.6084/m9.figshare.14312588
title: Figure 2B datasource file.xlsx

description: Endogenous CCDC137 protein quantification. Samples transfected with pFIN-Vpr WT or pFIN-Vpr R80A.
DOI: 10.6084/m9.figshare.14312588.v1
title: Figure 2B datasource file.xlsx

description: Endogenous CCDC137 protein quantification. Samples transfected with pFIN-Vpr WT or pFIN-Vpr R80A.
DOI: 10.6084/m9.figshare.14312594
title: Figure 3B datasource file.xlsx

description: G2/M cell cycle arrest in HeLa cells treated with scramble, CCDC137 or MCM10 siRNAs.
DOI: 10.6084/m9.figshare.14312594.v1
title: Figure 3B datasource file.xlsx

description: G2/M cell cycle arrest in HeLa cells treated with scramble, CCDC137 or MCM10 siRNAs.
DOI: 10.6084/m9.figshare.14312600
title: Figure 3C datasource file.xlsx

description: phospho CDK1(Y15) protein levels in 293FT cells the presence or absence of Vpr
DOI: 10.6084/m9.figshare.14312600.v1
title: Figure 3C datasource file.xlsx

description: phospho CDK1(Y15) protein levels in 293FT cells the presence or absence of Vpr
DOI: 10.5517/ccdc.csd.cc238hjf
title: CCDC 1944584: Experimental Crystal Structure Determination

description: Related Article: Afsaneh Khansari, Macguire R. Bryant, Daniel R. Jenkinson, Geoffrey B. Jameson, Omid T. Qazvini, Lujia Liu, Andrew D. Burrows, Shane G. Telfer, Christopher Richardson|2019|CrystEngComm|21|7498|doi:10.1039/C9CE01669D
DOI: 10.5517/ccdc.csd.cc238hkg
title: CCDC 1944585: Experimental Crystal Structure Determination

description: Related Article: Afsaneh Khansari, Macguire R. Bryant, Daniel R. Jenkinson, Geoffrey B. Jameson, Omid T. Qazvini, Lujia Liu, Andrew D. Burrows, Shane G. Telfer, Christopher Richardson|2019|CrystEngComm|21|7498|doi:10.1039/C9CE01669D
DOI: 10.5517/ccdc.csd.cc238hlh
title: CCDC 1944586: Experimental Crystal Structure Determination

description: Related Article: Afsaneh Khansari, Macguire R. Bryant, Daniel R. Jenkinson, Geoffrey B. Jameson, Omid T. Qazvini, Lujia Liu, Andrew D. Burrows, Shane G. Telfer, Christopher Richardson|2019|CrystEngComm|21|7498|doi:10.1039/C9CE01669D
DOI: 10.5281/zenodo.4638202
title: Establishing a Search String to Detect SecondaryStudies in Software Engineering

description: Support documents of the study Establishing a Search String to Detect SecondaryStudies in Software Engineering. It contains: Extracted data from included tertiary studies used as the basis of our analysis; Supplementary tables; Selected secondary studies through the execution of the validation process - Step 2
DOI: 10.5281/zenodo.4638201
title: Establishing a Search String to Detect SecondaryStudies in Software Engineering

description: Support documents of the study Establishing a Search String to Detect SecondaryStudies in Software Engineering. It contains: Extracted data from included tertiary studies used as the basis of our analysis; Supplementary tables; Selected secondary studies through the execution of the validation process - Step 2
DOI: 10.6084/m9.figshare.14312603
title: Figure 3D datasource file.xlsx

description: phosphoCDK1 (Y15) protein levels in 293FT cells in the presence of scramble or CCDC137 siRNA
DOI: 10.6084/m9.figshare.14312603.v1
title: Figure 3D datasource file.xlsx

description: phosphoCDK1 (Y15) protein levels in 293FT cells in the presence of scramble or CCDC137 siRNA
DOI: 10.25919/k798-4735
title: Parkes observations for project P1061 semester 2020OCTS_22

description: Fast Radio Bursts (FRBs) have extremely high brightness temperature, owing to their short-duration and prominent flux from the distant universe. The studies on emission mechanism of FRBs have met bottleneck for a long time unless a complete spectrum is measured. We propose to observe a new repeating FRB source, FRB 180301, using the Parkes ultra-wide-bandwidth receiver (UWL). This source was initially found by Parkes multibeam receivers and confirmed repetition by the FAST telescope. The source is still active until Jun 2020 from FAST follow-ups. It’s an ideal opportunity to capture comprehensive spectral information using the Parkes UWL. We demonstrate that the beam coverage is feasible and 30-hr observations are required for at least one detection.
DOI: 10.6084/m9.figshare.14312597
title: Figure 4b datasource file.xlsx

description: Endogenous CCDC137 and MCM10 protein levels in the presence of DMSO or CDK1 inhibitor Ro3306.
DOI: 10.6084/m9.figshare.14312597.v1
title: Figure 4b datasource file.xlsx

description: Endogenous CCDC137 and MCM10 protein levels in the presence of DMSO or CDK1 inhibitor Ro3306.
DOI: 10.5281/zenodo.4638203
title: Supporting Information for "Utilizing Environmental Tracers to Reduce Groundwater Flow Transport Model Parameter Uncertainties"

description: Supplementary Tables and Figures for manuscript "Utilizing Environmental Tracers to Reduce Groundwater Flow Transport Model Parameter Uncertainties" submitted to Water Resources Research June 2020.
DOI: 10.5281/zenodo.4638220
title: A complex genetic architecture in zebrafish relatives Danio quagga and D. kyathit underlies development of stripes and spots

description: Genotype and phenotype matrices used for QTL identification and plotting in R/qtl2.
DOI: 10.5281/zenodo.4635708
title: Super.FELT_external_dataset

description: External dataset for Super.FELT
DOI: 10.17632/rkbbz27vsd.1
title: Data for: Contributions of phenological groups of wild bees as an indicator of food availability in urban wastelands

description: Database of bee species found in Bydgoszcz in 2016-2018.
DOI: 10.25493/mh37-1x8
title: Transitions between different naturally and artificially-induced brain states in in vivo rats

description: The aim of the present experiments is to illustrate the cortical and sub-cortical dynamics underlying the natural-induced (sleep) and artificially-induced (anesthesia) conditions in the freely moving chronic implanted rat. The characterization of the transitions between states (Slow Oscillations, Slow Wave Sleep, REM, Awake, …) under these conditions is something that still needs to be further explore and the current dataset could help in that. The dataset contains the entire sessions for 3 different subjects, two of them belong to anesthesia (different concentrations of Ketamine + Medetomidine) and the other belongs to natural sleep.
DOI: 10.6084/m9.figshare.14312618.v1
title: example.tar.gz

description: A simulated data set with 3000 insertions.
DOI: 10.6084/m9.figshare.14312618
title: example.tar.gz

description: A simulated data set with 3000 insertions.
DOI: 10.6084/m9.figshare.14312717
title: Ribosomal protein database of Staphylococcus haemolyticus (strain JCSC1435)

description: This work presents the ribosomal protein database of <i>Staphylococcus haemolyticus </i>(strain JCSC1435). Original data for the work came from the annotated proteome data of the bacterium downloaded from UniProt. Using an in-house MATLAB ribosomal protein database analysis software, the original proteome data file was parsed to extract protein name and amino acid sequence of all ribosomal proteins in the species. The database also includes calculated variables such as number of residues, molecular weight, and nucleotide sequence. Overall, the presented database could serve as a ribosomal protein mass fingerprint for use in microbial identification, or it could be used in fundamental studies seeking to uncover new insights into ribosomal protein biology.
DOI: 10.6084/m9.figshare.14312717.v1
title: Ribosomal protein database of Staphylococcus haemolyticus (strain JCSC1435)

description: This work presents the ribosomal protein database of <i>Staphylococcus haemolyticus </i>(strain JCSC1435). Original data for the work came from the annotated proteome data of the bacterium downloaded from UniProt. Using an in-house MATLAB ribosomal protein database analysis software, the original proteome data file was parsed to extract protein name and amino acid sequence of all ribosomal proteins in the species. The database also includes calculated variables such as number of residues, molecular weight, and nucleotide sequence. Overall, the presented database could serve as a ribosomal protein mass fingerprint for use in microbial identification, or it could be used in fundamental studies seeking to uncover new insights into ribosomal protein biology.
DOI: 10.5281/zenodo.4638248
title: In pursuit of a better world: crop improvement and the CGIAR - SUPPLEMENTARY MATERIALS

description: <strong>Supplementary Material for manuscript with the same name published at JXB.</strong>
DOI: 10.5281/zenodo.4323546
title: In pursuit of a better world: crop improvement and the CGIAR - SUPPLEMENTARY MATERIALS

description: <strong>Supplementary Material for manuscript with the same name published at JXB.</strong>
DOI: 10.25345/c5cr5d
title: MassIVE MSV000087101 - Polymyxin resistance in colibactin-producing Escherichia coli induces host genotoxicity
title: The complex reservoir of metabolite-producing bacteria in the gastrointestinal tract contributes tremendously to human health and disease. Bacterial composition, and by extension gut metabolomic composition, is undoubtably influenced by the use of modern antibiotics. Herein, we demonstrate that polymyxin B, a last resort antibiotic used for chronic multidrug resistant infections infections, influences the production of the genotoxic metabolite colibactin from adherent-invasive Escherichia coli (AIEC) NC101. Colibactin can augment colorectal cancer (CRC) through DNA double stranded breaks and interstrand crosslinks. While the structure and biosynthesis of colibactin has been elucidated, chemical-induced regulation of its biosynthetic gene cluster and subsequent production of the genotoxin by pathogenic E. coli are largely unexplored. This research highlights the regulation of the colibactin-producing biosynthetic gene cluster under polymyxin stress. Using a multi-omic approach, we have identified that polymyxin stress enhances the abundance of colibactin biosynthesis proteins (Clbs) in multiple pks+ E. coli strains, including pro-carcinogenic AIEC: NC101, the probiotic strain: E. coli Nissle 1917, and the antibiotic testing strain: E. coli ATCC 25922. Expression analysis via qPCR revealed that increased transcription of clb genes likely contributes to elevated Clb protein levels in NC101. Enhanced production of Clbs by NC101 under polymyxin stress matched an increased production of the colibactin prodrug motif, a proxy for the mature genotoxic metabolite. Furthermore, E. coli with heightened tolerance for polymyxin antibiotics induced greater DNA damage, assessed by quantification of yH2AX staining in cultured intestinal epithelial cells. This study establishes a key link between the polymyxin B stress response and colibactin production in pks+ E. coli. Ultimately, our findings will inform future studies investigating colibactin regulation, the microbial response to antibiotics in the gut, and the ability of seemingly innocuous commensal microbes to induce host disease.
DOI: 10.21227/c7f5-9j96
title: January-28-Dong-Jiawei

description: January-28-Dong-Jiawei
DOI: 10.5517/ccdc.csd.cc24y90f
title: CCDC 1994354: Experimental Crystal Structure Determination

description: Related Article: Qing-Rong Kong, Dong Li, Xiao-Lin Liu, Hai-Xia Zhao, Yan-Ping Ren, La-Sheng Long, Lan-Sun Zheng|2021|Inorg.Chem.|60|3565|doi:10.1021/acs.inorgchem.0c02549
DOI: 10.5517/ccdc.csd.cc24y91g
title: CCDC 1994355: Experimental Crystal Structure Determination

description: Related Article: Qing-Rong Kong, Dong Li, Xiao-Lin Liu, Hai-Xia Zhao, Yan-Ping Ren, La-Sheng Long, Lan-Sun Zheng|2021|Inorg.Chem.|60|3565|doi:10.1021/acs.inorgchem.0c02549
DOI: 10.5517/ccdc.csd.cc24y95l
title: CCDC 1994359: Experimental Crystal Structure Determination

description: Related Article: Qing-Rong Kong, Dong Li, Xiao-Lin Liu, Hai-Xia Zhao, Yan-Ping Ren, La-Sheng Long, Lan-Sun Zheng|2021|Inorg.Chem.|60|3565|doi:10.1021/acs.inorgchem.0c02549
DOI: 10.5517/ccdc.csd.cc24y97n
title: CCDC 1994361: Experimental Crystal Structure Determination

description: Related Article: Qing-Rong Kong, Dong Li, Xiao-Lin Liu, Hai-Xia Zhao, Yan-Ping Ren, La-Sheng Long, Lan-Sun Zheng|2021|Inorg.Chem.|60|3565|doi:10.1021/acs.inorgchem.0c02549
DOI: 10.5517/ccdc.csd.cc25zcp7
title: CCDC 2025189: Experimental Crystal Structure Determination

description: Related Article: Yun Ye, Jie Zhu, Yinhua Huang|2021|Org.Lett.|23|2386|doi:10.1021/acs.orglett.1c00748
DOI: 10.5517/ccdc.csd.cc25zcq8
title: CCDC 2025190: Experimental Crystal Structure Determination

description: Related Article: Yun Ye, Jie Zhu, Yinhua Huang|2021|Org.Lett.|23|2386|doi:10.1021/acs.orglett.1c00748
DOI: 10.5517/ccdc.csd.cc261wgm
title: CCDC 2027600: Experimental Crystal Structure Determination

description: Related Article: Xiao-Jing Zhao, Zi-Hao Li, Tong-Mei Ding, Jin-Miao Tian, Yong-Qiang Tu, Ai-Fang Wang, Yu-Yang Xie|2021|Angew.Chem.,Int.Ed.|60|7061|doi:10.1002/anie.202015001
DOI: 10.25919/dsc8-9v73
title: CCS - CCS_SF_03 Mooring data May 2019 deployment EDGE System

description: This bio-acoustic data was collected between the 7th May 2019 and the 18th November 2019 at the proposed site for subsea CCS off Gippsland, Victoria using the EDGE system. Data summary: Turret system experienced problems where rotation of the system failed sometime after deployment. E&T sent a team to fix this. EDGE System: The EDGE system comprises a Simrad WBAT self contained echosounder connected to a Simrad ES70-7CD 70 kHz 7 degree transducer. The transducer is set atop a turret where a belt driven motor rotates the transducer through 360 degrees over a 20 minute period. A second rotation of 20 minuts occurs to take the transducer back to the starting postion. The rotation comprises steps of 7 degrees rotation where 20 pings are recorded at each step. The EDGE system was mounted to seafloor lander 2 (CCS_SF_03) and was deployed on the 7th of May 2019 in approximately 120m of water at site proposed for subsea CCS (38.2566S, 147.4247E). Parameter | Value Transducer manufacturer | Simrad Transducer model | ES70-CD Transducer serial number | 120 Transceiver manufacturer | Simrad Transceiver model | WBAT Transceiver serial number | 253667 Frequency (kHz) | Power (W) | Pulse duration (ms) | Ping Rate (pings per second) | Ping Rate (pings per second) 70 | 500 | 2.048 | 450 | 1.2 Echosounder system was uncalibrated.
DOI: 10.6084/m9.figshare.14298860
title: Supplementary of Original western blots.docx

description: Supplementary of Original western blots
DOI: 10.5281/zenodo.4638267
title: Dataset and Results for Deep Emulators for Differentiation, Forecasting and Parameterization in Earth Science Simulators

description: To understand and predict large, complex and chaotic systems, Earth scientists build simulators from physical laws. Simulators generalize better to new scenarios, require fewer tunable parameters and are more interpretable than non-physical deep learning, but procedures for obtaining their derivatives with respect to their inputs are often unavailable. These missing derivatives limit the application of many important tools for forecasting, model tuning, sensitivity analysis or sub-grid-scale parameterization. Here we propose to overcome this limitation with deep emulator networks that learn to calculate the missing derivatives. By training directly on simulation data without analyzing source code or equations, this approach supports simulators in any programming language on any hardware without specialized routines for each case. To demonstrate the effectiveness of our approach, we train emulators on complete or partial system states of the chaotic Lorenz-96 simulator, and evaluate the accuracy of their dynamics and derivatives as a function of integration time and training dataset size. We further demonstrate that emulator-derived derivatives enable accurate 4D-Var data assimilation and closed-loop training of parametrizations. These results provide a basis for further combining the unique inductive biases of physical models with the power and flexibility of machine learning.<br> <br> This archive contains the code, simulated data and numerical results of our study.
DOI: 10.5281/zenodo.4638266
title: Dataset and Results for Deep Emulators for Differentiation, Forecasting and Parameterization in Earth Science Simulators

description: To understand and predict large, complex and chaotic systems, Earth scientists build simulators from physical laws. Simulators generalize better to new scenarios, require fewer tunable parameters and are more interpretable than non-physical deep learning, but procedures for obtaining their derivatives with respect to their inputs are often unavailable. These missing derivatives limit the application of many important tools for forecasting, model tuning, sensitivity analysis or sub-grid-scale parameterization. Here we propose to overcome this limitation with deep emulator networks that learn to calculate the missing derivatives. By training directly on simulation data without analyzing source code or equations, this approach supports simulators in any programming language on any hardware without specialized routines for each case. To demonstrate the effectiveness of our approach, we train emulators on complete or partial system states of the chaotic Lorenz-96 simulator, and evaluate the accuracy of their dynamics and derivatives as a function of integration time and training dataset size. We further demonstrate that emulator-derived derivatives enable accurate 4D-Var data assimilation and closed-loop training of parametrizations. These results provide a basis for further combining the unique inductive biases of physical models with the power and flexibility of machine learning.<br> <br> This archive contains the code, simulated data and numerical results of our study.
DOI: 10.6084/m9.figshare.14312585
title: Figure 1D datasource file.xlsx

description: Figure 1D supporting .fcs filesHela cells transfected with pFIN-GFP or pFIN-Vpr and treated with DMSO or MLN4924
DOI: 10.6084/m9.figshare.14312585.v1
title: Figure 1D datasource file.xlsx

description: Figure 1D supporting .fcs filesHela cells transfected with pFIN-GFP or pFIN-Vpr and treated with DMSO or MLN4924
DOI: 10.6084/m9.figshare.14312816
title: Figure 4A .fcs datasource files

description: Figure 4A. BV421 fluorescence from HeLa cells treated with DMSO or 1-10 microM CDK1 inhibitor Ro3306.
DOI: 10.6084/m9.figshare.14312816.v1
title: Figure 4A .fcs datasource files

description: Figure 4A. BV421 fluorescence from HeLa cells treated with DMSO or 1-10 microM CDK1 inhibitor Ro3306.
DOI: 10.6084/m9.figshare.14312834
title: Figure 3B .fcs filesource data

description: Figure 3B. BV421 fluorescence data from HeLa cells treated with either scramble, CCDC137 or MCM10 siRNA.
DOI: 10.6084/m9.figshare.14312834.v1
title: Figure 3B .fcs filesource data

description: Figure 3B. BV421 fluorescence data from HeLa cells treated with either scramble, CCDC137 or MCM10 siRNA.
DOI: 10.6084/m9.figshare.14312828.v1
title: A laminated microbial ecosystem at the summit of the Cambrian Explosion

description: The Guojiaba Formation (Cambrian Stage 3), composed of laminated sandstones, siltstones, and mudstones mainly, is characterized by two units of MISS (biolamination) in the north margin of Yangzi plate. Biolamination arises from the microbial growth and it is characterized by alternation of light layers and dark layers in polished slides and thin sections. The light layers represent the normal background deposition where the development of microbial community is inhibited; whereas, the dark layers are rich in organic materials. SEM examination on the dark layers identified seven types of microorganisms in morphology confirmed the development of microbial community. The occurrence of the biolamination in Guojiaba Formation indicates a complex microbial ecosystem within epibenthic microbial mats in a relatively semi-closed to closed sedimentary environments at the summit of the Cambrian Explosion.
DOI: 10.6084/m9.figshare.14312828
title: A laminated microbial ecosystem at the summit of the Cambrian Explosion

description: The Guojiaba Formation (Cambrian Stage 3), composed of laminated sandstones, siltstones, and mudstones mainly, is characterized by two units of MISS (biolamination) in the north margin of Yangzi plate. Biolamination arises from the microbial growth and it is characterized by alternation of light layers and dark layers in polished slides and thin sections. The light layers represent the normal background deposition where the development of microbial community is inhibited; whereas, the dark layers are rich in organic materials. SEM examination on the dark layers identified seven types of microorganisms in morphology confirmed the development of microbial community. The occurrence of the biolamination in Guojiaba Formation indicates a complex microbial ecosystem within epibenthic microbial mats in a relatively semi-closed to closed sedimentary environments at the summit of the Cambrian Explosion.
DOI: 10.26180/14273243
title: Figure 4 dataset images

description: Figure 4 dataset images
DOI: 10.26180/14273243.v1
title: Figure 4 dataset images

description: Figure 4 dataset images
DOI: 10.26180/14178629.v1
title: Supplementary Figure 2 data

description: Supplementary Figure 2 data