cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15151/esrf-es-1079480257
title: Structure of metalloproteins, membrane proteins, filamentous sarcomer proteins, and virus particles

description: Our work focusses on biological nitrogen fixation by Nitrogenase, on metalloenzymes and integral membrane proteins of bacterial and archaeal respiratory systems (Andrade/Einsle/Wohlwend), the working mechanism and regulation of medically relevant membrane proteins and complexes and their defects leading to pathologies (Hunte), bacterial antibiotic resistance factors and viral and bacterial proteins bound to their targets or inhibitors, and their interactions with glycans (Stehle), human S100 proteins involved in nutritional immunity, USP18 enforcing the endogenous antiviral interferon response, and the respiratory complex NQR of V. cholerae (Fritz), LDL lipoprotein particles with low resolution data collection and phasing to find envelopes of parts of membrane proteins escaping conventional methods (Baumstark/Lunin), and on multi-domain components of the sarcomeric filamentous protein titin and their binding to the E3 ubiquitin ligase MuRF1 and the central myosin rod-domain (Mayans).
DOI: 10.5281/zenodo.7651524
title: Dispersion in SiN microrings

description: Modal dispersion calculated with Comsol for a silicon nitride microring. Ring dimensions: radius 50 um, height 800 nm, width 1 um. Contains the dispersion of TE and TM fundamental modes, with and without material dispersion.
DOI: 10.5281/zenodo.7651525
title: Dispersion in SiN microrings

description: Modal dispersion calculated with Comsol for a silicon nitride microring. Ring dimensions: radius 50 um, height 800 nm, width 1 um. Contains the dispersion of TE and TM fundamental modes, with and without material dispersion.
DOI: 10.18434/mds2-2940
title: Experimental Measurements for Pyrolysis Model Validation - Anaerobic Gasification of PMMA Under External Thermal Radiation
DOI: 10.13020/hyd7-c792
title: Shipboard turbulence and temperature profiles from the Near Inertial Coastal Experiment (NICE), 2017-2019

description: The Near Inertial Coastal Experiment (NICE) observed the physical properties of western Lake Superior from 2016-2020. The aim was to observe near-inertial internal waves and vertical mixing due to turbulence. Using the R/V Blue Heron as an observing platform during the summers of 2017, 2018, and 2019, a Rockland Scientific VMP-250 recorded 5,813 profiles of temperature, salinity, fluorescence, turbidity, and the turbulent kinetic energy dissipation rate, and an RBR fastDuet recorded 3,974 profiles of temperature. These profiles are archived here. Additional underway data from the R/V Blue Heron is available at the Rolling deck 2 Repository (R2R; https://www.rvdata.us/search/vessel/Blue%20Heron). Moored data from the NICE experiment was documented by Austin and Elmer (2022).
description: This archive contains processed vertical profiles of turbulence and temperature collected from the R/V Blue Heron during cruises in 2017, 2018, and 2019. The collection methods are described in "RSI Technical Note 049: Tow-yoing with the VMP-250-IR" (https://rocklandscientific.com/wp-content/uploads/2021/12/TN_049_Tow_yo.pdf). The VMP-250 had 2 shear probes along with temperature, salinity, pressure, turbidity, and fluorometer sensors. The data were converted from raw voltages to meaningful quantities using Rockland Scientific's ODAS library version 4.4.09. The only modifications to the Rockland software are (1) using the freshwater equations of state and (2) computing mass diffusivity via Osborne 1980. The processed data is saved as Matlab binary files. The RBR fastDuet had a temperature and pressure sensor. Data in the native RBR format and saved as Matlab binaries files. All data is time-stamped in UTC. The locations of each profile can be determined from R/V Blue Heron GPS data available through the Rolling deck 2 Repository (R2R; https://www.rvdata.us/search/vessel/Blue%20Heron). When analysis of this data is published, post processing scripts will be archived.
DOI: 10.34943/d21d8919-92fe-4168-9d0e-d1b88aa2ee09
title: Westshore Coal Terminal Oceanographic Radar System Deployed 2019-07-30

description: The CODAR SeaSonde 25MHz VCOL was deployed on 2019-07-30 at Westshore Coal Terminal. The Westshore Coal Terminal CODAR station contributes to an array of CODARs to monitor surface currents in Strait of Georgia. This device is a Oceanographic Radar System. Oceanographic radars measure the ocean surface currents and waves in near real-time, by timing reflected radio waves, and contribute to an accurate prediction of severe weather conditions. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.34943/7bcba06e-171a-4ff5-877e-7e4a82b18e54
title: Strait of Georgia Oceanographic Radar System Deployed 2016-03-23

description: The Strait of Georgia CODAR Array was deployed on 2016-03-23 at Strait of Georgia. Strait of Georgia is located between Vancouver Island and the mainland of British Columbia. There are many narrow channels and islands in this region. Located at the south end are the Gulf Islands and San Juan Islands. The Discovery Islands and Discovery Passage are located at the north end. This device is a Oceanographic Radar System. Oceanographic radars measure the ocean surface currents and waves in near real-time, by timing reflected radio waves, and contribute to an accurate prediction of severe weather conditions. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.7295/w9cil50644
title: CIL:50644, Mus musculus, Opn4Cremouse brain tissue, miniSOG inmelanopsin retinal ganglion cells , neurites
DOI: 10.5281/zenodo.7651540
title: Cavity-waveguide coupling gap

description: Extrinsic coupling loss of a microring coupled to a waveguide as a function of the gap between the structures. Data simulated with Comsol.
DOI: 10.5281/zenodo.7651539
title: Cavity-waveguide coupling gap

description: Extrinsic coupling loss of a microring coupled to a waveguide as a function of the gap between the structures. Data simulated with Comsol.
DOI: 10.6084/m9.figshare.21823455.v18
title: The ReptileEvolution.com Project

description: Taxon exclusion is the number one problem currently vexing paleontology. The search for pterosaur, turtle, bat, snake, whale, reptile and tetrapod ancestors continues to unnecessarily befuddle paleontologists who continue to work from cherry-picked, textbook and traditional taxon lists that overlook and omit pertinent taxa. That’s why the large reptile tree (LRT), the nearly completely resolved cladogram at the heart of www.ReptileEvolution.com, includes 2212 taxa. Larger taxon numbers minimize taxon exclusion issues. Results indicate the simple act of adding taxa resolves all phylogenetic issues.
DOI: 10.6084/m9.figshare.21823455.v19
title: The ReptileEvolution.com Project

description: Taxon exclusion is the number one problem currently vexing paleontology. The search for pterosaur, turtle, bat, snake, whale, reptile and tetrapod ancestors continues to unnecessarily befuddle paleontologists who continue to work from cherry-picked, textbook and traditional taxon lists that overlook and omit pertinent taxa. That’s why the large reptile tree (LRT), the nearly completely resolved cladogram at the heart of www.ReptileEvolution.com, includes 2212 taxa. Larger taxon numbers minimize taxon exclusion issues. Results indicate the simple act of adding taxa resolves all phylogenetic issues.
DOI: 10.6084/m9.figshare.21737420
title: Reference Data

description: Reference data used to edit sample information. <br> Files include; <br> identifiers_lookup_post_new.csv - gene identifiers and the associated antibiotic or antibiotic class they are expected to confer resistance to. <br> antibioitic_classes.csv - key describing antibiotics and antibiotic class. <br> urine_lookup_post.csv - key matching sample diagnosis descriptions with whether the label indicates a positive UTI diagnosis. <br>
DOI: 10.6084/m9.figshare.21737420.v1
title: Reference Data

description: Reference data used to edit sample information. <br> Files include; <br> identifiers_lookup_post_new.csv - gene identifiers and the associated antibiotic or antibiotic class they are expected to confer resistance to. <br> antibioitic_classes.csv - key describing antibiotics and antibiotic class. <br> urine_lookup_post.csv - key matching sample diagnosis descriptions with whether the label indicates a positive UTI diagnosis. <br>
DOI: 10.5517/ccdc.csd.cc27ycxh
title: CCDC 2083817: Experimental Crystal Structure Determination

description: Related Article: Hui Liu|2021|CSD Communication|||
description: Related Article: Hui Liu, Zhi-Fen Liang, Han-Jian Liu, Jin-Xi Liao, Li-Jun Zhong, Yuan-Hong Tu, Qing-Ju Zhang, Bin Xiong, Jian-Song Sun|2023|J.Am.Chem.Soc.|145|3682|doi:10.1021/jacs.2c13018
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: 10.7295/w9cil54605
title: CIL:54605, Mus musculus, NG2-CreER<sup>TM</sup>:Rosa<sup>tdTomato/+</sup>:Cx3cr1<sup>GFP/+</sup>, astrocyte, oligodendrocyte, endothelial cell, microglia
DOI: 10.5281/zenodo.7651568
title: Climate-associated change in the abundance of Shrimp in Puget Sound, USA

description: This is the clean and raw data files needed to replicate the analysis for our paper. The data contains Pacific Decadal Oscillation and El Nino/La Nina data, as well as data from a long running trawl survey in central Puget Sound, Washington, USA. The trawl data contains counts of invertebrate species from the trawls, as well as metadata about the trawls and the conditions during trawling. The trawl is conducted yearly by the School of Aquatic and Fishery Sciences, University of Washington.
DOI: 10.5281/zenodo.7651567
title: Climate-associated change in the abundance of Shrimp in Puget Sound, USA

description: This is the clean and raw data files needed to replicate the analysis for our paper. The data contains Pacific Decadal Oscillation and El Nino/La Nina data, as well as data from a long running trawl survey in central Puget Sound, Washington, USA. The trawl data contains counts of invertebrate species from the trawls, as well as metadata about the trawls and the conditions during trawling. The trawl is conducted yearly by the School of Aquatic and Fishery Sciences, University of Washington.
DOI: 10.6084/m9.figshare.22120511
title: Wungong_macroinvertebrates_20162017.xlsx

description: Freshwater macroinvertebrate assemblages from the Wungong Brook catchment in Southwestern Australia. Collections from perennial streams, and formerly-perennial, now intermittent streams impacted by climate drying.
DOI: 10.6084/m9.figshare.22120511.v2
title: Wungong_macroinvertebrates_20162017.xlsx

description: Freshwater macroinvertebrate assemblages from the Wungong Brook catchment in Southwestern Australia. Collections from perennial streams, and formerly-perennial, now intermittent streams impacted by climate drying.
DOI: 10.6084/m9.figshare.22120511.v1
title: Wungong_macroinvertebrates_20162017.xlsx

description: Freshwater macroinvertebrate assemblages from the Wungong Brook catchment in Southwestern Australia. Collections from perennial streams, and formerly-perennial, now intermittent streams impacted by climate drying.
DOI: 10.6084/m9.figshare.21737288
title: Sample information for AMR analysis.

description: For files; fg_metadata.csv - metadata for samples, including; sample ID, host animal species name, host animal common name, source tissue, veterinary diagnosis of animal and urinary tract infection diagnosis. <br> fg_genotype.csv - genotype information for samples, including; sample id, host animal common name, gene name, gene identifier, gene family, gene type, and antibiotic to which it confers resistance. <br> fg_phenotype - phenotype information for samples, describing what antibiotic a sample is resistant to. Phenotype labels are Sensitive, Resistance, WT, or Non-WT. <br> <br>
DOI: 10.5281/zenodo.7651594
title: A social niche breadth score reveals niche range strategies of generalists and specialists

description: <strong>Abstract</strong> Generalists can survive in many environments whereas specialists are restricted to a single environment. Although a classical concept in ecology, niche breadth has remained challenging to quantify for microbes because it depends on an objective definition of the environmental conditions. Here, by defining the environment of a microbe as the community it resides in, we integrated information from over 22 thousand environmental sequencing samples to derive a quantitative measure of the niche, which we call ‘social niche breadth’. At the level of genera, we explored niche range strategies throughout the prokaryotic tree of life. We found that social generalists include opportunists that stochastically dominate local communities, while social specialists are stable but low in abundance. Social generalists have a more diverse and open pan genome than social specialists, but we found no global correlation between social niche breadth and genome size. Instead, we observed two distinct evolutionary strategies, where specialists have relatively small genomes in habitats with low local diversity, but relatively large genomes in habitats with high local diversity. Together, our analysis shines data-driven light on microbial niche range strategies. <strong>Inside this repository</strong> This is the directory structure and code used to generate all data and figures in the paper "A social niche breadth score reveals niche range strategies of generalists and specialists" by F. A. Bastiaan von Meijenfeldt, Paulien Hogeweg, and Bas E. Dutilh. The code was made by F. A. Bastiaan von Meijenfeldt. The code inside the ./MGnify directory was used to download the MGnify data. The code inside the ./niche_breadth directory was used to generate all other data and uses the MGnify data. The code inside the ./figures directory was used to generate all figures.<br> Each directory in ./MGnify and ./niche_breadth contains a commands.sh that if run, and if source files are present, will generate all content in that directory. No files are written outside the directory. For example running ./MGnify/commands.sh will generate all files within ./MGnify. The generated files are source files for some of the scripts in ./MGnify/2019-08-20_extra and ./MGnify/2019-08-20_extra/commands.sh can now be run to generate all files within. Source files for the ./niche_breadth subdirectories can be from the ./MGnify directory or from other subdirectories within ./niche_breadth. The ./figures directory and its subdirectories contain *.ipynb Jupyter Notebook files that if run, and source files are present, will generate the vector files that were used as raw input for the final figures.<br> The file ./figures/mappings.Figure_to_Notebook.txt contains the mapping of the figure to the notebook that was used to generate the figure. In some cases only part of the notebook output was used in the final figures.
DOI: 10.5281/zenodo.7651593
title: A social niche breadth score reveals niche range strategies of generalists and specialists

description: <strong>Abstract</strong> Generalists can survive in many environments whereas specialists are restricted to a single environment. Although a classical concept in ecology, niche breadth has remained challenging to quantify for microbes because it depends on an objective definition of the environmental conditions. Here, by defining the environment of a microbe as the community it resides in, we integrated information from over 22 thousand environmental sequencing samples to derive a quantitative measure of the niche, which we call ‘social niche breadth’. At the level of genera, we explored niche range strategies throughout the prokaryotic tree of life. We found that social generalists include opportunists that stochastically dominate local communities, while social specialists are stable but low in abundance. Social generalists have a more diverse and open pan genome than social specialists, but we found no global correlation between social niche breadth and genome size. Instead, we observed two distinct evolutionary strategies, where specialists have relatively small genomes in habitats with low local diversity, but relatively large genomes in habitats with high local diversity. Together, our analysis shines data-driven light on microbial niche range strategies. <strong>Inside this repository</strong> This is the directory structure and code used to generate all data and figures in the paper "A social niche breadth score reveals niche range strategies of generalists and specialists" by F. A. Bastiaan von Meijenfeldt, Paulien Hogeweg, and Bas E. Dutilh. The code was made by F. A. Bastiaan von Meijenfeldt. The code inside the ./MGnify directory was used to download the MGnify data. The code inside the ./niche_breadth directory was used to generate all other data and uses the MGnify data. The code inside the ./figures directory was used to generate all figures.<br> Each directory in ./MGnify and ./niche_breadth contains a commands.sh that if run, and if source files are present, will generate all content in that directory. No files are written outside the directory. For example running ./MGnify/commands.sh will generate all files within ./MGnify. The generated files are source files for some of the scripts in ./MGnify/2019-08-20_extra and ./MGnify/2019-08-20_extra/commands.sh can now be run to generate all files within. Source files for the ./niche_breadth subdirectories can be from the ./MGnify directory or from other subdirectories within ./niche_breadth. The ./figures directory and its subdirectories contain *.ipynb Jupyter Notebook files that if run, and source files are present, will generate the vector files that were used as raw input for the final figures.<br> The file ./figures/mappings.Figure_to_Notebook.txt contains the mapping of the figure to the notebook that was used to generate the figure. In some cases only part of the notebook output was used in the final figures.
DOI: 10.5281/zenodo.7651605
title: Ring-ring coupling gap

description: Coupling coefficients of two coupled microrings as a function of the gap between the structures. Data simulated with Comsol.
DOI: 10.5281/zenodo.7651604
title: Ring-ring coupling gap

description: Coupling coefficients of two coupled microrings as a function of the gap between the structures. Data simulated with Comsol.
DOI: 10.6084/m9.figshare.22106189
title: Ultrasonic P-wave to Acquire Parameters of Boise Sandstone

description: Phase velocity and the quality factor of P-wave in water-saturated Boise sandstone, as well as the squirt coefficient.
DOI: 10.6084/m9.figshare.22106189.v2
title: Ultrasonic P-wave to Acquire Parameters of Boise Sandstone

description: Phase velocity and the quality factor of P-wave in water-saturated Boise sandstone, as well as the squirt coefficient.
DOI: 10.6084/m9.figshare.22106189.v1
title: Ultrasonic P-wave to Acquire Parameters of Boise Sandstone

description: Phase velocity and the quality factor of P-wave in water-saturated Boise sandstone, as well as the squirt coefficient.
DOI: 10.5517/ccdc.csd.cc2cmg7q
title: CCDC 2193443: Experimental Crystal Structure Determination

description: Related Article: Hui Liu, Zhi-Fen Liang, Han-Jian Liu, Jin-Xi Liao, Li-Jun Zhong, Yuan-Hong Tu, Qing-Ju Zhang, Bin Xiong, Jian-Song Sun|2023|J.Am.Chem.Soc.|145|3682|doi:10.1021/jacs.2c13018
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.cc2cx4bs
title: CCDC 2201785: Experimental Crystal Structure Determination

description: Related Article: Ye Yuan, Muliang Zhang, Xiaodong Tang, Jared L. Piper, Zhi-Hui Peng, Jun-An Ma, Jie Wu, Fa-Guang Zhang|2023|Org.Lett.|25|883|doi:10.1021/acs.orglett.3c00115
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.cc2cylc9
title: CCDC 2203181: Experimental Crystal Structure Determination

description: Related Article: Andrew Ritchhart, Alexander S. Filatov, Ie-Rang Jeon, John S. Anderson|2023|Inorg.Chem.|62|2817|doi:10.1021/acs.inorgchem.2c03991
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.cc2cyldb
title: CCDC 2203182: Experimental Crystal Structure Determination

description: Related Article: Andrew Ritchhart, Alexander S. Filatov, Ie-Rang Jeon, John S. Anderson|2023|Inorg.Chem.|62|2817|doi:10.1021/acs.inorgchem.2c03991
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.cc2d19sk
title: CCDC 2205798: Experimental Crystal Structure Determination

description: Related Article: M. Carla Aragoni, Enrico Podda, Veronica Caria, Silvia A. Carta, M. Francesca Cherchi, Vito Lippolis, Simone Murgia, Germano Orrù, Gabriele Pippia, Alessandra Scano, Alexandra M. Z. Slawin, J. Derek Woollins, Anna Pintus, Massimiliano Arca|2023|Inorg.Chem.|62|2924|doi:10.1021/acs.inorgchem.2c04410
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.cc2d19tl
title: CCDC 2205799: Experimental Crystal Structure Determination

description: Related Article: M. Carla Aragoni, Enrico Podda, Veronica Caria, Silvia A. Carta, M. Francesca Cherchi, Vito Lippolis, Simone Murgia, Germano Orrù, Gabriele Pippia, Alessandra Scano, Alexandra M. Z. Slawin, J. Derek Woollins, Anna Pintus, Massimiliano Arca|2023|Inorg.Chem.|62|2924|doi:10.1021/acs.inorgchem.2c04410
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.