cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7749765
title: Data From: B1 Field inhomogeneity correction for qDESS T2 mapping: application to rapid bilateral knee imaging

description: <strong>Purpose</strong>: T2 mapping is a powerful tool for studying osteoarthritis (OA) changes and bilateral imaging may be useful in investigating the role of between-knee asymmetry in OA onset and progression. The quantitative double-echo in steady-state (qDESS) can provide fast simultaneous bilateral knee T2 and high-resolution morphometry for cartilage and meniscus.<br> The qDESS uses an analytical signal model to compute T2 relaxometry maps, which require knowledge of the flip angle (FA). <br> In the presence of B1 inhomogeneities, inconsistencies between the nominal and actual FA can affect the accuracy of T2 measurements.<br> We propose a pixel-wise B1 correction method for qDESS T2 mapping exploiting an auxiliary B1 map to compute the actual FA used in the model.<br> <br> <strong>Methods</strong>: The technique was validated in a phantom and in vivo with simultaneous bilateral knee imaging. <br> T2 measurements of femoral cartilage (FC) of both knees of six healthy participants were repeated longitudinally to investigate the association between T2 variation and B1. <strong>Results</strong>: The results showed that applying the B1 correction mitigated T2 variations that were driven by B1 inhomogeneities. <br> Specifically, T2 left-right symmetry increased following the B1 correction (rc = 0.74 &gt; rc = 0.69). Without the B1 correction, T2 values showed a linear dependence with B1. The linear coefficient decreased using the B1 correction (from 24.3 \(\pm\) 1.6 ms to 4.1 \(\pm\) 1.8) and the correlation was not statistically significant after the application of the Bonferroni correction (p-value &gt; 0.01).<br> <br> <strong>Conclusion</strong>: the study showed that B1 correction could mitigate variations driven by the sensitivity of the qDESS T2 mapping method to B1, therefore increasing the sensitivity to detect real biological changes. The proposed method may improve the robustness of bilateral qDESS T2 mapping, allowing for an accurate and more efficient evaluation of OA pathways and pathophysiology through longitudinal and cross-sectional studies. <strong>This repository contains the raw data for reproducing the results reported in the paper. The data are provided in NIFTI format. The repository also contains the MALTAB scripts used to compute B<sub>1</sub> maps from the NIFTI data.</strong>
DOI: 10.5281/zenodo.7478225
title: Data From: B1 Field inhomogeneity correction for qDESS T2 mapping: application to rapid bilateral knee imaging

description: <strong>Purpose</strong>: T2 mapping is a powerful tool for studying osteoarthritis (OA) changes and bilateral imaging may be useful in investigating the role of between-knee asymmetry in OA onset and progression. The quantitative double-echo in steady-state (qDESS) can provide fast simultaneous bilateral knee T2 and high-resolution morphometry for cartilage and meniscus.<br> The qDESS uses an analytical signal model to compute T2 relaxometry maps, which require knowledge of the flip angle (FA). <br> In the presence of B1 inhomogeneities, inconsistencies between the nominal and actual FA can affect the accuracy of T2 measurements.<br> We propose a pixel-wise B1 correction method for qDESS T2 mapping exploiting an auxiliary B1 map to compute the actual FA used in the model.<br> <br> <strong>Methods</strong>: The technique was validated in a phantom and in vivo with simultaneous bilateral knee imaging. <br> T2 measurements of femoral cartilage (FC) of both knees of six healthy participants were repeated longitudinally to investigate the association between T2 variation and B1. <strong>Results</strong>: The results showed that applying the B1 correction mitigated T2 variations that were driven by B1 inhomogeneities. <br> Specifically, T2 left-right symmetry increased following the B1 correction (rc = 0.74 &gt; rc = 0.69). Without the B1 correction, T2 values showed a linear dependence with B1. The linear coefficient decreased using the B1 correction (from 24.3 \(\pm\) 1.6 ms to 4.1 \(\pm\) 1.8) and the correlation was not statistically significant after the application of the Bonferroni correction (p-value &gt; 0.01).<br> <br> <strong>Conclusion</strong>: the study showed that B1 correction could mitigate variations driven by the sensitivity of the qDESS T2 mapping method to B1, therefore increasing the sensitivity to detect real biological changes. The proposed method may improve the robustness of bilateral qDESS T2 mapping, allowing for an accurate and more efficient evaluation of OA pathways and pathophysiology through longitudinal and cross-sectional studies. <strong>This repository contains the raw data for reproducing the results reported in the paper. The data are provided in NIFTI format. The repository also contains the MALTAB scripts used to compute B<sub>1</sub> maps from the NIFTI data.</strong>
DOI: 10.6075/j09c6xmj
title: Large Area Imagery Collection & Processing Standard Operating Procedures - Version 3.0 (2021). In Standard Operating Procedure Documents for Coral Reef Ecological Monitoring

description: This document contains the standard operating procedures for large area imaging of 100m^2 plots. The methods describe here include image collection, model processing, and ecological data extraction.
DOI: 10.6075/j05m65xn
title: Large Area Imagery Collection & Processing Standard Operating Procedures - Version 2.0 (2018). In Standard Operating Procedure Documents for Coral Reef Ecological Monitoring

description: This document contains the standard operating procedures for large area imaging of 100m^2 plots. The methods describe here include image collection, model processing, and ecological data extraction.
DOI: 10.6075/j01v5f5w
title: Large Area Imagery Collection & Processing Standard Operating Procedures - Version 1.0 (2017). In Standard Operating Procedure Documents for Coral Reef Ecological Monitoring

description: This document contains the standard operating procedures for large area imaging of 100m^2 plots. The methods describe here include image collection, model processing, and ecological data extraction.
DOI: 10.25921/astc-2f95
title: EM2040 Water Column Sonar Data Collected During H13624
DOI: 10.18739/a2zp3w211
title: Eastern Khanty Bear Ceremonialism, Western Siberia, Russian Federation (2019-2023)

description: The four Eastern Khanty bear ceremonies that are the subject of this project took place in Surgut Region, KhMAO-Iugra between 1995 and 2021. Three of these were documented prior to the grant period --1995 Larlomkiny, R. Bolʹshoi Iugan; 2010, 2016 Kiniamino, R. Malyi Iugan – and one, 2021 Pesikova Settlement, R. Pim, during the grant period. Publicly available materials in this dataset include a description of the eastern Khanty Bear Festival as well as an annotated trilingual transcription of the “Song of the Coming of the Bear” available online at https://eloka-arctic.org/bears/eastern-khanty. Materials not yet available for public dissemination include photographic and raw video documentation of these Eastern Khanty Bear Festivals filmed by the researcher or made available to him, as well as transcriptions of songs and skits in Khanty language with rough translations in Russian, and some also in English: from 1995 Larlomkiny, 31 songs and 16 skits; from 2010 Kiniamino, 21 songs; from 2016 Kiniamino, one; 2021 Pesikova, 4 songs. Conservation regimes and governmental relations with Indigenous peoples both vary widely. Successfully resolving conficts arising from human-wildlife interactions (HWI) is complicated by the existence of multiple ontologies not only among various publics but within historically-marginalized and fragmented Indigenous communities. Current models of HWI are being reevaluated in order to better understand how humans and animals, including large carnivores, have learned to coexist. We outline the potential of such an ethos for developing moreinclusive and just management policies and practices focused on tolerance and coexistence, while also identifying some limitations on developing such policies that emerge from acculturative stresses
DOI: 10.5281/zenodo.7892375
title: Supplementary Material

description: Supplementary material
DOI: 10.5281/zenodo.7892374
title: Supplementary Material

description: Supplementary material
DOI: 10.5281/zenodo.7897667
title: Staged Snakemake Workflow: stage

description: This is a a snapshot of the outputs of a Snakemake workflow
DOI: 10.5281/zenodo.7897666
title: Staged Snakemake Workflow: stage

description: This is a a snapshot of the outputs of a Snakemake workflow
DOI: 10.5281/zenodo.7897655
title: SDO/AIA cutout images for 2-April-2022 solar filament eruption

description: This entry contains sets of "cutout" images for the solar filament eruption that took place on 2-April-2022 around 13:30 UT. The images are from the Atmospheric Imaging Assembly (AIA) instrument onboard the Solar Dynamics Observatory (SDO). AIA takes full-disk images, and the cutout images were obtained from the Joint Science Operations Center (JSOC) website's cutout service. Tar files are available for the 304 angstrom and 131 angstrom AIA channels. These images were used to generate movies for a paper by M. Janvier et al. that was submitted to the journal Astronomy & Astrophysics in 2023.
DOI: 10.5281/zenodo.7897654
title: SDO/AIA cutout images for 2-April-2022 solar filament eruption

description: This entry contains sets of "cutout" images for the solar filament eruption that took place on 2-April-2022 around 13:30 UT. The images are from the Atmospheric Imaging Assembly (AIA) instrument onboard the Solar Dynamics Observatory (SDO). AIA takes full-disk images, and the cutout images were obtained from the Joint Science Operations Center (JSOC) website's cutout service. Tar files are available for the 304 angstrom and 131 angstrom AIA channels. These images were used to generate movies for a paper by M. Janvier et al. that was submitted to the journal Astronomy & Astrophysics in 2023.
DOI: 10.6073/pasta/56491d9a56214ca7d7f3f26487faf510
title: Aboveground net primary productivity data for Saddle grid, 1992 - ongoing.

description: Total aboveground live vascular biomass was clipped from 50x20 cm plots in areas near the saddle grid permanent plots on Niwot Ridge to measure net primary productivity. NDVI measurements were also included in some years.
DOI: 10.6073/pasta/82b9b3561cc34a1cba2e30b469def4db
title: NGE01 Chronic Addition of Nitrogen Gradient Experiment (ChANGE): Assessing threshold responses of plant community composition and ecosystem processes at Konza Prairie

description: Chronic nutrient additions can lead to drastic shifts in the plant community through time, both within tallgrass prairie in other grassland ecosystems worldwide. Nutrient addition experiments have answered many questions about patterns of diversity loss and community shifts; however, the level of nutrients which must be added to cause community shifts is unknown. To date, all nitrogen (N) addition experiments at Konza have added 10 g m-2 (e.g., NutNet Plots; Phosphorus (P) Plots; Belowground Plots), yet current rates of N deposition are one-tenth of that level. Even predicted rates of future N deposition in grasslands are not expected to exceed 5 g m-2 by the year 2050 and will likely be around 2 g m-2 for most of the US. This mismatch begs the question will 10 g/m2 affect grasslands the same way 2 or 5 g m-2 will? There are two main goals for this long-term experiment (1) to identify the nutrient threshold needed to drive plant community change with nutrient additions, and (2) to determine what factors underlie those threshold responses (build up of nutrients, mycorrhizal loss, invertebrate herbivory). Konza ChANGE is part of a multi-site experiment spanning grasslands on two different continents: North America – tallgrass prairie (KNZ) and shortgrass steppe (SGS), and China – three sites in Inner Mongolia. By including multiple grasslands, we expand our ability to make generalizations about how grasslands are affected by N additions, and whether thresholds, if they exist, vary with precipitation, natural nutrient availability, and species identity/composition. Research Questions: (1) Do ecosystems have N tolerance thresholds above which community composition will change, and does that differ between grassland types (i.e. mesic and xeric grasslands)? (2) Does adding a large amount of nutrients in one season result in an equivalent community change as adding a small amount over multiple years? (For example does 5 g m-2 for 6 years create the same community change as 30 g m-2 for 1 year or 15 g m-2 for 2 years?) (3) Will predicted levels of N deposition (2.5 g m-2 or 5 g m-2) elicit a community change? (4) Are there different thresholds for different plant functional types? For example, does a small amount of nutrients cause a decrease in N-fixing forb composition, while a larger amount of nutrients are necessary to reduce the abundance of the dominant C4 grasses? At what point does the community change state from a perennial grassland to the predicted annual forb community? Is it a gradual linear change or an abrupt transition? (5) Is decreased light availability due to increased ANPP the primary determinant leading to community shifts (like it is for species loss), or do other factors determine when nutrients cause a shift in community composition and structure such as interactions with invertebrate herbivory or loss of mycorrhizal symbionts.
DOI: 10.5281/zenodo.7897670
title: Complementary Dataset for ICIS2023 Submission

description: Complementary Dataset for ICIS2023 Submission
DOI: 10.5281/zenodo.7897669
title: Complementary Dataset for ICIS2023 Submission

description: Complementary Dataset for ICIS2023 Submission
DOI: 10.15482/usda.adc/1528959
title: Immigration and cyclical bottlenecks: High inbreeding despite high genetic diversity in an oscillating population of the biting midge, Culicoides sonorensis (Diptera: Ceratopogonidae)

description: These data represent the microsatellite peak calls generated after genotyping the specimens, as well as, the outputs from downstream analyses and the metadata used to construct some of the figures and tables. The microsatellite data can be found in "Shults_2023_peak_calls.xlsx" and contains the identity of each peak scored scored using Geneious v.9.1 software. An "x" represents no peak call at that marker for that individual. These data were used as input for all of the subsequent population genetic analyses. All of the data used to create the tables and figures of the manuscript can be found in "Shults_2023_tables_figs.xlsx".
Resources in this dataset:


Resource Title: Microsatellite peak calls
File Name: Shults_2023_peak_calls.xlsx
Resource Description: Contained in this file are all of the individual specimens (rows) genotype during this project. An "x" represents an uncalled peak for that specific marker.


Resource Title: Tables and Figures
File Name: Shults_2023_tables_figs.xlsx
Resource Description: Contained in this file are all of the metadata used to create the tales and figures from the manuscript. Each tab is labeled with the corresponding information and IBT stands for isolation by time.
DOI: 10.5517/ccdc.csd.cc23xx0z
title: CCDC 1964191: Experimental Crystal Structure Determination

description: Related Article: Yanyu Zhu, Tianyang Ding, Xu Zhang, Yanan Zhou, Jiahui Yu, Xin Li, Hanwen Zheng, Zhengang Sun, Chengqi Jiao|2023|Inorg.Chem.Front.|10|2818|doi:10.1039/D3QI00251A
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.cc29y76q
title: CCDC 2143253: Experimental Crystal Structure Determination

description: Related Article: Timothy J. Boyle, Paris C. Reuel, Dora K. Wiemann, Taylor Settecerri, Michael A. Omana, Roger E. Cramer|2023|CSD Communication|||
description: Related Article: Timothy J. Boyle, Paris C. Reuel, Dora K. Wiemann, Taylor Settecerri, Michael A. Omana, Roger E. Cramer|2022|Polyhedron|223|115958|doi:10.1016/j.poly.2022.115958
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.7897689
title: TOM.D: Taking Advantage of Microclimate Data for Urban Building Energy Modeling

description: Data required to rebuild the study: "TOM.D: Taking Advantage of Microclimate Data for Urban Building Energy Modeling". In this dataset of New York City, one can find building footprints, monthly energy consumption data for each of these buildings, and matching / cleaned microclimate data from a variety of data sources which are referenced in the work. Among them, thermal infrared measurements may be found, climate models from NOAA and ERA5 may be found, and preprocessed vision systems from Google are used.
DOI: 10.5281/zenodo.7897688
title: TOM.D: Taking Advantage of Microclimate Data for Urban Building Energy Modeling

description: Data required to rebuild the study: "TOM.D: Taking Advantage of Microclimate Data for Urban Building Energy Modeling". In this dataset of New York City, one can find building footprints, monthly energy consumption data for each of these buildings, and matching / cleaned microclimate data from a variety of data sources which are referenced in the work. Among them, thermal infrared measurements may be found, climate models from NOAA and ERA5 may be found, and preprocessed vision systems from Google are used.
DOI: 10.25919/hf95-rt37
title: RV Investigator Voyage IN2022_V02 End of Voyage (EOV) Archive

description: This record describes the End of Voyage (EOV) data archive from the Marine National Facility (MNF) RV Investigator voyage IN2022_V02, titled "Sedimentation at its extreme: how powerful are submarine caldera-forming eruptions (Kermadec arc)?" The voyage took place between March 19, 2022 and April 19, 2022 (AEST), departing from Hobart and returning to Hobart. Piggy-back projects: BGC and Standard Argo float deployments. Natural iron fertilisation of oceans around Australia: Linking terrestrial dust and bushfires to marine biogeochemistry. For further information please refer to the voyage documentation links. Instruments used and data collected include: Regular measurements: Acoustic Doppler Current Profiler (ADCP; 75, 150 KHz ), Greenhouse Gas Analysers (Picarro), Cloud Condensation Nuclei counter (CCN), Condensation Particle Counters (CPC), Disdrometer, Radon sensor, Scanning Mobility Particle Sizers (SMPS), CTD, Hydrochemistry, Fisheries Echosounder (EK60/EK80, ME70), Multibeam Echosounder (EM710, EM122), Sub-bottom Profiler (SBP120), GPS Positioning System, Doppler Velocity Log, Thermosalinographs (TSG), Fluorometer, Oxygen Optode, Infrared Sea Surface Temperature Autonomous Radiometer (ISAR), pCO2, Gravimeter, Multiangle Absorption Photometer (MAAP), Ozone Sensor, Nephelometer, Atmospheric Temperature, Humidity, Pressure, Wind and Rain sensors, Photosynthetically Active Radiation (PAR) sensor, Precision Infrared Radiometer (PIR), Precision Spectral Pyranometer (PSP), Starboard and Portside Radiometers, Air Sampler, Ultra Short BaseLine Underwater Positioning System (USBL), Weather Radar. Voyage-specific measurements: Giant Piston Corer (GPC), Rock Dredge, Seismic, Deep Towed Camera (DTC), Wildlife Observations (seabirds, cetaceans and seals). The archive for the IN2022_V02 EOV raw data is curated by the CSIRO National Collections and Marine Infrastructure (NCMI) Information and Data Centre (IDC) in Hobart, with a permanent archive at the CSIRO Data Access Portal (https://data.csiro.au/dap/), providing access to voyage participants and processors of the data collected on the voyage. All voyage documentation is available electronically to MNF support via the local network. Access to voyage documentation for non-CSIRO participants can be made via NCMI_DataLibrarians@csiro.au.
DOI: 10.5281/zenodo.7897708
title: aglantha_digitale_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.7897707
title: aglantha_digitale_spades_01.fasta.gz

description: .
DOI: 10.25921/45wr-yw27
title: EM2040 Water Column Sonar Data Collected During H13620
DOI: 10.26183/tqg2-2x04
title: Pelvic girdle pain in pregnancy dataset

description: Study Design: Cross-sectional study conducted between December 2017 and October 2019 Objective: To determine the prevalence and risk factors associated with pregnancy-related pelvic girdle pain (PPGP) in Australia. Summary of Background Data: Pregnancy-related pelvic girdle pain (PPGP) is a common condition worldwide yet the prevalence and associated risk factors are not known in Australia. Methods: A random sample of pregnant women (N=780) of (mean (SD)) 31 (5) years of age between 14 and 38 weeks gestation attending ante-natal care in a tertiary referral hospital in Sydney, Australia was conducted. The main outcome measure was point-prevalence of PPGP as classified by recommended guidelines including a physical examination. A number of potential risk factors, including socio-demographic characteristics, country of birth, ethnicity, history of low back pain (LBP) and PPGP, family history of PPGP, occupational factors and physical activity were investigated with logistic regression. Results: The point-prevalence of PPGP in a random sample of 780 Australian women was 44% with the odds of having PPGP increasing with each additional week of gestation (odds ratio (OR)) (OR 1.02). Increasing parity (p = 0.03, OR 1.15), country of birth (p = 0.03) and greater duration of time spent standing (p = 0.009, OR 1.06) were associated with PPGP. The strongest predictors of PPGP were previous LBP and/or PPGP both pregnancy (p < 0.001, OR 4.35) and not pregnancy related (p < 0.001, OR 2.24), and a family history of PPGP (p < 0.001, OR 3.76). Conclusion: The prevalence of PPGP in Australian women was high with almost half the sample classified with PPGP, matching data reported worldwide. The identified risk factors associated with PPGP can be included in routine ante-natal care to screen women and identify those at risk of this common and disabling condition.

A de-identified version of the data can be discussed by contacting the author at Dragana Ceprnja <D.Ceprnja@westernsydney.edu.au> ORCID 0000-0002-1955-9096
DOI: 10.25345/c5z60cc0r
title: MassIVE MSV000091861 - Loss of hRpn13 reconfigures the proteome and transcriptome of multiple myeloma cells
title: hRpn13 is an established proteasome substrate receptor but is also present off proteasomes and the possibility of it assuming cellular functions beyond its activities at the proteasomes has been long hypothesized. Herein, we demonstrate that hRpn13 deletion by gene-editing leads to alterations in the transcriptome that correlate with proteome alterations and moreover, that these effects are cell type-specific. We find that the hRpn13 Pru region directly interacts with two regulators of protein expression; namely the histone deacetylase HDAC8, which we also find is inhibited by hRpn13 in cells and a catalytic assay, and the bone marrow-specific protein arginine deamidase PADI4. In multiple myeloma cells, PADI4 and proteins of the cytoskeleton, immune response, calcium signaling, metabolitic and epigenetic pathways are sensitive to hRpn13 deletion by gene-editing. These proteins are also depleted by proteasome inhibition with carfilzomib or the hRpn13 PROTAC XL5-VHL-2. Altogether, we provide evidence for a multi-layered regulatory network involving arginine deamidation, histone deacetylation, proteasome activity and hRpn13Pru that confers a unique cell survival mechanism for multiple myeloma cells.
DOI: 10.5281/zenodo.7897740
title: cryptochiton_stelleri_spades_01.fasta.gz

description: .