cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22238443.v1
title: observer_reliability_statistics_no_id_for_reviewers_only.xlsm from Neotropical mixed-species bird flocks in a community context

description: Mixed-species flocks are an important component of bird communities, particularly in the Neotropics, where flocks reach their highest diversity. The extent to which mixed-species flocks represent unique functional or ecological roles within communities, and how these attributes change over environmental gradients, however, is not well understood. We use a trait-based approach to examine functional aspects of flocking assemblages as they relate to those observed in the larger avian community across a 3000 m elevational gradient. Our results reveal similar ecological strategies among flocking species and the communities in which they occur, at the scale of the regional pool and across elevations. Trait variation in flocking and non-flocking assemblages is structured along two major axes defined by size- and resource-related traits. The trait space occupied by flocking species, however, represents only half (51%) that of the larger community. Similarly, the trait space of flocks across elevations is restricted compared to non-flocking species. The shared trait space across flock types represents small-bodied invertivores foraging in lower forest strata, traits associated with increased vulnerability to predation. The concentration of flocking species in functional trait space suggests high niche packing and either more overlap in ecological strategies or more finely divided niches relative to non-flocking species.This article is part of the theme issue ‘Mixed-species groups and aggregations: shaping ecological and behavioural patterns and processes’.
DOI: 10.6084/m9.figshare.22238446
title: Hypervolume estimation for the trait space of the flocks from Neotropical mixed-species bird flocks in a community context

description: Following the best practices recommended in Mammola et al. (2018) and to facilitate repeatability, we included the hypervolume objects
DOI: 10.6084/m9.figshare.22238446.v1
title: Hypervolume estimation for the trait space of the flocks from Neotropical mixed-species bird flocks in a community context

description: Following the best practices recommended in Mammola et al. (2018) and to facilitate repeatability, we included the hypervolume objects
DOI: 10.5281/zenodo.7663738
title: Simulation data for "Chain Sliding versus β-Sheet Formation upon Shearing Single α-Helical Coiled Coils"

description: <strong>Content</strong> <strong>- Input</strong> and <strong>output</strong> files of the steered molecular dynamics simulations; python, VMD/Tcl <strong>scripts</strong> to produce the figures containing simulation data presented in the main text and in the SI of the associated publication. <strong>Movies</strong> of two simulation runs of the A5<sub>N3</sub>B5<sub>N3</sub> coiled coil at <em>v</em><sub>pull</sub>=0.01 nm/ns: two movies of different durations of a simulation run where the alpha-to-beta transition occurs (A5B5_BetaSheet-1min30sec.gif and A5B5_BetaSheet-30sec.gif); one movie of a simulation run where the alpha-to-beta transition does not occur (A5B5_noBetaSheet-23sec.gif). The movies can be played by dragging-and-dropping into a web browser (e.g., Firefox). <strong>Instructions</strong> Usage of this dataset necessitates basic knowledge of python, LaTex, VMD/Tcl and Gromacs. Unzip all files in the same directory. - analysis05/dataverse-simulation-figures.pdf contains all figures with simulation data shown in the main text and in the SI of the associated publication. - analysis05/dataverse-simulation-figures.tex can be consulted to determine the names of each figure. With a few exceptions, any output files produced by a script share the same prefix as the script name. E.g., figure s027_v04_A4B4_vE-2_ForceTrace_vs_z-L0.pdf was produced by script s027_v04*py; vmd04_v01*.dat was produced by vmd04_v01*.tcl. The exceptions are the few figures that were produced interactively, and the output files of scripts vmd001_interchainHBs_*.tcl (because sometimes bad days happen, and imperfectly-named progress is better than no progress at all). - The simulation trajectories that gave origin to the simulation data presented in each figure can be identified from the input files listed within each script.
DOI: 10.5281/zenodo.7663737
title: Simulation data for "Chain Sliding versus β-Sheet Formation upon Shearing Single α-Helical Coiled Coils"

description: <strong>Content</strong> <strong>- Input</strong> and <strong>output</strong> files of the steered molecular dynamics simulations; python, VMD/Tcl <strong>scripts</strong> to produce the figures containing simulation data presented in the main text and in the SI of the associated publication. <strong>Movies</strong> of two simulation runs of the A5<sub>N3</sub>B5<sub>N3</sub> coiled coil at <em>v</em><sub>pull</sub>=0.01 nm/ns: two movies of different durations of a simulation run where the alpha-to-beta transition occurs (A5B5_BetaSheet-1min30sec.gif and A5B5_BetaSheet-30sec.gif); one movie of a simulation run where the alpha-to-beta transition does not occur (A5B5_noBetaSheet-23sec.gif). The movies can be played by dragging-and-dropping into a web browser (e.g., Firefox). <strong>Instructions</strong> Usage of this dataset necessitates basic knowledge of python, LaTex, VMD/Tcl and Gromacs. Unzip all files in the same directory. - analysis05/dataverse-simulation-figures.pdf contains all figures with simulation data shown in the main text and in the SI of the associated publication. - analysis05/dataverse-simulation-figures.tex can be consulted to determine the names of each figure. With a few exceptions, any output files produced by a script share the same prefix as the script name. E.g., figure s027_v04_A4B4_vE-2_ForceTrace_vs_z-L0.pdf was produced by script s027_v04*py; vmd04_v01*.dat was produced by vmd04_v01*.tcl. The exceptions are the few figures that were produced interactively, and the output files of scripts vmd001_interchainHBs_*.tcl (because sometimes bad days happen, and imperfectly-named progress is better than no progress at all). - The simulation trajectories that gave origin to the simulation data presented in each figure can be identified from the input files listed within each script.
DOI: 10.6084/m9.figshare.16633838
title: Research integrity guidelines and safeguards in Brazil

description: Brazilian research output has been growing annually, and so have its domestic and international research collaborations. Accordingly, it is essential to harmonize research integrity guidance and regulations to ensure research quality. Therefore, this study aims to collect and analyze guidance documents on research integrity from Brazilian research performing organizations (RPO). Research integrity guidance documents, regulations, and policies were retrieved from 60 randomly selected universities in Brazil. The search was conducted via the universities’ websites and confirmed by e-mail. The documents were analyzed based on inductive content analysis. Relevant documents from 20 RPOs were identified. 28% of the included institutions have developed their own guidelines or adopted some guidance document on research integrity. Best practices, misconduct and misbehaviors, principles, and institutional policies regarding sanctions differ between universities. The RPOs where research integrity guidance documents could be identified are concentrated mainly in the southeastern and southern areas. The number and distribution heterogeneity highlights the need to increase awareness and create regulatory documents on research integrity in Brazilian universities. Further Research Performing and Funding Organizations’ initiatives are needed to foster research integrity in Brazil and harmonize it with international standards.
DOI: 10.6084/m9.figshare.16633838.v1
title: Research integrity guidelines and safeguards in Brazil

description: Brazilian research output has been growing annually, and so have its domestic and international research collaborations. Accordingly, it is essential to harmonize research integrity guidance and regulations to ensure research quality. Therefore, this study aims to collect and analyze guidance documents on research integrity from Brazilian research performing organizations (RPO). Research integrity guidance documents, regulations, and policies were retrieved from 60 randomly selected universities in Brazil. The search was conducted via the universities’ websites and confirmed by e-mail. The documents were analyzed based on inductive content analysis. Relevant documents from 20 RPOs were identified. 28% of the included institutions have developed their own guidelines or adopted some guidance document on research integrity. Best practices, misconduct and misbehaviors, principles, and institutional policies regarding sanctions differ between universities. The RPOs where research integrity guidance documents could be identified are concentrated mainly in the southeastern and southern areas. The number and distribution heterogeneity highlights the need to increase awareness and create regulatory documents on research integrity in Brazilian universities. Further Research Performing and Funding Organizations’ initiatives are needed to foster research integrity in Brazil and harmonize it with international standards.
DOI: 10.18119/n9ks4h
title: Chronic cellular senescence course - Homeostasis imbalance process ontology (HOIP)
DOI: 10.18119/n9g31j
title: Chronic cellular senescence course associated with type 2 diabetes mellitus - Homeostasis imbalance process ontology (HOIP)
DOI: 10.18119/n9b892
title: Acute cellular senescence course associated with type 2 diabetes mellitus - Homeostasis imbalance process ontology (HOIP)
DOI: 10.18119/n96k75
title: Acute cellular senescence course - Homeostasis imbalance process ontology (HOIP)
DOI: 10.18119/n92s4v
title: Senolytics course - Homeostasis imbalance process ontology (HOIP)
DOI: 10.18119/n9z328
title: Adult cellular senescence course - Homeostasis imbalance process ontology (HOIP)
DOI: 10.18119/n9t89d
title: Cellular senescence course - Homeostasis imbalance process ontology (HOIP)
DOI: 10.18119/n9pk7h
title: Embryonic cellular senescence - Homeostasis imbalance process ontology (HOIP)
DOI: 10.17909/7cnj-5y94
title: Kamieneski et al. 2023b JWST/HST
DOI: 10.34740/kaggle/dsv/5132126
title: 💥📰 Daily Breaking News Twitter Dataset
DOI: 10.5281/zenodo.7710361
title: CongDong2023_Macroscale regionalized ensemble estimation and analyses of wave periods across Canada

description: Data for temporal variabilities and trends of Canadian wave periods.
DOI: 10.5281/zenodo.7710360
title: CongDong2023_Macroscale regionalized ensemble estimation and analyses of wave periods across Canada

description: Data for temporal variabilities and trends of Canadian wave periods.
DOI: 10.34740/kaggle/dsv/5132195
title: 🇺🇦 Ukraine Conflict Twitter Dataset
DOI: 10.5281/zenodo.7710540
title: Safe and just ESB for groundwater

description: Global data for annual groundwater recharge volumes and the changes to groundwater storage over the 2003-2016 period.
DOI: 10.5281/zenodo.7710539
title: Safe and just ESB for groundwater

description: Global data for annual groundwater recharge volumes and the changes to groundwater storage over the 2003-2016 period.
DOI: 10.25955/22238860
title: master_table_lit_search_analysis_basic_155_models_20230225.xlsx

description: This spreadsheet was produced following a literature search conducted across the Scopus, EBSCOhost, and Web of Science (WoS) databases. The search targeted peer-reviewed papers, books, and book chapters published globally from January 2015 to December 2021. The search string "<strong>(estimat* OR predict*) AND (yield* OR product*) AND (wheat OR barley OR canola OR oilseed* OR rapeseed* OR cereal*) AND model*</strong> " was applied across the three databases and a separate EndNote data base accumulated over the period 01/01/2020 – 31/12/2021 using ad hoc searches and publisher alerts. The Scopus data base was searched first, followed by searches across the EBSCOhost, WoS and EndNote databases in that order. After duplicate records were removed, search results were filtered using the following criteria: The paper, book chapter or book was peer reviewed and written in English The primary purpose of the paper, book chapter or book was the development and testing of a yield prediction model The location, crop, yield units, input and prediction scale and extent were thoroughly documented The models targeted either wheat, barley, or canola (or some combination of these crops) The model output resolution was at sub-paddock scale or higher (e.g. paddock regional, national), but excluded plot scale models The model was applied across extensive areas (&gt; 100km x 100km) Input data (for running the model) was limited to accessible published data. Model development and calibration may use in situ data, but the model must not rely on in situ data to run. In this study, the data typically included publicly available, satellite-based, remotely sensed data and spatially continuous meteorological, soil moisture, landform, soil, and agronomic data as well as crop maps. Data collected by, UAV or other airborne sensors, paddock scale in situ measurements or private farmer records, were excluded. The search identified a total of 11,908 papers. After removing duplicate records and filtering based on title and the abstract, this was reduced to 388 papers. Another 46 papers were identified and added from the EndNote database. After a detailed scrutiny of the papers and strict application of the search criteria, 118 papers were identified that fitted the literature review criteria. Some of these papers described models for multiple crop types and a range of spatial resolution. This resulted in the review identifying 155 models. <br>
DOI: 10.25955/22238860.v1
title: master_table_lit_search_analysis_basic_155_models_20230225.xlsx

description: This spreadsheet was produced following a literature search conducted across the Scopus, EBSCOhost, and Web of Science (WoS) databases. The search targeted peer-reviewed papers, books, and book chapters published globally from January 2015 to December 2021. The search string "<strong>(estimat* OR predict*) AND (yield* OR product*) AND (wheat OR barley OR canola OR oilseed* OR rapeseed* OR cereal*) AND model*</strong> " was applied across the three databases and a separate EndNote data base accumulated over the period 01/01/2020 – 31/12/2021 using ad hoc searches and publisher alerts. The Scopus data base was searched first, followed by searches across the EBSCOhost, WoS and EndNote databases in that order. After duplicate records were removed, search results were filtered using the following criteria: The paper, book chapter or book was peer reviewed and written in English The primary purpose of the paper, book chapter or book was the development and testing of a yield prediction model The location, crop, yield units, input and prediction scale and extent were thoroughly documented The models targeted either wheat, barley, or canola (or some combination of these crops) The model output resolution was at sub-paddock scale or higher (e.g. paddock regional, national), but excluded plot scale models The model was applied across extensive areas (&gt; 100km x 100km) Input data (for running the model) was limited to accessible published data. Model development and calibration may use in situ data, but the model must not rely on in situ data to run. In this study, the data typically included publicly available, satellite-based, remotely sensed data and spatially continuous meteorological, soil moisture, landform, soil, and agronomic data as well as crop maps. Data collected by, UAV or other airborne sensors, paddock scale in situ measurements or private farmer records, were excluded. The search identified a total of 11,908 papers. After removing duplicate records and filtering based on title and the abstract, this was reduced to 388 papers. Another 46 papers were identified and added from the EndNote database. After a detailed scrutiny of the papers and strict application of the search criteria, 118 papers were identified that fitted the literature review criteria. Some of these papers described models for multiple crop types and a range of spatial resolution. This resulted in the review identifying 155 models. <br>
DOI: 10.6084/m9.figshare.22239406
title: Advice Giving and Sex Communication

description: This dataset examines advice giving during conversations about sex between close friends.
DOI: 10.6084/m9.figshare.22239406.v1
title: Advice Giving and Sex Communication

description: This dataset examines advice giving during conversations about sex between close friends.
DOI: 10.25345/c5fb4ww8s
title: MassIVE MSV000091448 - LC-MS/MS based identification of molecular biomarkers involved in neoplastic progression of gallbladder inflammatory lesions to invasive cancer
title: A total of 20 homogenous samples, including ten gallbladder cancer tissues (stage 2, adenocarcinoma) and ten gallbladder inflammatory lesions ( chronic cholecystitis) were taken up for label-free LC-MS/MS run in technical duplicates. The raw data generated from 40 files were checked in X calibur software and analyzed through Proteome Discoverer 2.4 using the sequest HT algorithm.
DOI: 10.6084/m9.figshare.22089632
title: Ultrastructural changes in resistance arterioles of normotensive and hypertensive premenopausal women with uterine fibroids

description: The association between uterine smooth muscle fibroids and systemic arterial hypertension is poorly understood. Therefore, we explored possible concomitant myocyte pathology of systemic resistance-sized arterioles (200 to 400 μm), isolated from omental samples donated by 19 women (mean age 42 y; SE 1) undergoing fibroid surgery. Vessels of 17 women (8 hypertensives) were available for transmission electron microscopy. We found ultrastructural vessel wall abnormalities in all patients, albeit with greater severity in hypertensives. In the endothelium, this ranged from moderate mitochondrial and endoplasmic reticulum stress in normotensives, to necrosis and sloughing in hypertensives. Myocyte-like cells were observed to migrate across the internal elastic lamina, with isolated subendothelial myocytes in normotensives, and focal subendothelial multicellular aggregates or myo-intimal “cushions” in hypertensives. Medial myocytes of all patients showed abnormalities similar to fibroids, with dilated sarco-endoplasmic reticulum, elongated mitochondria, and myofilament loss involving focal areas or entire cells. To our knowledge, the first study on the ultrastructure of systemic resistance arterioles of women with fibroids indicates that severe abnormalities are present that likely affect blood pressure regulation. Whether these perturbations are induced by fibroids, or represent systemic pathology that affects myocytes of both uterine and vascular tissue warrants further exploration.
DOI: 10.6084/m9.figshare.22089632.v1
title: Ultrastructural changes in resistance arterioles of normotensive and hypertensive premenopausal women with uterine fibroids

description: The association between uterine smooth muscle fibroids and systemic arterial hypertension is poorly understood. Therefore, we explored possible concomitant myocyte pathology of systemic resistance-sized arterioles (200 to 400 μm), isolated from omental samples donated by 19 women (mean age 42 y; SE 1) undergoing fibroid surgery. Vessels of 17 women (8 hypertensives) were available for transmission electron microscopy. We found ultrastructural vessel wall abnormalities in all patients, albeit with greater severity in hypertensives. In the endothelium, this ranged from moderate mitochondrial and endoplasmic reticulum stress in normotensives, to necrosis and sloughing in hypertensives. Myocyte-like cells were observed to migrate across the internal elastic lamina, with isolated subendothelial myocytes in normotensives, and focal subendothelial multicellular aggregates or myo-intimal “cushions” in hypertensives. Medial myocytes of all patients showed abnormalities similar to fibroids, with dilated sarco-endoplasmic reticulum, elongated mitochondria, and myofilament loss involving focal areas or entire cells. To our knowledge, the first study on the ultrastructure of systemic resistance arterioles of women with fibroids indicates that severe abnormalities are present that likely affect blood pressure regulation. Whether these perturbations are induced by fibroids, or represent systemic pathology that affects myocytes of both uterine and vascular tissue warrants further exploration.
DOI: 10.6084/m9.figshare.22239445.v1
title: 22Rv1_ATAC_ENZ3w_naked-DNA_rep1

description: 22Rv1_ATAC_ENZ3w_naked-DNA_rep1
DOI: 10.6084/m9.figshare.22239445
title: 22Rv1_ATAC_ENZ3w_naked-DNA_rep1

description: 22Rv1_ATAC_ENZ3w_naked-DNA_rep1
DOI: 10.5281/zenodo.7710631
title: 324a6207-70bd-4a59-be2b-25001d1af9e3

description: These data sets are one of the workflows in manabuishii/yevis-getting-started.
DOI: 10.5281/zenodo.7710630
title: 324a6207-70bd-4a59-be2b-25001d1af9e3

description: These data sets are one of the workflows in manabuishii/yevis-getting-started.
DOI: 10.6084/m9.figshare.22239460
title: 22Rv1_ATAC_naked-DNA_rep1

description: 22Rv1_ATAC_naked-DNA_rep1
DOI: 10.6084/m9.figshare.22239460.v1
title: 22Rv1_ATAC_naked-DNA_rep1

description: 22Rv1_ATAC_naked-DNA_rep1
DOI: 10.6084/m9.figshare.22239463
title: VCaP_ATAC_0nM_rep1

description: VCaP_ATAC_0nM_rep1
DOI: 10.6084/m9.figshare.22239463.v1
title: VCaP_ATAC_0nM_rep1

description: VCaP_ATAC_0nM_rep1
DOI: 10.6084/m9.figshare.22239466
title: VCaP_ATAC_0nM_rep2

description: VCaP_ATAC_0nM_rep2
DOI: 10.6084/m9.figshare.22239466.v1
title: VCaP_ATAC_0nM_rep2

description: VCaP_ATAC_0nM_rep2
DOI: 10.25345/c59p2wg6w
title: MassIVE MSV000091449 - Systems-wide adaptations in Arabidopsis thaliana plant lines grown in 1g and in microgravity environments, GC-MS Metabolomics
title: This research used Arabidopsis thaliana, aiming to identify systems-wide adaptations when plant lines are grown in 1g and microgravity environments. Both leaf and stem samples of WT plants and arogenate dehydratase mutants (adt5, adt45, adt3456) as well as carbon capturing mutants WTCCM and adt3456CCM were grown and analyzed for two separate repeat experiments on board the International Space Station (ISS) as compared to plants grown at 1 g at Kennedy Space Center (KSC). These two experiments are named Flight 1 and Flight 2. This work builds upon our recent progress in a) modulating lignin contents and vascular apparatus performance, via manipulating the arogenate dehydratase (ADT) multi-gene family, and b) enhancing carbon concentrating mechanisms (CCMs) to improve photosynthetic carbon assimilation and water use efficiency (WUE), alone and/or in combination with altered lignin levels. The knowledge gained will be essential for optimizing plants for spaceflight exploration and utilization (such as on Moon or Mars bases), as well as gaining new insights and knowledge into the various network interdependencies including, for example, photo-/gravi-tropisms, lignification, and WUE. Samples are extracts from a modified Folch extraction. This is the GC-MS metabolomics analysis of the methanol:H2O (polar) fraction.
DOI: 10.34740/kaggle/dsv/5132611
title: The impacts of COVID-19 policy on people's SWB
DOI: 10.34740/kaggle/dsv/5132708
title: Elon Musk Tweets