cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.11105629
title: Raw model output presented and analyzed in: "Ancient Stratified Thermochemical Piles due to High Intrinsic Viscosity"

description: Summary

This archive contains the raw model output for all cases presented in the manuscript titled "Ancient Stratified Thermochemical Piles due to High Intrinsic Viscosity".

The output files are archived in hdf5 file format. The content of these files (one for each case) is as follows:



Temperature, viscosity and compositional fields, as well as the time-series of the lower heat-flux (from 4 billion years of model evolution onwards)

Age field at 5 billion years of model evolution

Time


The file mesh.h5 contains the x and y meshes of the models (called 'xmesh' and 'ymesh', respectively).

All data provided can be used to reproduce the results and figures in the manuscript, as detailed in the main and supplementary text. 

 

 
description: Information




hdf5 key
time
T
bs
eta
age
t_CMBhflux


description
 time
temperature
basalt fraction
viscosity
age
time and bottom heat-flux 




units

s
K
n/a
Pa s
s
s and W / (m^2)




notes

 
 
 
 
Values at the final time step
The first column contains time, the second column contains the heatflux




 
description: Naming conventions




drhoLM
270
310
350
390


delta [%]
1
2
3
4




 




z
001
01
1
10
100


zeta
-3
-1
0
1
2
DOI: 10.5281/zenodo.13144875
title: Recordings of zebra finch group behaviors with manually annotated vocal segments

description: This dataset contains recording files and manually annotated vocal segments of freely behaving zebra finches in the BirdPark. The files contain animal-borne accelerometer, microphone and video channels. Birds are housed in groups of different sizes (2, 4, or 8 birds, (one 7-mins file per group). The dataset contains 112 mins of recordings from 4 different experiments.


The dataset is published as an appendix of the following paper:

Rüttimann, L., Wang, Y., Rychen, J., Tomka, T., Hörster, H., Rocha, M. D., & Hahnloser, R. H. (2024). Multimodal system for recording individual-level behaviors in songbird groups. bioRxiv.

See the README.pdf file for a detailed description.
DOI: 10.5281/zenodo.7702405
title: Fabrication of low loss III-V Bragg-reflection waveguides for parametric down-conversion

description: Measurements of sidewall roughness (AFM), optical losses (transmission) and photon pair coincidence counts (coinc) of Bragg-reflection waveguides. Data are contained in .csv files. Example plots are .pdf or .png format. RF: with reflow step No RF: without reflow step Coinc: Coincidence Counts
DOI: 10.5440/1696801
title: Plant Physiology, Alder and Willow Species, Seward Peninsula, Alaska, 2019

description: Photosynthetic parameters (Vcmax and Jmax), CO2 response (ACi) curves and dark respiration (Rdark) measurements of tundra shrub species. Data were collected at the NGEE-Arctic Kougarok and Teller study sites on the Seward Peninsula, AK, USA in July 2019. Four species were measured using LI-COR LI-6400 portable gas exchange systems: Alnus viridis ssp. fruticosa, Salix richardsonii and Salix pulchra. The data package files include data files, metadata files, dGPS locations and the complete instrument output for all gas exchange measurements in .csv format. See the related data packages for foliar trait data (leaf mass per area, leaf nitrogen concentration), and leaf spectral reflectance data collected simultaneously on the same shrubs (NGA210, NGA212).The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).
DOI: 10.6073/pasta/1030af44239528ce4e17f7f585d00462
title: Hubbard Brook Experimental Forest: Annual measurements on marked northern red oak seedlings, 2014-ongoing

description: Marked individual northern red oak seedlings were individually marked and mapped at 20 valleywide transects starting in summer 2011. This data set includes detailed seedling measures starting in summer 2014. The data were used to examine the impact of previous year seedling condition on whether the seedling survived in the next season.
 
 These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
DOI: 10.6073/pasta/1de25c7fd5bc23dc39171d66b29652ac
title: Hubbard Brook Experimental Forest: Oak seedling demography, 2011 - ongoing

description: This data set was built from a larger data set of marked northern red oak seedlings surveyed from 2011-2023. In this data set, only seedlings marked in their year of germination with full environmental and seedlings measures were kept (N = 937). The data set was built for an accelerated failure time model of seedling survival that found year of germination, seedling density, shrub cover and elevation to have the largest effect on survival time. The status of the seedling acorn (attached or missing) was also important.
 These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
DOI: 10.6084/m9.figshare.23692359
title: Data.rar

description: Dataset for validating multiplexed wavefront sensing with a thin diffuser.
DOI: 10.6084/m9.figshare.23929626
title: Cornea and phantom datasets for: “Possible depth-resolved reconstruction of shear moduli in the cornea following collagen crosslinking (CXL) with optical coherence tomography and elastography.

description: Raw OCT datasets for corneal and phantom experiments
DOI: 10.6084/m9.figshare.25392130
title: Supplementary Material for: Prevalence and characteristics of known versus newly detected atrial fibrillation in ischemic stroke: a population-based study

description: Background: Atrial fibrillation (AF) is frequently diagnosed during the acute stage of ischemic (IS), and it may reflect undiagnosed AF before stroke, thus representing a missed opportunity for stroke prevention. This population-based study aimed to assess the prevalence of known AF (KAF) and AF diagnosed early after IS (AFDAS), and to compare clinical and brain/arterial imaging characteristics between patients. 
Methods: Among patients with acute IS recorded in the population-based Dijon Stroke Registry, France (2013-2020), we identified those with KAF or AFDAS. AFDAS was considered when AF was diagnosed during the initial work-up based on electrocardiograms, in-hospital continuous electrocardiographic and/or Holter monitoring. Clinical and imaging characteristics on brain CT-scan or angio-CT-scan when available including old parenchymal lesions, arterial territory of the index IS, and aortic arch, cervical and intracranial arteries atheroma were compared between groups (KAF versus AFDAS). Regression logistic models were used to assess factors associated with AFDAS (compared to KAF). 
Results: Among 1756 IS patients, 550 (31.3%) had AF (mean age: 83.6 ±10.3 years old, 60.5% women), of whom 367 (66.7%) presented with KAF and 183 (33.3%) had AFDAS. In multivariable model, hypertension (OR=0.37; 95% CI: 0.21-0.64, p&lt;0.001), chronic heart failure (OR=0.34; 95% CI: 0.18-0.67, p=0.002), previous stroke (OR=0.42; 95% CI: 0.26-0.67, p&lt;0.001), and preexisting dementia (OR=0.36; 95% CI: 0.21-0.63, p&lt;0.001), were inversely associated with AFDAS, whereas NIHSS score was associated with AFDAS (OR=1.02; 95% CI: 1.00-1.05, p=0.012). 
Conclusions: Our findings indicate a more advanced stage of the atrial cardiomyopathy in KAF as compared with AFDAS patients, and may thus contribute to the fact that in these latter patients AF had not been diagnosed prior to stroke. This group of patients undeniably represents a missed opportunity for stroke prevention.
DOI: 10.6084/m9.figshare.25432816
title: Supplementary.zip

description: Additional material in the manuscript. Supplementary 1，Supplementary 2， and Supplementary 3.
DOI: 10.6084/m9.figshare.26026873
title: Comparing Information Theory Analysis with Cross-Correlation and Minimum Variance Analysis of the Solar Wind Structures Rev--Figures and data

description: This is the data set for the JGR Paper: Comparing Information Theory Analysis with Cross-Correlation and Minimum Variance Analysis of the Solar Wind Structures
DOI: 10.6084/m9.figshare.26043940
title: Supplementary Material for: European Portuguese version of the Game Addiction Scale-7 (GAS-7-PT): Factor structure and psychometric properties

description: Introduction: Game addiction (GA) can be described as a compulsive and excessive usage of computers or video games that causes emotional and or social problems. The current study tested the factor structure and psychometric properties of the European Portuguese Game Addiction Scale (GAS-7-PT) short version. 
Methods: The sample encompassed 375 participants, 233 women (62.1%) and 142 men (37.9%), with a mean age of 21.71 (SD=5.82) years old. Participants completed a set of self-report measures online: the GAS-7-PT, the Scale of Involvement in Video Games and the Patient Health Questionnaire-4.
Results: Confirmatory factor analyses confirmed a biological sex invariant single-factor structure with a very good fit to the data. The GAS-7-PT showed good reliability and test-retest reliability. Correlations with related and unrelated measures suggested convergent validity, and partial correlation results pointed to incremental validity. Men showed significantly higher scores than women. 
Conclusion: The GAS-7-PT is a self-report instrument with suitable psychometric properties for clinical and research contexts. The availability of a European Portuguese version confirms the GAS-7 robust consistency and allows further cross-cultural clinical research.
DOI: 10.15129/9fff8e03-d6c0-4164-a258-01a5d4469f39
title: Data for: "Single-frequency optical parametric oscillator intracavity-pumped by a visible VECSEL for low-noise down-conversion to 1.55 μm"

description: The dataset presented here corresponds to the experimental data reported in the manuscript "Single-frequency optical parametric oscillator intracavity-pumped by a visible VECSEL for low-noise down-conversion to 1.55 μm" to be published in Optics Express (https://doi.org/10.15129/9fff8e03-d6c0-4164-a258-01a5d4469f39). The following manuscript describes the design and operation of the first optical parametric oscillator (OPO) pumped by a visible (red) AlGaInP-based vertical-external-cavity surface-emitting-laser (VECSEL) with emission at 690.6 nm; of interest for quantum optics experiments and quantum light state applications. Firstly, it includes the VECSEL fundamental tuning performance (plotted in Fig. 1b) and the (resolution-limited) full-width at half-maximum (FWHM) linewidth of the VECSEL emission at 690.6 nm (plotted in Fig. 1b, inset). Secondly, the normalized intensity spectra of the VECSEL fundamental, and OPO signal (1245.2 nm) and idler (1550.8 nm) are plotted (see Fig. 2a) as well as the tuning characteristics of the OPO (plotted in Fig. 2b). Thirdly, in the absence of resonant idler output-coupling, the OPO power and conversion efficiency is characterized (plotted in Fig. 3a) as well the intracavity VECSEL power when the OPO is switched "on" and switched "off" (plotted in Fig. 3b). Alternatively, in the presence of resonant idler output-coupling, Fig. 4a and Fig. 4b present the OPO power transfer and OPO conversion and extraction efficiencies, respectively. When the OPO is pumped by the multi-longitudinal-mode VECSEL, we demonstrate a (short-term) passive power stability of the VECSEL fundamental over 5 ms (plotted in Fig. 5a) and a (long-term) passive power stability of the OPO signal output over 4000 s (plotted in Fig. 5b). On top of that, Fig. 6 shows the normalized Fabry-Perot interferometer (FPI) transmission traces and reference cavity PZT voltages as a function of time for the VECSEL fundamental, and OPO signal and idler; providing the first direct evidence of single-frequency (longitudinal-mode) operation of an OPO pumped by a VECSEL laser. Finally, the passive power stability results of the single-frequency VECSEL-pumped OPO (plotted in Fig. 7) are presented over a timescale of 500 s.
DOI: 10.17632/f5y9cggnxy.2
title: k-mers 1D and 2D representation dataset of SARS-CoV-2 nucleotide sequences

description: The dataset provides five types of k-mers genome representation characterized as k-mers count 1D, k-mers probability 1D, k-mers count 2D, k-mers probability 2D, and k-mers image. The dataset is composed of 1557 virus instances of SARS-CoV-2. Besides, the dataset also provides a data stream of 11540 viruses from the Virus-Host DB dataset and the other three Riboviria viruses from NCBI (Betacoronavirus RaTG13, bat-SL-CoVZC45, and bat-SL-CoVZXC21).
DOI: 10.17632/zbk2wz5zsj.1
title: SARS-CoV-2 CGR Genome Image Dataset

description: This dataset comprises image representations generated through the Chaos Game Representation (CGR) of SARS-CoV-2 complete genome sequences. Designed to support a wide array of computational biology and deep learning tasks, it facilitates not only the classification of viral variants but also opens avenues for diverse analytical studies due to its rich, image-based genomic encoding.
DOI: 10.5066/p9jxhmo2
title: Earth Observing One (EO-1) - Hyperion

description: The Earth-Observing One (EO-1) satellite was decommissioned March 2017. The EO-1 satellite was launched on November 21, 2000 with the NASA's New Millennium Program (NMP). The NMP was an advanced-technology development program created a new generation of technologies and mission concepts into future Earth and space science missions. For more information on the final phase of the EO-1 mission go to: https://eo1.gsfc.nasa.gov/EO-1%20Phase-F%20Report%2020160617%20Final.docx. All EO-1 ALI and Hyperion historical data will continue to be available through EarthExplorer for the foreseeable future.
DOI: 10.5281/zenodo.10207035
title: SPA_modeling_paper_archive

description: This archive contains data in support of the paper "The South Pole-Aitken basin: Constraints on impact excavation, melt, and ejecta" by Citron et al., submitted to GRL. 
The archive consists of:

ANEOS input files for the equations of state used in the numerical models.
DOI: 10.5281/zenodo.1048275
title: Energy Intensity Data For Public Water Supply In The United States

description: Empirical observations of water use, electricity use, and supporting data describing energy requirements of public water systems in the United States.
DOI: 10.5281/zenodo.11195759
title: Data for "Antiferromagnetic phase transition in a 3D fermionic Hubbard model"

description: This dataset is for research article "Antiferromagnetic phase transition in a 3D fermionic Hubbard model".
DOI: 10.5281/zenodo.12528901
title: Flow cytometry of mesenteric lymph nodes, small and large intestinal lamina propria, and spinal cord cells from fibre-rich and fiber-free diet-fed gnotobiotic mice at baseline and after experimental autoimmune encephalomyelitis (EAE) induction

description: We perform profiling of different immune cell populations in the small (SILP) and large intestine lamina propria (CLP), mesenteric lymph nodes (MLN) and spinal cords (SC). We are specifically interested to evaluate the impact of dietary fiber deprivation followed by mucus erosion on the immune cell profiles of T helper cells (Th cells, T cell population) of gnotobiotic mice fed a fiber-rich (FR) or fiber-free (FF) diet. This dataset aims to assess the impact of microbiome and diet on disease course in a mouse model of multiple sclerosis (experimental autoimmune encephalomyelitis, EAE) via T cell populations. Mice are either germ-free or colonized by intragastric gavage with a defined variation of a 14-member synthetic human gut microbiome (doi: 10.1016/j.cell.2016.10.043 and 10.1016/j.xpro.2021.100607): SM01 (Akkermansia muciniphila monocolonisation), SM03 (Bacteroides caccae, Bacteroides thetaiotaomicron, Barnesiella intestinihominis), SM04 (B. caccae, B. thetaiotaomicron, B. intestinihominis, A. muciniphila), SM12 (full community except mucin-specialists B. intestinihominis and A. muciniphila), SM13 (full community except mucin specialist A. muciniphila), or SM14 (full community: Roseburia intestinalis, Faecalibacterium prausnitzii, Marvinbryantia formatexigens, Collinsella aerofaciens, Desulfovibrio piger, B. caccae, B. thetaiotaomicron, Bacteroides ovatus, Bacteroides uniformis, B. intestinihominis, Eubacterium rectale, Clostridium symbiosum, Escherichia coli, and A. muciniphila). At age 5 to 8 weeks, mice were colonized with SM combinations while fed an FR diet. Mice were either maintained on an FR diet or switched to an FF diet at 5 days after initial colonization, until the end of experiment. Baseline samples were collected 20 days following the diet switch. Otherwise, EAE induction was performed 15 days after the diet switch and samples were collected 30 days after the induction.
DOI: 10.5281/zenodo.1434068
title: Human Hyperpolarization Activated Cyclic Nucleotide Gated Ion Channel 4 (HCN4); A Target Enabling Package

description: HCN4 is one of four hyperpolarisation activated cyclic nucleotide gated ion channels. It is responsible for the pacemaker or funny (If) current in the heart and is required for maintenance of a stable heartbeat. Mutations in HCN4 lead to a number of arrhythmias. HCN4 is the target for the angina drug ivabradine, which reduces HCN4 activity. However, ivabradine is non-selective, affecting all of the four HCN channels. HCN4 is a close homologue of HCN2, which is a target for neuropathic and inflammatory pain treatment. We have solved the structure of HCN4 both in complex with cyclic AMP and without nucleotide. Comparison of our HCN4 structure with that of the related HCN1 channel (86% identity) allows us to suggest ways to design selectivity for small molecule inhibitors between these closely related channels.
DOI: 10.5281/zenodo.3376310
title: Postgraduate education among family and community physicians in Brazil: the Trajetórias MFC project

description: Dataset analyzed in the "Postgraduate education among family and community physicians in Brazil: the <em>Trajetórias MFC</em> project" manuscript. File "family_physicians" has personally identifiable data on family and community physicians in Brazil, more specifically on their specialization (medical residency, specialist certification) and their master's and PhD degrees. File "postgraduate_programs" has data on the master's and PhD programs the family and community physicians graduated from. All spreadsheets are in the CSV (comma-separated values) format, delmited with semicolons and encoded in UTF-8 (there are special characters due to the Portuguese language) with the byte-order mark (BOM). The spreadsheets can be opened with desktop or Web application software (LibreOffice Calc, Microsoft Excel, Google Sheets) or with statistical software such as R. Each dataset is accompanied with a data dictionary for interpreting the columns. See also the manuscript for background.
DOI: 10.5281/zenodo.5095284
title: mit-ll/AlphaSeq_Antibody_Dataset: Initial release of AlphaSeq Antibody Dataset

description: Dataset with quantitative binding scores of scFv-format antibodies against SARS-CoV-2 target peptide.
DOI: 10.5281/zenodo.6560537
title: Data and simulation files for: "Optimization of diamond optomechanical crystal cavities"

description: Data and simulation files for the article "Optimization of diamond optomechanical crystal cavities".
description: This work was supported by São Paulo Research Foundation (FAPESP) through grants 2020/00100- 9, 2020/00119-1, 2018/15580-6, 2018/15577-5, 2018/25339-4, 2021/10249-2, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) (Finance Code 001), Conselho Nacional de Desenvolvimento Científico e Tecnológico, and Financiadora de Estudos e Projetos (Finep).
DOI: 10.5281/zenodo.8390942
title: Dataset for: Multi-mode Heterodyne Laser Interferometry Realized via Software Defined Radio

description: Repository of data plotted in figures for the journal publication "Multi-mode Heterodyne Laser Interferometry Realized via Software Defined Radio" (doi: 10.1364/OE.500077 ).


Please see metadata file for details on individual data files.
DOI: 10.6084/m9.figshare.11844789
title: Mua.txt

description: Broadband optical absorption coefficient of different porcine organs obtained using time-domain diffuse optical spectroscopy. Measurements were performed on three different spatial locations of each organ, the mean value and the standard deviation over the three values are presented here.
DOI: 10.6084/m9.figshare.25624422
title: Supplementary Material for: Analysis of the characteristics of coexisting lesions in colorectal cancer patients in an international study: A subgroup analysis of the ATLAS trial

description: Introduction: We investigated coexisting lesion types in patients with invasive colorectal cancer (CRC) in a multinational study for comprehending the adenoma-carcinoma and serrated pathway about the development of CRC. 
Methods: We retrospectively reviewed 3050 patients enrolled in the international randomized controlled trial (ATLAS study) to evaluate the colorectal polyp detection performance of image-enhanced endoscopy in 11 institutions in four Asian countries/regions. In the current study, as a subgroup analysis of the ATLAS study, 92 CRC patients were extracted and compared to 2958 patients without CRC to examine the effects of age, sex, and coexisting lesion types (high-grade adenoma [HGA], low-grade adenoma with villous component [LGAV], 10 adenomas, adenoma ≥10 mm, sessile serrated lesions [SSL], and SSL with dysplasia [SSLD]). Additional analyses of coexisting lesion types were performed according to sex and location of CRC (right- or left-sided). 
Results: A multivariate analysis showed that HGA (odds ratio [95%confidence interval] 4.29 [2.16-8.18]; p&lt;0.01), LGAV (3.02 [1.16-7.83], p=0.02) and age (1.04 [1.01-1.06], p=0.01) were independently associated with CRC. According to sex, the coexisting lesion types significantly associated with CRC were LGAV (5.58 [1.94-16.0], p&lt;0.01) and HGA (4.46 [1.95-10.20], p&lt;0.01) in males and HGA (4.82 [1.47-15.80], p&lt;0.01) in females. Regarding the location of CRC, SSLD (21.9 [1.31-365.0], p=0.03) was significant for right-sided CRC, and HGA (5.22 [2.39-11.4], p&lt;0.01) and LGAV (3.46 [1.13-10.6], p=0.02) were significant for left-sided CRC. 
Conclusions: The significant coexisting lesions in CRC differed according to sex and location. These findings may contribute to comprehending the pathogenesis of CRC.