cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20555163
title: Supplementary Material for: Consistencies and Differences in Intermediate Physiological Phenotypes of Vascular Ageing between Ischaemic Stroke Aetiologies

description: <b><i>Objective:</i></b> Arterial stiffness, cerebral pulsatility, and beat-to-beat blood pressure variability partly mediate the relationship between hypertension and stroke, but it is unknown if these intermediate phenotypes of vascular ageing differ between stroke aetiologies. We therefore aimed to characterize differences in these intermediate cardiovascular phenotypes between patients presenting with strokes of different aetiologies. <b><i>Methods:</i></b> In consecutive patients on best medical management 1 month after TIA or nondisabling stroke (Oxford Vascular Study), arterial stiffness (PWV) was measured by applanation tonometry (Sphygmocor), middle cerebral blood flow velocity, and pulsatility index (MCA-PI) were measured by transcranial ultrasound (TCD, DWL Doppler Box), and beat-to-beat BP variability was measured with a Finometer. Differences between patients with large artery (LAS), small vessel (SVD), cardioembolic (CE), or undetermined events were derived, including adjustment for cardiovascular risk factors. Relationships were characterized by mixed linear models. <b><i>Results:</i></b> In 909 eligible patients, MCA-PI, PWV, and SBPV were all positively skewed. Mean values were greatest in LAS than CE and lowest in SVD (<i>p</i> &lt; 0.001). However, after adjustment for age, sex, and risk factors, PI was greatest in LAS and lowest in CE stroke, whilst PWV was greatest in SVD and undetermined stroke (<i>p</i> &lt; 0.001). In multivariate linear models, age was more strongly associated with PWV and PI in patients with small vessel stroke than other aetiologies, particularly under the age of 65, but SBPV was only weakly associated with demographic indices in all stroke subtypes. <b><i>Conclusions:</i></b> Intermediate cardiovascular phenotypes of vascular ageing had similar demographic associations between stroke aetiologies, but these were particularly strong in patients with small vessel stroke under the age of 65, implying a potential role of these phenotypes in increasing stroke risk in this patient group.
DOI: 10.13012/b2idb-8842653_v1
title: Datasets for "Dense sampling of taxa and characters improves phylogenetic resolution among deltocephaline leafhoppers (Hemiptera: Cicadellidae: Deltocephalinae)"

description: The following files were used to reconstruct the phylogeny of the leafhopper subfamily Deltocephalinae, using IQ-TREE v1.6.12 and ASTRAL v 4.10.5. Taxon_sampling.csv: contains the sequencing ids (1st column) and the taxonomic information (2nd column) of each sample. Sequencing ids were used in the alignment files and partition files. concatenated_nt.phy: concatenated nucleotide alignment used for the maximum likelihood analysis of Deltocephalinae by IQ-TREE v1.6.12. The file lists the sequences of 163,365 nucleotide positions from 429 genes in 730 samples. Hyphens are used to represent gaps. concatenated_nt_partition.nex: the partitions for the concatenated nucleotide alignment. The file partitions the 163,365 nucleotide characters into 429 character sets, and defines the best substitution model for each character set. concatenated_aa.phy: concatenated amino acid alignment used for the maximum likelihood analysis of Deltocephalinae by IQ-TREE v1.6.12. The file gives the sequences of 53,969 amino acids from 429 genes in 730 samples. Hyphens are used to represent gaps. concatenated_aa_partition.nex: the partitions for the concatenated amino acid alignment. The file partitions the 53,969 characters into 429 character sets, and defines the best substitution model for each character set. concatenated_nt_106taxa.phy: a reduced concatenated nucleotide alignment representing 107 samples x 86 genes. This alignment is used to estimate the divergence times of Deltocephalinae using MCMCTree in PAML v4.9. The file lists the sequences of 79,239 nucleotide positions from 86 genes in 107 samples. Hyphens are used to represent gaps. concatenated_nt_106taxa_partition.nex: the partitions for the nucleotide alignment concatenated_nt_106taxa.phy. The file partitions the 79,239 nucleotide characters into 86 character sets, and defines the best substitution model for each character set. Individual_gene_alignment.zip: contains 429 FAS files, one for each of the partitioned nucleotide character sets in the concatenated_nt_partition.nex file. Hyphens are used to represent gaps. These files were used to construct gene trees using IQ-TREE v1.6.12, followed by multispecies coalescent analysis using ASTRAL v 4.10.5.
DOI: 10.17632/ws3cdn28n8.4
title: Harvard Forest CNDD in ECM species 2019

description: To test the strength of density dependence and whether it affects seedling community diversity in a temperate forest, we tracked the survival of seedlings of three ectomycorrhizal-associated species experimentally planted beneath conspecific and heterospecific adults. We compared these results to evidence of CNDD from observed sapling survival patterns of 28 species over approximately 8 years in a 35-hectare forest plot in Massachusetts, USA. We then used the observational sapling survival to compare species-specific estimates of CNDD to mycorrhizal association, shade tolerance, and local abundance. Experimental seedling survival was always lower under conspecific adults, which increased seedling community diversity in one of six treatments. In our observational sapling analysis, we found evidence of significant, negative CNDD in 23 of 28 species. Contrary to our expectations, ectomycorrhizal-associated species generally exhibited stronger (e.g. more negative) CNDD than arbuscular mycorrhizal- associated species. CNDD was also stronger in more shade tolerant species but was not associated with local abundance.
DOI: 10.6084/m9.figshare.20624376
title: Supplementary Material for: Substance Use, Substance Use Disorders, and Co-Occurring Psychiatric Disorders in Recently Incarcerated Men: A Comparison with the General Population

description: <b><i>Introduction:</i></b> The rates of alcohol and illegal drug use and the prevalence of alcohol and illegal drug use disorders (AUDs and DUDs) are high in prison populations, particularly in men entering jail. However, these rates have never been exhaustively assessed and compared to those of the general population in France. <b><i>Methods:</i></b> We based our research on two surveys, conducted in the same French region, which included a total of 630 men entering jail and 5,793 men recruited from the general population. We used the Mini-International Neuropsychiatric Interview to assess alcohol and drug use, AUD, DUD, as well as co-occurring psychiatric disorders, and we examined differences in prevalence rates between the two populations. Logistic regression models were performed to (i) identify the factors associated with AUD and DUD and (ii) test whether the interaction between admission to jail and the presence of AUD, DUD, or both is linked to the presence of at least one co-occurring psychiatric disorder. <b><i>Results:</i></b> Compared to the general population sample, the prevalence of AUD (33.8% vs. 8.7%, <i>p</i> &lt; 0.001) and DUD (at least one type of drug: 28.7% vs. 5.0%, <i>p</i> &lt; 0.001; cannabis: 24.0% vs. 4.7%, <i>p</i> &lt; 0.001; opioids: 6.8% vs. 0.4%, <i>p</i> &lt; 0.001; stimulants: 5.2% vs. 0.8%, <i>p</i> &lt; 0.001) was significantly higher in the jail population sample, as well as the rates of past-year use of various substances (alcohol: 62.1% vs. 56.4%, <i>p</i> = 0.007; at least one type of illegal drug: 50.0% vs. 14.4%, <i>p</i> &lt; 0.001; cannabis: 45.6% vs. 13.9%, opioids: 9.4% vs. 0.7%; stimulants: 8.6% vs. 1.9%). Admission to jail was associated with a higher risk of AUD (aOR = 3.80, 95% CI: 2.89–5.01, <i>p</i> &lt; 0.001) or DUD (aOR = 4.25, 95% CI: 3.10–5.84, <i>p</i> &lt; 0.001). History of trauma was also associated with both AUD (aOR = 1.81, 95% CI: 1.53–2.14, <i>p</i> &lt; 0.001) and DUD (aOR = 2.15, 95% CI: 1.74–2.65, <i>p</i> &lt; 0.001), whereas history of migration was only associated with DUD (aOR = 1.38, 95% CI: 1.12–1.71, <i>p</i> = 0.003). AUDs and DUDs were more strongly associated with co-occurring psychiatric disorders in incarcerated men than in the general population. Among individuals with AUD, DUD, or both, co-occurring anxiety and mood disorders were particularly more frequent in jail than in the general population. <b><i>Discussion/Conclusion:</i></b> As in most countries, AUD and DUD are highly prevalent among men entering jail in France. Our results also suggest that incarceration constitutes an independent vulnerability factor for a dual disorder, which supports a systematic assessment and treatment of psychiatric disorders in men entering jail and diagnosed with an AUD or DUD.
DOI: 10.5281/zenodo.1220364
title: Research Data For: On The Persistent Shape And Coherence Of Pulsating Auroral Patches

description: Data for the research article: On the persistent shape and coherence of pulsating auroral patches in Journal of Geophysical Research: Space physics. For example all-sky imager movies of 557.7 nm pulsating/fluctuating aurora on 1 March 2012.
DOI: 10.5281/zenodo.1256716
title: Time-lapse photograph dataset: complementation of ago7 mutant A. thaliana plants with truncated promoter transgenes

description: This transgenic complementation experiment is described in a paper by Hoyer et al. (2019): https://doi.org/10.1002/pld3.102

Time-stamped photographs are provided in twelve directories by camera (twelve overlapping fields of view) and a manifest file with file SHA-1 sums is included.

Metadata have been made available separately, to facilitate updates -- see https://github.com/jshoyer/raspi-photo-and-leaf-scan-metadata, archived as https://doi.org/10.5281/zenodo.1340636

Seed was plated and growth started on 2016-08-26.
DOI: 10.5281/zenodo.5825885
title: Dataset for train and test BRITTANY (Biometric RecognITion Through gAit aNalYsis)

description: This dataset can be used train and test the BRITTANY tool. Information contained in the dataset is especially suitable to be used as train and test data for neural network-based classifiers. This dataset contains 198 Rosbag files, of 5 seconds duration, recorded in different locations (kitchen, livingroom-window and livingroom-door) with Orbi-One robot stood still. Two sorts of Rosbag files have been recorded. In 90 Rosbag files (train*.bag), data recorded correspond to a person walking in a straight line in front of the robot. Data from five different people have been recorded. For each location and person, six Rosbag files have been recorded. In 108 Rosbag files (test*.bag), data recorded correspond to a person walking in a straight line in front of the robot. Data from six different people have been recorded. Five of those six people are the same as in the other rosbags and the other one is not registered in the system to evaluate the false-positive cases in the system.
DOI: 10.5281/zenodo.6376566
title: Zellige example dataset: Drosophila pupal wing and abdomen

description: <strong>Drosophila pupa imaged at around 24h after puparium formation. </strong> The z-stack image encompasses a distal portion of the wing and a portion of the abdomen. The four distinct surfaces are the abdomen cuticle, the abdomen epithelium, the wing cuticle and the wing epithelium. The z-stack was acquired with a spinning disk confocal microscope (Yokogawa W1) equipped with a Nikon Plan-Apochromat 60x lens (NA=1.4). Pixel size 0.183 µm, z step &lt;1 µm. This dataset contains both the ground-truth height maps and the height maps generated with Zellige.The Zellige parameters used are: \(T_{A}=6, T_{otsu}=1, S_{min}=5, \sigma_{xy}=5, \sigma_{z}=1, T_{OSE1}=0.7, R_{1}=10, C_{1}=0.8, T_{OSE2}=0.1, R_{2}=5, C_{2}=0.9.\) Nota: to compare the ground truth height map with the Zellige height map, one first needs to substrat 1 to all values of the Zellige height map. See the accompanying paper: Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software tool. Trébeau <em>et al.</em> 2022: https://doi.org/10.1101/2022.04.05.485876
DOI: 10.5281/zenodo.6556998
title: Data for "Transparent Josephson Junctions in Higher-Order Topological Insulator WTe2 via Pd Diffusion"

description: Data for the publication "Transparent Josephson Junctions in Higher-Order Topological Insulator WTe<sub>2</sub> via Pd Diffusion". Updated version as accepted by Physical Review Materials.
DOI: 10.5281/zenodo.6590345
title: Overcoming contrast reversals in focused probe ptychography of thick materials: an optimal pipeline for efficiently determining local atomic structure in materials science

description: Files concerning the publication "Overcoming contrast reversals in focused probe ptychography of thick materials: an optimal pipeline for efficiently determining local atomic structure in materials science"(arxiv:2205.13308 )
DOI: 10.5281/zenodo.6598713
title: Raw Data to "Theoretical Study on the Photoacidity of Hydroxypyrene Derivatives in DMSO Using ADC(2) and CC2"

description: This data is a supplement to the publication entitled "Theoretical Study on the Photoacidity of Hydroxypyrene Derivatives in DMSO Using ADC(2) and CC2" in the The Journal of Physical Chemistry A (DOI: 10.1021/acs.jpca.2c04436). It contains the structures (as '.xyz' files) and HF/DFT energies from the quantum chemical (QC) calculations using TURBOMOLE (version 7.4). Additional information on the file structure is given in the README file.
DOI: 10.5525/gla.researchdata.1274
title: Snapshot Volumetric Imaging with Engineered Point-Spread functions

description: PSF and raw image data, along with python notebooks, used to generate manuscript figures.
DOI: 10.6084/m9.figshare.20709214
title: Supplementary Material for: Signal Alteration of the Inner Ear on High-Resolution Three-Dimensional Constructive Interference in Steady State Sequence in Patients with Ménière’s Disease and Labyrinthitis

description: <b><i>Introduction:</i></b> The aim of this study is to evaluate signal alteration in the inner ear using three-dimensional (3D)-constructive interference in steady state (CISS) sequence in patients with Ménière’s disease and labyrinthitis and its correlation with clinical and audiological parameters. <b><i>Methods:</i></b> The medical records of the department of otorhinolaryngology were searched for patients with Ménière’s disease or labyrinthitis who underwent MRI with 3D-CISS sequence. Blinded analysis of these patients and of MRI from control subjects without middle or inner ear symptoms was performed to detect any signal asymmetry of the inner ear structures. The results were correlated with clinical symptoms and results of audiological and vestibular tests. <b><i>Results:</i></b> Fifty-eight patients with definite Ménière’s disease and 5 patients with labyrinthitis as well as 41 control exams were included. A separate analysis was performed for patients with probable Ménière’s disease (<i>n</i> = 68). A total of 172 3D-CISS sequences were analyzed by 2 blinded independent neuroradiologists. A CISS-hypointense signal of the inner ear structures was found in 3 patients with definite Ménière’s disease (5.2%), in 4 patients with probable Ménière’s disease (5.9%), and 2 patients with labyrinthitis (40%). No CISS hypointensity was found in the control group. Although no significant difference in symptoms or audiological test results was found between patients with and without this signal change, the side of hypointensity was frequently correlated with the symptomatic side and with hearing impairment. <b><i>Discussion/Conclusion:</i></b> CISS hypointensity of the inner ear structures was evident in patients with clinical conditions other than vestibular schwannoma – more frequently in labyrinthitis than in Ménière’s disease. This signal alteration was frequently encountered on the same symptomatic side as that of the pathological audiology tests, but it is not a predictor for hearing or vestibular impairment.
DOI: 10.5281/zenodo.5013856
title: Nanopore Translocation Signal

description: This dataset contains a set of nanopore translocation current traces. It is divided in two parts. <strong>Part I:</strong> This part contains artificially generated traces with different levels of background noise (SNR = 4, 2, 1, 0.5, and 0.25) For each noise level, three parameters are varied in data generation: a. Twenty different concentrations of nanoparticles as the analytes (Cnp): 0.013, 0.016, 0.020, 0.025, 0.032, 0.040, 0.050, 0.063, 0.080, 0.1, 0.13, 0.16, 0.20, 0.25, 0.32, 0.40, 0.50, 0.63, 0.80, and 1, with the unit of nano-molar, [nM]. b. Fifteen different diameters of the nanoparticles (Dnp): 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, and 17, with the unit of nanometer, [nm]. c. Five different translocation durations (Duration): 0.5, 1.0, 1.5, 3.0, and 5.0, with the unit of millisecond, [ms]. In total we have 20*15*5=1500 current traces for each SNR. There are three datasets: training, validation and test. Traces in training datasets are of 20 seconds, traces in validation and test datasets are 10 seconds long. For SNR = 4, training, validation and test datasets are provided. For other SNRs, only test traces are provided. <strong>Pert II</strong>: This part contains real experimental datasets, the translocation of Lambda DNA and Streptavidin with 6 current traces each at different bias voltages. Each Lambda DNA trace has 71 seconds, while each Streptavidin trace has 126 seconds. Two truncated pyramid shape nanopores were used in our experiments, one with a side length of 7.5 nm and another 16 nm, both in a 55 nm-thick silicon layer, for DNA and protein streptavidin translocation, respectively. The DNA and streptavidin were dispersed in 500 mM KCl electrolyte with a concentration of 78 pM and 84 nM, respectively. <br> Details of artificially generated data and experimental data can be found in our paper: Dario Dematties, Chenyu Wen, Mauricio David Pérez, Dian Zhou, Shi-Li Zhang. Deep learning of nanopore sensing signals using a bi-path network. arXiv:2105.03660. <strong>Trained and Validated Models</strong> In this data set we also include all the trained and best validated models evaluated in our paper.
description: The Artificial data set is compressed and split into "n" .zip files. Once you downloaded such files you can use the following sequence of commands for joining and unzipping them: zip -F Artificial_Data.zip --out single-archive.zip unzip single-archive.zip
DOI: 10.5281/zenodo.6583640
title: Analysis of regional CO2 contributions at the high Alpine observatory Jungfraujoch by means of atmospheric transport simulations and δ13C

description: The data set complementary to manuscript "Analysis of regional CO<sub>2</sub> contributions at the high Alpine observatory Jungfraujoch by means of atmospheric transport simulations and δ<sup>13</sup>C" in <em>Atmospheric Chemistry and Physics</em> (https://acp.copernicus.org).
DOI: 10.6073/pasta/292e47940d0b0b07c3be7e9026c12c66
title: Lyford Mapped Tree Plot at Harvard Forest since 1969

description: Permanent forest plots provide an empirical understanding of forest change over time, and are an invaluable part of forestry and ecological research. Walter Lyford began measurements of a 2.88 ha red oak-red maple forest on the Prospect Hill Tract of Harvard Forest in 1969. All trees over 2 inches (5 cm) were mapped on very large-scale (1 inch = 5 feet) hand-drawn maps, and included live and dead trees, stumps, windthrows and other features such as stone walls, boulders, soil moisture and a damage boundary from the 1938 hurricane. All living and dead trees have been re-located and measured (diameter at breast height, canopy class for live trees; condition, decay class, diameter, bole length and stem orientation for fallen dead trees) in 1969, 1975, 1987-1992, 2001, and 2011. In 2001, the original, hand-drawn maps were digitized using ArcView GIS. From 1969 to 2011, red oak (Quercus rubra) increased its dominance of the stand’s total basal area from 52% to 60%; however, red maple (Acer rubrum) has become relatively less abundant, decreasing from 30% to 23%. While red oak and red maple continue to account for the majority of the basal area in the stand, the secondary species experienced a dramatic increase in relative abundance of individuals in the stand; yellow birch (Betula alleghaniensis), black birch (Betula lenta), American chestnut (Castanea dentata), American beech (Fagus grandifolia), witch hazel (Hamamelis virginiana), eastern white pine (Pinus strobus), and eastern hemlock (Tsuga canadensis) have increased from comprising 25% of the individuals in the stand in 1969 to comprising 52% in 2011. The total biomass of living individuals is increasing linearly (R2=0.99, p=0.0002), which implies that the stand has not yet experienced an age-induced decrease in biomass accumulation.
DOI: 10.5281/zenodo.5548555
title: LANID-US: Landsat-based Irrigation Dataset for the United States

description: <strong>Annual 30-m resolution irrigation maps, derivative products, and ground reference locations for the United States, 1997-2017</strong>, including: (1) lanidYYYY (binary): Annual irrigation layer for the year YYYY (ranging from 1997 to 2017), e.g., lanid2017 is the irrigation map for the year 2017. (2) irrFreq (1-21): The number of years irrigated during 1997-2017. (3) irrFreqPasture_West: irrFreq of pasture/hay for the western CONUS. (4) maxIrrExt (binary): Croplands that have been irrigated at least once during 1997-2017. (5) irrFreqChange (1-21): The difference of number of years irrigated between 1998-2007 and that of between 2008-2017 (i.e., irrFreq<sub>2008-2017</sub> - irrFreq<sub>1998-2007</sub>). (6) irrAreaGain (-1684-2333): LANID-derived irrigation gain (in hectare) from 1998-2007 to 2008-2017 at the 6km×6km scale. (7) formerIrr (binary): Not irrigated anytime in 2015-2017, but irrigated at least 3 times prior. (8) irrWholePeriod (binary): Irrigated at least once for both 1997-1999 and 2015-2017. (9) intermittentIrr (binary): Irrigated at least once for both 1997-1999 and 2015-2017, and irrigation frequency ≤ 18. (10) irrSamples_eastCONUS: Sample locations of center pivot fields in the eastern CONUS (4976 sample locations). (11) rainfedSamples_eastCONUS: Sample locations of stable rainfed fields in the eastern CONUS (4978 sample locations). <strong>For technical details that used to create the dataset, please refer to <em>https://doi.org/10.1016/j.rse.2021.112445</em>; Data description details are available via <em>https://essd.copernicus.org/preprints/essd-2021-207/</em>.</strong>
DOI: 10.5281/zenodo.6376542
title: Zellige example dataset: mouse embryonic cochlea stained for F-actin

description: <strong>Mouse embryonic cochlea stained for F-actin at embryonic stage E16.5. </strong> The z-stack image encompasses an epithelial surface and a thick mesh of mesenchymal cells. It was acquired with a swept-field confocal microscope (Bruker OpterraII) equipped with a Nikon Plan-Apochromat 60x lens (NA=1.4). Pixel size 0.133 µm, z step &lt;1 µm. This dataset contains both the ground-truth height map and the height map generated with Zellige, along with the parameters used to generate the latter one. The Zellige parameters used are: \(T_{A}=1, T_{otsu}=1, S_{min}=5, \sigma_{xy}=4, \sigma_{z}=1, T_{OSE1}=0.1, R_{1}=5, C_{1}=0.7, T_{OSE2}=0.1, R_{2}=10, C_{2}=0.8.\) Nota: to compare the ground truth height map with the Zellige height map, one first needs to substrat 1 to all values of the Zellige height map. See the accompanying paper: Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software tool. Trébeau <em>et al.</em> 2022: https://doi.org/10.1101/2022.04.05.485876