cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14029286
title: ROSMAP meQTL Results for Neurons with CpGs

description: This dataset contains methylation quantitative trait loci (meQTL) results for the following study:

"regionalpcs improve discovery of DNA methylation associations with complex traits"

Tiffany Eulalio*1, Min Woo Sun1, Olivier Gevaert1, Michael D. Greicius2, Thomas J. Montine3, Daniel Nachun*‡3, Stephen B. Montgomery*‡1,3

‡ These authors contributed equally as senior authors

* Corresponding authors: Tiffany Eulalio (eulalio@alumn.stanford.edu), Daniel Nachun (dnachun@stanford.edu), Stephen B. Montgomery (smontgom@stanford.edu)

 Author affiliations:

1.     Department of Biomedical Data Science, Stanford University, Stanford, CA

2.     Department of Neurology & Neurological Sciences, Stanford University, Stanford, CA

3.     Department of Pathology, Stanford University, Stanford, CA

 

Dataset description:

This dataset contains QTL results generated from FastQTL, organized by region type (full gene, gene body, preTSS, and promoters) and summary types (averages and regional principal components).

Contents:



Parquet tar files: These compressed archives contain output files in Parquet format from FastQTL, split by chromosome. parquet1 includes chromosomes 1-10, and parquet2 includes chromosomes 11-22.

cis_qtl_summary_stats.csv: Provides summary statistics for each phenotype-variant pair, including effect sizes, p-values, TSS distances, and additional details.

cis_qtl.signif_pairs.csv: Contains the significant QTL results identified by FastQTL.

cis_qtls.time_to_run.txt: Reports the running time for FastQTL analysis.

cis_qtls.cis_qtl.txt.gz: Contains comprehensive results for all cis QTLs.


This dataset is intended to support replication and further exploration of QTL associations across different genomic regions and summary methods.
DOI: 10.5281/zenodo.14133221
title: Code for simple BTSP models
DOI: 10.5281/zenodo.3518036
title: Copernicus Global Land Service: Land Cover 100m: collection 3: epoch 2017: Globe

description: Consolidated epoch 2017 from the Collection 3 of annual, global 100m land cover maps. Other available epochs: 2015 2016 2018 2019 Produced by the global component of the Copernicus Land Service, derived from PROBA-V satellite observations and ancillary datasets. The maps include a main discrete classification with 23 classes aligned with UN-FAO's Land Cover Classification System, a set of versatile cover fractions: percentage (%) of ground cover for the 10 main classes a forest type layer quality layers on input data density and on the confidence of the detected land cover change Click here to view the maps More information about the land cover maps Product User Manual
DOI: 10.5281/zenodo.6008487
title: Orientation-dependent propulsion of active Brownian spheres: from self-advection to programmable cluster shapes

description: Supplemental data for the following manuscript: Stephan Bröker, Jens Bickmann, Michael te Vrugt, Michael E. Cates, Raphael Wittkowski, "Orientation-dependent propulsion of active Brownian spheres: from self-advection to programmable cluster shapes".
description: M.t.V. thanks the Studienstiftung des deutschen Volkes for financial support. M.E.C. is funded by the Royal Society. R.W. is funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - 283183152 (WI 4170/3-2). The simulations for this work were performed on the computer cluster PALMA II of the University of Münster.
DOI: 10.5281/zenodo.6549887
title: Data set for the article "Self-oscillation and Synchronisation Transitions in Elasto-Active Structures"

description: This is the data set for the article "Self-oscillation and Synchronisation Transitions in Elasto-Active Structures", https://doi.org/10.48550/arXiv.2106.05721 Is contains raw images and processed data from images used to describe the self-oscillations under study in this article. All zip files corresponds to the single chain experiment except "Double_chain_Experiment.zip".
DOI: 10.5281/zenodo.7660587
title: Stability and cooling of the C_7^2- dianion

description: The files found here are text files with data related to the article: "Stability and cooling of the C_7^2- dianion" to published in Physical Review Letters (2023). The files contain the information necessary to reproduce all figures containing data from the experiment or from the described calculations. Each file contains a header explaining the data sets which follow.
DOI: 10.5281/zenodo.8060040
title: Data of "Thermodynamics of Quantum Trajectories on a Quantum Computer"

description: The uploaded files contain the data of the simulations presented in the figures of the publication "Thermodynamics of Quantum Trajectories on a Quantum Computer".
DOI: 10.5291/ill-data.5-32-921
title: Exploring Chemical and Magnetic Disorders in the Triangular Antiferromagnet Yb(Mg/Zn)GaO4
DOI: 10.5440/1129476
title: Plant community composition and vegetation height, Utqiagvik (Barrow), Alaska, Ver. 1

description: This dataset contains i) the results of field surveys of plant community composition and vegetation height made between 17th and 29th July 2012 in 48, 1 x 1 m plots located in areas A-D of Intensive Site 1 at the Next-Generation Ecosystem Experiments (NGEE) Arctic site near Utqiagvik (Barrow), Alaska and ii) results of a mapping exercise undertaken in August 2013 using two perpendicular transects across each polygon containing vegetation plots to determine the boundaries of vegetation communities described in 2012. This dataset includes six csv files, three pdf files, and a zipped folder of vegetation photos.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/316203040ea1b8ece89673985ab431b7
title: North Temperate Lakes LTER: Physical Limnology of Primary Study Lakes 1981 - current

description: Parameters characterizing the physical limnology of the eleven primary lakes (Allequash, Big Muskellunge, Crystal, Sparkling, Trout, bog lakes 27-02 [Crystal Bog] and 12-15 [Trout Bog], Mendota, Monona, Wingra and Fish) are measured at one station in the deepest part of each lake at 0.25-m to 1-m depth intervals depending on the lake. Measured parameters in the data set include water temperature, vertical penetration of photosynthetically active radiation (PAR; not measured on lakes Mendota, Monona, Wingra, and Fish), dissolved oxygen, as well as the derived parameter percent oxygen saturation. Sampling Frequency: fortnightly during ice-free season - every 6 weeks during ice-covered season for the northern lakes. The southern lakes are similar except that sampling occurs monthly during the fall and typically only once during the winter (depending on ice conditions). Number of sites: 11
DOI: 10.6084/m9.figshare.26117344
title: Growing meat on vegetables: plants with natural biomimetic micro-patterns as edible meat-engineering scaffolds

description: LC-MS raw data for Chinese chive, Shiitake mushroom and loofah exacts
DOI: 10.6084/m9.figshare.26406205.v1
title: Abundance and occupancy data for invertebrate species associated to intertidal mussel patches

description: This file contains data on the abundance and occupancy of invertebrate species found in intertidal mussel patches in Nova Scotia, Canada.
DOI: 10.6084/m9.figshare.28093631
title: Supplementary Material for: BEYOND THE LIMIT: SALVAGING THE POSTERIOR CIRCULATION TERRITORY VIA LATE ENDOVASCULAR THROMBECTOMY

description: Introduction: Posterior circulation infarctions, particularly basilar artery occlusions, contribute significantly to morbidity and mortality in ischemic stroke. However, literature supporting mechanical thrombectomy in the posterior circulation, especially beyond the 24-hour window, is limited. 
Case Presentation: We present the case of a 64-year-old male diagnosed with basilar artery occlusion who underwent a successful mechanical thrombectomy 11 days after symptom onset. Despite complications such as hemorrhagic transformation and herniation, the patient was stabilized and showed functional improvement 3 months post-stroke, 
Conclusion: This case suggests that delayed thrombectomy may provide benefits for selected patients, even beyond the recommended 24-hour window. Further research is essential to refine treatment strategies and potentially extend the intervention window for posterior circulation strokes.
DOI: 10.6084/m9.figshare.28130084
title: Supplementary Material for: Severe hypomagnesemia in a patient treated using carboplatin co-administered with vonoprazan

description: Introduction: We describe a case of severe hypomagnesemia that occurred during treatment with carboplatin (CBDCA) and nanoparticle albumin-bound paclitaxel (nab-PTX) for lung adenocarcinoma when co-administered with vonoprazan. Case Presentation: A man in his 70s was diagnosed with stage IIIA lung adenocarcinoma and received CBDCA and nab-PTX as the first-line treatment. The patient had been taking omeprazole 10 mg once daily (for &gt;3 years) for gastroesophageal reflux disease, but it was switched to lansoprazole 15 mg because of hospital's adopted medication. During the first treatment cycle, his serum creatinine levels increased from 1.0 to 1.5 mg/dL, suggesting CBDCA-associated renal impairment. Because of gastric discomfort on day 15 of the second cycle, lansoprazole was switched to vonoprazan 10 mg once daily. On day 23 of the second cycle, he developed torsades de pointes and was hospitalized; severe hypomagnesemia (0.4 mg/dL) was detected to be causing the symptoms. Discontinuation of vonoprazan and a single intravenous infusion of 60 mEq magnesium sulfate raised serum magnesium levels to 3.7 mg/dL and the arrhythmia disappeared. Mild hypomagnesemia (1.4 mg/dL) reappeared five days later, and an additional intravenous infusion of 20 mEq magnesium sulfate with subsequent oral magnesium oxide (1980 mg/day) resolved the symptoms. CBDCA was discontinued and nab-PTX monotherapy was continued. Vonoprazan was resumed owing to gastric discomfort relapse; however, grade ≥2 hypomagnesemia did not reappear later. Conclusions: This case highlights the risk of severe hypomagnesemia in patients with CBDCA and vonoprazan co-administration; therefore, regular monitoring of serum magnesium levels during the treatment is crucial.
DOI: 10.15151/esrf-es-1578705079
title: Temperature evolution of crystallographic parameters in tetragonal tungsten bronzes

description: A large group of materials are known to crystallize in the tetragonal tungsten bronze (TTB) structure, having the general formula A12A24C4B12B28O30. Depending on the chemistry and structure a wide range of interesting magnetic and electronic properties are known to exist among these materials, including ferroelectricity. However, there is no general consensus on the origin of ferroelectricity in these materials, and our understanding of the composition-structure-properties relationship is further complicated by the complex modulations, octahedral tilting patterns and mixed occupancy that is also known to exist for this class of materials. Here we propose a temperature dependent high-resolution X-ray powder diffraction investigation of the structures, modulations and mixed occupancies of a wide group of TTBs, namely ferroelectric Ba4A12Nb10O30 (A1 = Li, Na, K, Rb) and non-ferroelectric A24Bi2Nb10O30 (A2 = Na, K, Rb, Ba).
DOI: 10.17632/4zkgtwff5c.1
title: Geochemical compostions of subducted carbon from mantle plume in mid-ocean ridge basalts

description: Supplementary data for subducted carbon from mantle plume in mid-ocean ridge basalts
DOI: 10.17863/cam.83866
title: Data Moiré Nonlinearities

description: Data for figures in the paper. Please see ReadMe file for detailed description
DOI: 10.17863/cam.84678
title: Experimental realization of a fermionic spin-momentum lattice [Dataset and Code].

description: Data and code for figures in the paper and supplementary material. Please see ReadMe.txt file for detailed description.
DOI: 10.3886/icpsr01100
title: Collective Bargaining Contracts in the Canadian Public Sector, 1964-1987
title: Archival Version

description: These data and/or computer programs are part of ICPSR's Publication-Related Archive and are distributed exactly as they arrived from the data depositor. ICPSR has not checked or processed this material. Users should consult the INVESTIGATOR(S) if further information is desired.
description: Datasets: 
 
 DS1: Dataset
DOI: 10.48436/zyqxm-62108
title: Data for: "Waterfalls: umbilical cords at the birth of Hubbard bands"

description: Context and methodology



This repository contains raw data from the associated research work. It serves the purpose of aiding interested readers to reproduce the results of the related work and verify their validity.

The research area in which this dataset is created is that of condensed matter, strongly correlated electron systems, ARPES, cuprates, and nickelates.

This dataset was created using the w2dynamics code for DMFT calculations, the ana_cont package for analytic continuation, and the DGApy code for DGA calculations. 


Technical details



For each figure there is a corresponding folder in data folder containing the data shown in the figure. Data files are of type hk, hdf5, npz, and txt and named logically after data they contain.

Reading the data requires python (version 3.10.13, numpy version 1.26.0) with h5py (version 3.10.0).

The detailed content of the data files can found in a README file.


w2dynamics calculations



DMFT calculations are done in three iterations, each involving different numbers of DMFT steps and statistics.

Corresponding input files _Parameters_dmft_iter.in, _Parameters_dmft_iter_2.in, and _Parameters_dmft_stat.in can be found in the folder input_files/w2dynamics/, and are executed in that order.

The output of the last iteration is contained in 1p-data.hdf5, including the self-energy on the Matsubara axis.


DGApy calculations



 In addition to the single-particle data in 1p-data.hdf5, DGApy requires the two-particle DMFT data contained in g4iw_sym.hdf5.

The corresponding input file _Parameters_vertex.in for w2dynamics can be found in input_files/w2dynamics/. Note that the DMFT output will contain the full Vertex.hdf5. To get g4iw_sym.hdf5 one needs to execute sym1b (part of DGApy) in the same folder where Vertex.hdf5 is located.

The resulting self-energy on the Matsubara axis is contained in siwk_dga.npy files.


ana_cont



Analytical continuation of the self-energy to the real-frequency axis was performed using MaxEnt as implemented in the ana_cont python package; model for fitting was flat and chi2kink method was used to determine the hyperparameter alpha.

For temperatures T = 100/t and T = 15/t, number of fermionic Matsubara frequencies taken was 800 and 200, while the real-frequency grid was taken to be linear with 1001 points in the range [-50,50].

Errors for DMFT self-energies can be found in 1p-data.hdf5, while for DGA results it is taken to be 1e-3; preblur was set to 1e-3 in all calculations.

Analyically continued DMFT self-energy is located in self_energy.npz files, while analytically continued DGA self-energy in self_energy_nw1001_nk400_delta0.04.npy. Note that the interpolation in both momentum and frequency space may be employed to get better resolution. In addition, a constant imaginary part of 0.04 was added to the DGA self-energy to improve stability of results.
DOI: 10.5281/zenodo.10075655
title: Compression-driven viscous fingering: Experimental and numerical data

description: These data are from experiments and numerical simulations of viscous fingering in a rigid, radial, oil-filled Hele-Shaw cell driven by the compression of a connected air reservoir. The methods and data are presented in the authors' joint-submissions and their supporting information:



L. C. Morrow, C. Cuttle, and C. W. MacMinn, Gas compression systematically delays the onset of viscous fingering, Physical Review Letters 131, 224002 (2023).

C. Cuttle, L. C. Morrow, and C. W. MacMinn, Compression-driven viscous fingering in a radial Hele-Shaw cell, Physical Review Fluids 8, 113904 (2023).


We here provide all raw data for 2 experimental repetitions and 5 numerical repetitions, over the full range of parameters reported.

See README file for full details.

VERSION 2: The pressure data are now given in the correct units of Pa. Note that the pressure data in Version 1 are identical, except for the fact that they are mistakenly given in units of PSI.
DOI: 10.5281/zenodo.1040168
title: TUT Acoustic scenes 2017, Evaluation dataset

description: TUT Acoustic Scenes 2017, evaluation dataset consists of 10-seconds audio segments from 15 acoustic scenes: Bus - traveling by bus in the city (vehicle) Cafe / Restaurant - small cafe/restaurant (indoor) Car - driving or traveling as a passenger, in the city (vehicle) City center (outdoor) Forest path (outdoor) Grocery store - medium size grocery store (indoor) Home (indoor) Lakeside beach (outdoor) Library (indoor) Metro station (indoor) Office - multiple persons, typical work day (indoor) Residential area (outdoor) Train (traveling, vehicle) Tram (traveling, vehicle) Urban park (outdoor) Each acoustic scene has 108 segments totaling 18 minutes of audio.
DOI: 10.5281/zenodo.10782550
title: Vegetation Photosynthesis and Respiration Model code and output for south-western Europe between 2001 and 2022

description: These datasets contain the Python code for executing the modified Vegetation Photosynthesis and Respiration Model (VPRM) including soil moisture effects on the Net ecosystem exchange (NEE), Gross Primary Production (GPP) and the Ecosystem respiration (RES); and the daily VPRM output between January 2001 and December 2022 for the south-western Europe domain. 

The compressed file VPRM_SWEurope.zip contains the Python programs for estimating the terrestrial ecosystem carbon fluxes (NEE, GPP and RES) using the modified VPRM detailed on the manuscript  "Heat and drought events alter biogenic capacity to balance CO2 budget in south-western Europe".  The code Offline_VPRM_modified_Mediterranean_SYNMAP_two_crops.py is employed to derive hourly fluxes at 9 km resolution, and aggregated over montly NetCDF files. The input of the model is located in the data directory, where MODIS vegetation indices are already provided in the MODIS_SYN directory. The meteorological drivers (air temperature, surface solar radiation downwards and soil moisture between 7 cm and 28 cm depth) are not provided but can be obtaind from the Copernicus Climate Data Store.

The Python program make_daily_sum.py transforms the output of the VPRM model from mol CO2 / (km^2 hour)  to g C /(m^2 day).

The compressed file Output_VPRM.zip contains the daily sum terrestrial ecosystem carbon fluxes (NEE, GPP and RES) modelled for the south-western European domain between January 2001 and December 2022. The units are in g C /(m^2 day).
DOI: 10.5281/zenodo.13350981
title: ApisTox

description: The global decline in bee populations poses significant risks to agriculture, biodiversity, and environmental stability. To bridge the gap in existing data, we introduce ApisTox, a comprehensive dataset focusing on the toxicity of pesticides to honey bees (Apis mellifera). This dataset combines and leverages data from existing sources such as ECOTOX and PPDB, providing an extensive, consistent, and curated collection that surpasses the previous datasets. ApisTox incorporates a wide array of data, including toxicity levels for chemicals, details such as time of their publication in literature, and identifiers linking them to external chemical databases. This dataset may serve as an important tool for environmental and agricultural research, but also can support the development of policies and practices aimed at minimizing harm to bee populations. Finally, ApisTox offers a unique resource for benchmarking molecular property prediction methods on agrochemical compounds, facilitating advancements in both environmental science and cheminformatics. This makes it a valuable tool for both academic research and practical applications in bee conservation.
DOI: 10.5281/zenodo.13969023
title: Theoretical simulations for: Emergence of exotic spin texture in supramolecular metal complexes on a 2D superconductor

description: Here you will find the information necessary to reproduce the theoretical data published on "Emergence of Exotic Spin Texture in Supramolecular Metal Complexes on a 2D Superconductor" paper

It contains:



the geometries used in the DFT calculations

inputs and outputs of the multiplet calculations implemented on matlab
DOI: 10.5281/zenodo.14020225
title: Regionalpcs ROSMAP Fine-mapped QTLs

description: This dataset contains DAP-G fine-mapped QTL results for the following study:

"regionalpcs improve discovery of DNA methylation associations with complex traits"

Tiffany Eulalio*1, Min Woo Sun1, Olivier Gevaert1, Michael D. Greicius2, Thomas J. Montine3, Daniel Nachun*‡3, Stephen B. Montgomery*‡1,3

‡ These authors contributed equally as senior authors

* Corresponding authors: Tiffany Eulalio (eulalio@alumn.stanford.edu), Daniel Nachun (dnachun@stanford.edu), Stephen B. Montgomery (smontgom@stanford.edu)

 Author affiliations:

1.     Department of Biomedical Data Science, Stanford University, Stanford, CA

2.     Department of Neurology & Neurological Sciences, Stanford University, Stanford, CA

3.     Department of Pathology, Stanford University, Stanford, CA

 

Dataset description:

The DAP-G results are organized by region type (full gene, gene body, preTSS, and promoters), cell type (astrocytes, endothelial cells, neurons, oligodendrocytes, and bulk), and summary type (averages and regionalpcs).