cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5007980
title: AIMNet-NSE test datasets

description: Ions-16 and ChEMBL-20 datasets used to test the performance of the AIMNet-NSE model. The datasets contain PBE0/ma-Def2-SVP energies and NBO atomic charges for the non-equilibrium conformers of neutral organic molecules randomly sampled from the PubChem database (Ions-16) and B97-3c optimized conformations of neutral organic molecules randomly sampled from the ChEMBL database (ChEMBL-20). The number in the dataset name corresponds to the maximum number of non-hydrogen atoms in the molecules. The dataset which was used for training the AIMNet-NSE model contains molecules up to 12 non-H atoms, whereas Ions-16 and ChEMBL-20 contain the molecules with 13 non-hydrogen atoms or more. The datasets are formatted as HDF5 files. Data group names have the format as <code>_???</code>, where <code>???</code> corresponds to the number of atoms in molecules. Each group contains data for M molecules, each with <code>N</code> atoms. The groups contain the following datasets: Name Data type Shape Description<br> mol_id S24 M Molecule ID<br> coord float32 M, N, 3 Cartesian coordinates, Å<br> numbers uint8 M, N Atomic numbers<br> charge int8 M Molecular charge<br> mult unit8 M Spin multiplicity<br> energy float64 M PBE0/ma-def2-SVP energy, eV<br> charges float32 M, N, 2 α and β NBO charges
DOI: 10.5281/zenodo.5007979
title: AIMNet-NSE test datasets

description: Ions-16 and ChEMBL-20 datasets used to test the performance of the AIMNet-NSE model. The datasets contain PBE0/ma-Def2-SVP energies and NBO atomic charges for the non-equilibrium conformers of neutral organic molecules randomly sampled from the PubChem database (Ions-16) and B97-3c optimized conformations of neutral organic molecules randomly sampled from the ChEMBL database (ChEMBL-20). The number in the dataset name corresponds to the maximum number of non-hydrogen atoms in the molecules. The dataset which was used for training the AIMNet-NSE model contains molecules up to 12 non-H atoms, whereas Ions-16 and ChEMBL-20 contain the molecules with 13 non-hydrogen atoms or more. The datasets are formatted as HDF5 files. Data group names have the format as <code>_???</code>, where <code>???</code> corresponds to the number of atoms in molecules. Each group contains data for M molecules, each with <code>N</code> atoms. The groups contain the following datasets: Name Data type Shape Description<br> mol_id S24 M Molecule ID<br> coord float32 M, N, 3 Cartesian coordinates, Å<br> numbers uint8 M, N Atomic numbers<br> charge int8 M Molecular charge<br> mult unit8 M Spin multiplicity<br> energy float64 M PBE0/ma-def2-SVP energy, eV<br> charges float32 M, N, 2 α and β NBO charges
DOI: 10.5281/zenodo.5007789
title: A Positive/Unlabeled Approach for the Segmentation of Medical Sequences using Point-Wise Supervision

description: Description<br> ------------ This archive contains data and results (model checkpoint, segmentation results, ...)<br> used and obtained in paper: Laurent Lejeune, Raphael Sznitman,<br> A Positive/Unlabeled Approach for the Segmentation of Medical Sequences using Point-Wise Supervision,<br> Medical Image Analysis,<br> 2021 (in preparation) Details<br> ------------ Each directory is named DatasetXY, where X denotes the type (surgical instrument, cochlea,<br> slitlamp, and brain), and Y denotes the index of the sequences (from 0 to 3). For the data.zip archive, we provide a CSV file that contains the 2d locations used in our experiments. For the results.zip archive, the checkpoint of our models are in PyTorch format.
DOI: 10.5281/zenodo.5007788
title: A Positive/Unlabeled Approach for the Segmentation of Medical Sequences using Point-Wise Supervision

description: Description<br> ------------ This archive contains data and results (model checkpoint, segmentation results, ...)<br> used and obtained in paper: Laurent Lejeune, Raphael Sznitman,<br> A Positive/Unlabeled Approach for the Segmentation of Medical Sequences using Point-Wise Supervision,<br> Medical Image Analysis,<br> 2021 (in preparation) Details<br> ------------ Each directory is named DatasetXY, where X denotes the type (surgical instrument, cochlea,<br> slitlamp, and brain), and Y denotes the index of the sequences (from 0 to 3). For the data.zip archive, we provide a CSV file that contains the 2d locations used in our experiments. For the results.zip archive, the checkpoint of our models are in PyTorch format.
DOI: 10.6084/m9.figshare.14815869
title: Supplementary Material

description: Supplementary Material for a manuscirpt
DOI: 10.6084/m9.figshare.14815869.v3
title: Supplementary Material

description: Supplementary Material for a manuscirpt
DOI: 10.6084/m9.figshare.14815869.v2
title: Supplementary Material

description: Supplementary Material for a manuscirpt
DOI: 10.5281/zenodo.5008043
title: Data accompanying the paper "Early habitability and crustal decarbonation of a stagnant-lid Venus"

description: Produced data from a coupled interior-atmosphere model depicting Venus' early evolution assuming stagnant-lid convection, CO<sub>2</sub> degassing, weathering, carbonate burial, and crustal decarbonation. The data accompanies the paper "Early habitability and crustal decarbonation of a stagnant-lid Venus", submitted to JGR: Planets.
DOI: 10.5281/zenodo.4600709
title: Data accompanying the paper "Early habitability and crustal decarbonation of a stagnant-lid Venus"

description: Produced data from a coupled interior-atmosphere model depicting Venus' early evolution assuming stagnant-lid convection, CO<sub>2</sub> degassing, weathering, carbonate burial, and crustal decarbonation. The data accompanies the paper "Early habitability and crustal decarbonation of a stagnant-lid Venus", submitted to JGR: Planets.
DOI: 10.6073/pasta/3cba4f75a923485a2f72c4333f79f192
title: Interagency Ecological Program San Francisco Estuary Spring Kodiak Trawl Survey 2002 - 2021

description: The Interagency Ecological Program San Francisco Estuary Spring Kodiak Trawl Survey was initiated by the California Department of Fish and Wildlife (CDFW) in 2002 to improve the detection rate of pre-spawning and mature Delta Smelt (hypomesus transpacificus). The survey began as the Spring Midwater Trawl Survey, an extension of the Fall Midwater Trawl Survey, in 1991 to assist with water management and export decisions in relation to the distribution of pre-spawning Delta Smelt. Net evaluations studies compared the relative catch efficiency of 3 types of nets and found that the Kodiak net was most effective for Sampling adult Delta Smelt. Objectives of SKT are to improve the ability to detect Delta Smelt, obtain maturity status for adult Delta Smelt, and provide results to scientist and managers on a near real-time basis to ais in resource management. SKT operates 6 monthly surveys December through May each lasting 4-5 days in length. Each survey, 40 fix sample locations are sampled using a standard 10 minute Kodiak trawl with a total length of 65 feet and a fully expanded mouth opening of 25 feet by 6 feet. The volume of water sampled is estimated using a General Oceanics flowmeter placed over the side of the boat. The net is constructed of green or black variable mesh ranging in dimension from 2 inches knoteted stretched mesh at the mouth and decreasing by ½ inch through a series of 5 panels to ¼ inch knotless stretched mesh at the cod-end. All fish sampled are identified to species and enumeration, Delta Smelt are staged in the field. At each station, environmental and water quality data are also collected, and include: temperature, electrical conductivity (normalized @ 25°C), water clarity, and tidal condition.
DOI: 10.5281/zenodo.4912673
title: GlobalFlowRatios

description: Datasets for the "Temperature and pH mediate stoichiometric constraints of organically-derived soil nutrients" manuscript.
DOI: 10.6084/m9.figshare.11815257
title: Adversity and REF in BPD

description: Dataset ( R format) coming from the EUropean Research NETwork investigating correlates of BPD in adolescence, the European Research Network on BPD, EURNET-BPD (Corcos et al., 2010; Corcos et al., 2013).<br>Code.R : Code to reproduce the analysis of our study
DOI: 10.6084/m9.figshare.11815257.v1
title: Dataset Borderline.rds

description: Dataset ( R format) coming from the EUropean Research NETwork investigating correlates of BPD in adolescence, the European Research Network on BPD, EURNET-BPD (Corcos et al., 2010; Corcos et al., 2013).<br>Code.R : Code to reproduce the analysis of our study
DOI: 10.5517/ccdc.csd.cc203lsj
title: CCDC 1850507: Experimental Crystal Structure Determination

description: Related Article: Wen-Jing Shi, Yan Huang, Wancui Liu, Dan Xu, Shu-Ting Chen, Fenggang Liu, Jiaqin Hu, Liyao Zheng, Kun Chen|2019|Dyes Pigm.|170|107566|doi:10.1016/j.dyepig.2019.107566
DOI: 10.5517/ccdc.csd.cc25wl0p
title: CCDC 2022502: Experimental Crystal Structure Determination

description: Related Article: K. Saminathan, R. Jagan, K. Sivakumar, K. Saravanan|2017|Springer Proceedings in Physics|189|553|
DOI: 10.5517/ccdc.csd.cc26l1rm
title: CCDC 2043140: Experimental Crystal Structure Determination

description: Related Article: Jais Kurian, Kanneth S. Shurooque, Venkatachalam Ramkumar, Lakshmi Chakkumkumarath, M. Muraleedharan Kannoth |2021|Org.Lett.|23|3354|doi:10.1021/acs.orglett.1c00827
DOI: 10.5517/ccdc.csd.cc26l1sn
title: CCDC 2043141: Experimental Crystal Structure Determination

description: Related Article: Jais Kurian, Kanneth S. Shurooque, Venkatachalam Ramkumar, Lakshmi Chakkumkumarath, M. Muraleedharan Kannoth |2021|Org.Lett.|23|3354|doi:10.1021/acs.orglett.1c00827
DOI: 10.25387/g3.14580009
title: Supplemental Material for Berg, et al., 2021

description: Supplemental data and analysis scripts for Berg et al. "The amino acid substitution affects cellular response to mistranslation"
DOI: 10.25387/g3.14580009.v1
title: Supplemental Material for Berg, et al., 2021

description: Supplemental data and analysis scripts for Berg et al. "The amino acid substitution affects cellular response to mistranslation"
DOI: 10.5281/zenodo.4979149
title: Stem cell hierarchies and developmental origins of rhabdomyosarcoma

description: Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma of childhood and is comprised of two major molecular subtypes. Here, we identify common developmental stages and hierarchies in this disease.
description: The compressed datasets contain all the single-cell RNA-seq and lineage tracing data in the manuscript "Stem cell hierarchies and developmental origins of rhabdomyosarcoma". After uncompressing, the root directory contains all the clustering annotation information and rhabdomyosarcoa gene modules. For each folder, there is the filtered count matrix output by Cell Ranger, and normalized and filtered Seurat RDS data, and raw velocity loom file together with processed velocity h5ad file for dynamical RNA velocity models. The scripts to analyze the datasets are available on GitHub https://github.com/qinqian/rms_analysis.
DOI: 10.5281/zenodo.4783316
title: Phase transition of interstellar CO ice

description: This collection contains the experimental data for the manuscript titled: "Phase transition of interstellar CO ice". This collection contains mid-infrared spectral data at a resolution of 1 cm<sup>-1</sup>. The temperature corresponding to each spectrum is marked in the "temperature" column or in the file name. The background spectrum of each experiment is taken to be the one measured right before the CO/CO2 deposition. There are three groups corresponding to three sets of experiments: 1. CO warm-up. RAIRS spectra of CO ice of different thicknesses during warm-up. The file is suffixed by the thickness, such as CO_warmUp_3ML.csv. The CO ices were deposited onto np-ASW at 6 K and warmed up at 0.2 K/minute. The temperature corresponding to each spectrum is marked in the "temperature" column. 2. CO:CO<sub>2</sub> mixture warm-up. RAIRS spectra of the mixture of 9 ML of CO and 1 ML of CO<sub>2</sub> during warm-up. The CO:CO<sub>2</sub> ice mixture was deposited onto np-ASW at 6 K and warmed up at 0.2 K/minute. The temperature corresponding to each spectrum is marked in the "temperature" column, file name co_co2_mix_warmup.csv. 3. CO:CO<sub>2</sub> mixture isotherm. RAIRS spectra of the mixture of 9 ML of CO and 1 ML of CO<sub>2</sub> deposited at 6 K and then flash heated to a target temperature to do isotherm experiments. The target temperatures are shown in the file name, such as CO_CO2_mix_isotherm_7.9K.csv.
DOI: 10.5281/zenodo.4783315
title: Phase transition of interstellar CO ice

description: This collection contains the experimental data for the manuscript titled: "Phase transition of interstellar CO ice". This collection contains mid-infrared spectral data at a resolution of 1 cm<sup>-1</sup>. The temperature corresponding to each spectrum is marked in the "temperature" column or in the file name. The background spectrum of each experiment is taken to be the one measured right before the CO/CO2 deposition. There are three groups corresponding to three sets of experiments: 1. CO warm-up. RAIRS spectra of CO ice of different thicknesses during warm-up. The file is suffixed by the thickness, such as CO_warmUp_3ML.csv. The CO ices were deposited onto np-ASW at 6 K and warmed up at 0.2 K/minute. The temperature corresponding to each spectrum is marked in the "temperature" column. 2. CO:CO<sub>2</sub> mixture warm-up. RAIRS spectra of the mixture of 9 ML of CO and 1 ML of CO<sub>2</sub> during warm-up. The CO:CO<sub>2</sub> ice mixture was deposited onto np-ASW at 6 K and warmed up at 0.2 K/minute. The temperature corresponding to each spectrum is marked in the "temperature" column, file name co_co2_mix_warmup.csv. 3. CO:CO<sub>2</sub> mixture isotherm. RAIRS spectra of the mixture of 9 ML of CO and 1 ML of CO<sub>2</sub> deposited at 6 K and then flash heated to a target temperature to do isotherm experiments. The target temperatures are shown in the file name, such as CO_CO2_mix_isotherm_7.9K.csv.
DOI: 10.6073/pasta/b7ac67d21ce911b4a0a40a89fb509e99
title: Rainfall at El Verde Field Station, Rio Grande, Puerto Rico since 1975

description: Rainfall has been measured at the El Verde Field Station since 1964. McDowell and Estrada-Pinto, 1988 presents a description of the collection procedures, raw data from 1964 to 1986, and some summary statistics for this period of record. Precipitation for this period showed some seasonality in monthly means, with a peak in May. Monthly averages for the period of 1975 to current chart can be found at this site. The highest values for the monthly averages for the period of 1975 to 2000 are from August to December with a low in October and November the highest. In this period the highest amount of total annual rainfall was in 1998 with 5293.61 mm and the minimum in 1994 with 1402.87 mm.
DOI: 10.6073/pasta/08d3b894e356b9abafa03d8ec3186753
title: Maximum temperature at El Verde Field Station, Rio Grande, Puerto Rico since October 1992

description: Daily emperature has been measured at the El Verde Field Station since 1975 (see methods). These data was divided into two data set: #16, having data from 1992 to current and #181 which has data from1975 till August 1992. Data-missing gaps where filled in by extrapolated data from other sources, making the subsequent manipulations less valuable for interpreting long term trends. Monthly averages have been calculated. Maximum values for maximum temperature were recorded from May to October with a range from 29 to 30 and peaks of 29.7 Centigrade in October. The months of October through December show the most dramatic increase, specially December (see chart). Highest average maximum temperatures during these years were recorded in 1998 and 1999 (See chart). Max monthly temperatures appear to be increasing from this years on.
DOI: 10.5281/zenodo.5007378
title: Probabilistic Reconstruction of Type Ia Supernova SN 2002bo

description: <strong>SN2002bo_emulator_paper_data</strong> The TARDIS configuration YAML file used as a template for the training spectra. HDF5 file of posterior samples of model parameters and their associated weights from the nested sampler. <strong>SN2002bo_emulator_paper_spectra</strong> Input grid of model parameters and corresponding spectra produced by TARDIS used to generate the training grid of the emulator.
description: For further questions, please contact John O'Brien at obrie278@msu.edu
DOI: 10.5281/zenodo.5007377
title: Probabilistic Reconstruction of Type Ia Supernova SN 2002bo

description: <strong>SN2002bo_emulator_paper_data</strong> The TARDIS configuration YAML file used as a template for the training spectra. HDF5 file of posterior samples of model parameters and their associated weights from the nested sampler. <strong>SN2002bo_emulator_paper_spectra</strong> Input grid of model parameters and corresponding spectra produced by TARDIS used to generate the training grid of the emulator.
description: For further questions, please contact John O'Brien at obrie278@msu.edu
DOI: 10.18739/a2zs2kd99
title: In situ Magnesium/Calcium (Mg/Ca) and oxygen isotope (d18O) measurements in Neogloboquadrina pachyderma shells collected in 2006 and 2007 in sediment traps moored in the Irminger Sea

description: This dataset includes chemical and isotopic measurements on shells of the planktic foraminifera Neogloboquadrina pachyderma sinistral collected in April 2006 and April 2007 from two sediment traps moored in the Irminger Sea (IRM-3, 59°14.86’North (N), 39°39.47’West (W) and IRM-4, 59°14.85’N, 39°39.47’W). Individual shells were analyzed in situ for their magnesium/calcium (Mg/Ca) ratios by Laser Ablation Inductively Coupled Mass Spectrometry (LA-ICP-MS), and for their stable oxygen isotope composition (d18O) by secondary ion mass spectrometry (SIMS). Hydrographic measurements reveal that the water column at sample location is isothermal and isohaline during the month prior to collection. The purpose of this project was to determine potential differences in the Mg/Ca or d18O composition of the lamellar calcite, formed and the upper water column, and the crust calcite, precipitated in deeper waters but at the same temperature and salinity than the lamellar calcite. Corresponding publication: Livsey, C.M., Kozdon, R., Bauch, D., Brummer, G.-J.A., Jonkers, L., Orland, I., Hill, T.M., Spero, H.J., 2020. High-resolution Mg/Ca and d18O patterns in modern Neogloboquadrina pachyderma from the Fram Strait and Irminger Sea. Paleoceanography and Paleoclimatology, 35(9): e2020PA003969.doi:10.18739/A2319S316.
DOI: 10.6084/m9.figshare.14587599
title: Supplementary_Table_5_Plasma_DE_analysis.xlsx

description: Supplementary Table 5. A. Expression levels and differential expression analysis of plasma miRNAs. B. Plasma levels of the DEmiRNAs identified in the analysis of stool samples. C. Correlation analysis between miRNA levels in stool and plasma samples.
DOI: 10.6084/m9.figshare.14587581
title: Supplementary_Table_2_Food_drink_nutrient_intake.xlsx

description: Supplementary Table 2. Dietary and lifestyle information of the analysed subjects. For continuous covariates the average and standard deviation are reported.
DOI: 10.6084/m9.figshare.14587584
title: Supplementary_Table_6_xenomiR_expression.xlsx

description: Supplementary Table 6. Analysis of xenomiR expression levels in stool (A) and in plasma samples (B). C) Set of RNA sequences aligned with gma-MIR6300 using BLAST. D) Homology analysis between detected xenomiRs and human miRNAs
DOI: 10.6084/m9.figshare.14587596
title: Supplementary_Table_1_Alignment_statistics.xlsx

description: Supplementary Table 1. Alignment statistics and information of the small RNA-Seq data in stool (A) and plasma (B) samples and alignment statistics and information of the stool shotgun metagenomic data (C).
DOI: 10.6084/m9.figshare.14587599.v2
title: Supplementary_Table_5_Plasma_DE_analysis.xlsx

description: Supplementary Table 5. A. Expression levels and differential expression analysis of plasma miRNAs. B. Plasma levels of the DEmiRNAs identified in the analysis of stool samples. C. Correlation analysis between miRNA levels in stool and plasma samples.
DOI: 10.6084/m9.figshare.14587584.v2
title: Supplementary_Table_6_xenomiR_expression.xlsx

description: Supplementary Table 6. Analysis of xenomiR expression levels in stool (A) and in plasma samples (B). C) Set of RNA sequences aligned with gma-MIR6300 using BLAST. D) Homology analysis between detected xenomiRs and human miRNAs
DOI: 10.6084/m9.figshare.14587581.v1
title: Supplementary_Table_2_Food_drink_nutrient_intake.xlsx

description: Supplementary Table 2. Dietary and lifestyle information of the analysed subjects. For continuous covariates the average and standard deviation are reported.
DOI: 10.6084/m9.figshare.14587584.v1
title: Supplementary_Table_6_xenomiR_expression.xlsx

description: Supplementary Table 6. Analysis of xenomiR expression levels in stool (A) and in plasma samples (B). C) Set of RNA sequences aligned with gma-MIR6300 using BLAST. D) Homology analysis between detected xenomiRs and human miRNAs
DOI: 10.6084/m9.figshare.14587602
title: Supplementary_Table_7_Enrichment_Analysis.xlsx

description: Supplementary Table 7. A. List of functional processes enriched in targets of different groups of stool miRNAs. B. Validated targets of stool miRNA analysed in the functional enrichment analysis.
DOI: 10.6084/m9.figshare.14587599.v1
title: Supplementary_Table_5_Plasma_DE_analysis.xlsx

description: Supplementary Table 5. A. Expression levels and differential expression analysis of plasma miRNAs. B. Plasma levels of the DEmiRNAs identified in the analysis of stool samples. C. Correlation analysis between miRNA levels in stool and plasma samples.
DOI: 10.6084/m9.figshare.14587611.v1
title: Supplementary_Table_3_Stool_DEmiRNAs.xlsx

description: Supplementary Table 3. A) Expression levels and differential expression analysis of stool miRNAs; B) Results of the differential expression analysis of the 49 stool DEmiRNAs considering different covariates in the DESeq2 model; C) Results of a correlation analysis between stool DEmiRNAs expression and subject age and years of non-omnivorous diet; D) HMDD annotations for the hairpin of stool DEmiRNAs; E) Differential expression analysis of stool DEmiRNAs considering an independent group of O subjects (O validation).
DOI: 10.6073/pasta/15e12e152d17d7ab925db6851955007c
title: Minimum temperature at El Verde Field Station, Rio Grande, Puerto Rico since 1975

description: Daily emperature has been measured at the El Verde Field Station since 1975 (see methods). Monthly averages have been calculated. Lowest average values for minimum temperature were recorded from January to April with nearly 18 Centigrades during this period of time (see chart). During these months, the lowest average minimum temperature was recorded in 1976 ranging from 20 to 22 Centigrades (see chart). Highest minimum montly average records are shown from June to October with peak in the vecinity of 20 Centigrades. The year with lowest minimum tempearture was 1995 and 2000 with the low values near 14 and 15 Centigrades, respectively.
DOI: 10.5283/epub.45068
title: Data archive of "Spin-orbit interaction induces charge beatings in a lightwave-STM -- single molecule junction", published in Physical Review B

description: Recent lightwave-STM experiments have shown space and time resolution of single molecule vibrations directly on their intrinsic length and timescales. We address here theoretically the electronic dynamics of a copper-phthalocyanine in a lightwave-STM explored within a pump-probe cycle scheme. The spin-orbit interaction in the metallic center induces beatings of the electric charge flowing through the molecule as a function of the delay time between the pump and the probe pulses. Interference between the quasidegenerate anionic states of the molecule and the intertwined dynamics of the associated spin and pseudospin degrees of freedom are the key aspects of such phenomenon. We study the dynamics directly in the time domain within a generalized master-equation approach.