cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.24378/exe.1023
title: The limits of the primitive equations of dynamics for warm, slowly rotating Small Neptunes and Super Earths (dataset)

description: We present significant differences in the simulated atmospheric flow for warm, tidally–locked small Neptunes and super Earths (based on a nominal GJ 1214b) when solving the simplified, and commonly used, primitive dynamical equations or the full Navier–Stokes equations. The dominant prograde, superrotating zonal jet is markedly different between the simulations which are performed using prac- tically identical numerical setups, within the same model. The differences arise due to the breakdown of the so–called ‘shallow–fluid’ and traditional approximations, which worsens when rotation rates are slowed, and day–night temperature contrasts are increased. The changes in the zonal advection between simulations solving the full and simplified equations, give rise to significant differences in the atmospheric redistribution of heat, altering the position of the hottest part of the atmosphere and temperature contrast between the day and night sides. The implications for the atmospheric chemistry and, therefore, observations need to be studied with a model including a more detailed treatment of the radiative transfer and chemistry. Small Neptunes and super Earths are extremely abundant and important, potentially bridging the structural properties (mass, radius, composition) of terrestrial and gas giant planets. Our results indicate care is required when interpreting the output of models solving the primitive equations of motion for such planets.
description: Netcdf output files of prognostic atmospheric fields for 3D simulations of a Super-Earth/Mini neptune Exoplanet based nominally on GJ1214b
description: The article associated with this dataset is located in ORE at: http://hdl.handle.net/10871/35082
DOI: 10.24378/exe.1604
title: Vibrational strong coupling with surface plasmons and the presence of surface plasmon stop bands (dataset)

description: We demonstrate strong coupling between surface plasmon resonances and molecular vibrational resonances of polymethyl methacrylate (PMMA) molecules in the mid-infrared range through the use of grating coupling, complimenting earlier work using microcavities and localised plasmon resonances. We choose the period of the grating so that we may observe strong coupling between the surface plasmon mode associated with a patterned gold film and the C=O vibrational resonance in an overlying polymer film. We present results from experiments and numerical simulations to show that surface plasmon modes provide convenient open cavities for vibrational strong coupling experiments. In addition to providing momentum matching between surface plasmon modes and incident light, gratings may also produce a modification of the surface plasmon properties, notably their dispersion. We further show that for the parameters used in our experiment, surface plasmon stop bands are formed, and we find that both stop-band edges undergo strong coupling.
description: Data associated with the figures in the Menghrajani et al. (2019) article "Vibrational strong coupling with surface plasmons and the presence of surface plasmon stop bands" published in ACS Photonics.
description: The article associated with these datasets is available in ORE at: http://hdl.handle.net/10871/38669
DOI: 10.24378/exe.503
title: A broadband stripline technique for characterizing relative permittivity and permeability (dataset)

description: We present a stripline design and calibration method allowing the extraction of relative permittivity of single dielectric samples in the 200 MHz – 50 GHz range. The simultaneous extraction of relative permittivity and permeability is also illustrated by characterizing a set of samples comprising magnetic inclusions over the same frequency range. The calibration method involves the use of seven measurements of the stripline scattering parameters (S-parameters) with different length shorts inserted. From these measurements, it is possible to determine the reflections at the transition regions of the stripline to correct the measured S-parameters for characterization. By quantifying a range of samples with increasing percentage volume filling of barium titanate in polyurethane for the case of dielectric samples, and carbonyl iron powder (CIP) for magnetic samples, this work demonstrates a reliable method for the broadband characterization of composite materials.
description: The article associated with this dataset is located in ORE at: http://hdl.handle.net/10871/33245
DOI: 10.24378/exe.4264
title: Numerical Investigation of Flexible Purcell-like Integrated Microfluidic Pumps (dataset)

description: This is the dataset used for the Binsley et al. (2022) article "Numerical Investigation of Flexible Purcell-like Integrated Microfluidic Pumps" published in the Journal of Applied Physics.
description: The "Numerical Investigation of Flexible Purcell-like Integrated Microfluidic Pumps" dataset. Data includes a COMSOL model and a Matlab file. Data formats are .m and .mph
description: The article associated with this dataset is available in ORE at: http://hdl.handle.net/10871/131254
DOI: 10.24378/exe.4347
title: 3D climate simulations of the Archean find that methane has a strong cooling effect at high concentrations (dataset)

description: Methane is thought to have been an important greenhouse gas during the Archean, although its potential warming has been found to be limited at high concentrations due to its high shortwave absorption. We use the Met Office Unified Model, a general circulation model, to further explore the climatic effect of different Archean methane concentrations. Surface warming peaks at a pressure ratio pCH4:pCO2 of approximately 0.1, reaching a maximum of up to 7\,K before significant cooling above this ratio. Equator-to-pole temperature differences also tend to increase up to pCH4≤300 Pa, which is driven by a difference in radiative forcing at the equator and poles by methane and a reduction in the latitudinal extend of the Hadley circulation. 3D models are important to fully capture the cooling effect of methane, due to these impacts of the circulation.
description: Here is the data set accompanying this publication, for all simulations. All data comes from climate simulation data from the Met Office Unified Model. All the data is here for results and appendix material.
description: The article associated with this dataset is available in ORE at: http://hdl.handle.net/10871/132519
DOI: 10.24378/exe.4384
title: High-dimensional spatial mode sorting using multi-plane light conversion (dataset)

description: This is the dataset used for the Kupianskyi et al. article "High-dimensional spatial mode sorting and optical circuit design using multi-plane light conversion" published in APL Photonics.
description: The dataset contains: - data for plots shown in the paper in form of .mat and .m MATLAB files; - experimental results in form of camera images used to analyse the performance of the system shown in the paper; - example commented Python code in form of a Jupyter notebook that demonstrates the gradient ascent phase mask optimisation procedure; - supplementary movies.
DOI: 10.5281/zenodo.15722171
title: ISMB/ECCB25 -  VT3 tutorial data

description: Tissues and organs are complex and highly-organized systems composed of diverse cells that work together to maintain homeostasis, drive development and mediate complex disease progression as Myocardial Infarction (Kuppe et al. 2022). A key focus of modern biology is understanding how heterogeneous populations of cells coexist and communicate with each other (intercellular signaling), how they properly respond (intracellular signaling) within a tissue and organ system and how these processes vary across different experimental conditions (comparative analysis). Recently, a rapid expansion of computational tools exploring the expression of ligand and receptor has enabled the systematic inference of cell-cell communication from single-cell transcriptomics and spatial transcriptomics data (Armingol et al. 2021; Armingol, Baghdassarian, and Lewis 2024). These are crucial in unravelling the complex landscape of biological systems.

This tutorial aims to provide a comprehensive introduction to computational approaches for cell-cell communication inference using high throughput transcriptomics data. It covers the fundamental concepts of cellular communication and assumptions underlying analysis focusing on the main computational methods used in the field. This includes computational approaches for inter-cellular communication inference (CellphoneDB (Efremova et al. 2020); LIANA (Dimitrov et al. 2022, 2024)) and for intra-cellular signals communication (scSeqComm (Baruzzo, Cesaro, and Di Camillo 2022); NicheNet (Browaeys, Saelens, and Saeys 2019)). Next, we will describe approaches for comparative analysis of cell-cell networks in distinct biological conditions (CrossTalkeR (Nagai et al. 2021)) and methods for spatially resolved cell-cell communications (Ischia (Regan-KomitoDaniel 2024); DeepCOLOR (Kojima et al. 2024)).

In the first part of the tutorial, participants will be introduced to the theoretical basis of state-of-the-art computational approaches and will learn how to use representative tools for inferring intercellular signaling and intracellular signaling pathways. In the second part, we will focus on the comparative analyses, i.e. changes of cell-cell communication in two conditions, and subsequently highlighting the unique insights spatial transcriptomics data can provide for understanding tissue architecture and cellular communication. Both sections will be followed by a hands-on component based on the analysis of single cell and spatial transcriptomics data from the myocardial infarction atlas (Kuppe et al. 2022). To promote transparency, all the codes, software tools and the datasets used throughout the tutorial will be available and accessible through open-access repositories (e.g. GitHub repositories or Zenodo platforms).

During the ISMB VT3 tutorial, we will work with data from the Myocardial Infarction atlas from Kuppe, C. et. al., 2022 . This is a subset with 23 snRNA and Visium 10x paired samples (samples with less than 1500 cells in the snRNA-seq data were filtered out), and 33 different cell subtypes
DOI: 10.5065/kqmb-hn20
title: ICARUS Chamber Experiment: Caltech Atmospheric Chamber_20201001_DECAMETHYLCYCLOPENTASILOXANE_Hydroxyl radical_Ammonium sulfate_C2

description: Goals: Measure SOA yield of D5Summary: Performed in the Caltech Near Bag, no NOx, low YOrganization: Caltech Atmospheric Chamber Lab Affiliation: California Institute of Technology, Pasadena, CA Chamber: Near Bag 2017Experiment Category: Aerosol formation Oxidant: Hydroxyl radical Reactants: DECAMETHYLCYCLOPENTASILOXANE Reaction Type: Photooxidation Relative Humidity: 5 Temperature: 26.5 Seed Name: Ammonium sulfate
DOI: 10.15468/dl.ens957
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dolichospermum flosaquae (Bréb. ex Bornet & Flahault) Wacklin, L.Hoffm. & Komárek",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((20.529 -24.0715,20.509 -24.0455,20.509 -24.0715,20.529 -24.0715))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065298-250525065834625/datasets/export for details.
DOI: 10.15468/dl.6kwv84
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dolichospermum flosaquae (Bréb. ex Bornet & Flahault) Wacklin, L.Hoffm. & Komárek",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((25.5395 -23.2724,25.1306 -24.0715,25.5395 -24.0715,25.5395 -23.2724))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065299-250525065834625/datasets/export for details.
DOI: 10.15468/dl.agve6j
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Canis lupus Linnaeus, 1758",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON((9.924338 43.237198, 11.815867 43.237198, 11.815867 44.512177, 9.924338 44.512177, 9.924338 43.237198))",
 "Year is greater than or equal to 2005",
 "Year is less than or equal to 2015"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065300-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9bdptw
title: Occurrence Download

description: A dataset containing 32300921 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Costa Rica",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 32300921 records from 1851 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065277-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18033969
title: Supplemental Material for: Relaminated subduction mélange beneath southern Tibet: A key to Lhasa ultrapotassic magmatism
DOI: 10.5281/zenodo.18033970
title: Supplemental Material for: Relaminated subduction mélange beneath southern Tibet: A key to Lhasa ultrapotassic magmatism
DOI: 10.6084/m9.figshare.28267697
title: Enhanced reactivity of <i>syn</i>-CH<sub>3</sub>CHOO with H<sub>2</sub>O by a roaming mechanism in the entrance channel

description: Experimental and Theoretical Supplementary Data.
DOI: 10.15468/dl.qax8kw
title: Occurrence Download

description: A dataset containing 625 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Cirolana parva Hansen, 1890",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 625 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015768-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ghht4q
title: Occurrence Download

description: A dataset listing the 2698 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Estonia",
 "GadmGid is EST.1.20_1",
 {
 "or" : [
 "Month is March",
 "Month is April",
 "Month is May",
 "Month is June",
 "Month is July"
 ]
 },
 "OccurrenceStatus is Present",
 "Year 2001-2021"
 ]
}

 The dataset's 2698 records were derived from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050050-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.oyqo3p
title: Occurrence Download

description: A dataset containing 578 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sorex veraepacis Alston, 1877"
 ]
}

 The dataset includes 578 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003285-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ubit71
title: Occurrence Download

description: A dataset containing 1311 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cercyonis oetus Boisduval, 1869"
 ]
}

 The dataset includes 1311 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005202-180730143533302/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rpxbrf
title: Occurrence Download

description: A dataset containing 1618707 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Argentina",
 {
 "or" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "DatasetKey is Instituto de Botánica Darwinion"
 ]
 }
 ]
}

 The dataset includes 1618707 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000343-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vt6x9r
title: Occurrence Download

description: A dataset containing 58 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Mimosa exalbescens Barneby",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 58 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049187-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.blmyqc
title: Occurrence Download

description: A dataset containing 103 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Poeciliopsis prolifica Miller, 1960"
 ]
}

 The dataset includes 103 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005202-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.evbnfm
title: Occurrence Download

description: A dataset containing 331 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Stylocheiron affine Hansen, 1910"
 ]
}

 The dataset includes 331 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0133164-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rjezzs
title: Occurrence Download

description: A dataset containing 950407 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Year 1000-2009",
 "DatasetKey is EOD – eBird Observation Dataset",
 "TaxonKey is Passer domesticus (Linnaeus, 1758)"
 ]
}

 The dataset includes 950407 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057075-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tdrhi2
title: Occurrence Download

description: A dataset containing 469 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Benin",
 "TaxonKey is Cochlospermum planchonii Hook.f. ex Planch."
 ]
}

 The dataset includes 469 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005202-190307172214381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j9bph9
title: Occurrence Download

description: A dataset containing 34269 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-110.21168 22.07889,-108.85161 23.14754,-112.33017 28.56637,-114.62057 32.89253,-117.47598 32.69598,-115.33209 27.25769,-110.21168 22.07889))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cathartes aura (Linnaeus, 1758)"
 ]
}

 The dataset includes 34269 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0150395-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g382ym
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States Minor Outlying Islands",
 "TaxonKey is Myrtales"
 ]
}

 The dataset includes 8 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057072-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fmyt7m
title: Occurrence Download

description: A dataset containing 754 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Prionailurus bengalensis (Kerr, 1792)"
 ]
}

 The dataset includes 754 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005202-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h07zvn
title: Occurrence Download

description: A dataset containing 57 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mammillaria petterssonii Hildm."
 ]
}

 The dataset includes 57 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000343-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ahhvu2
title: Occurrence Download

description: A dataset containing 782 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Year 1970-2020",
 "HasCoordinate is true",
 "TaxonKey is Vespa mandarinia Smith, 1852",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 782 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063979-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jvq4rc
title: Occurrence Download

description: A dataset containing 9231 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "TaxonKey is Polygala rupestris Pourr."
 ]
}

 The dataset includes 9231 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025824-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.itd2jo
title: Occurrence Download

description: A dataset listing the 35 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Cyprus",
 "TaxonKey is Elasmobranchii"
 ]
}

 The dataset's 35 records were derived from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035683-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wmp0ek
title: Occurrence Download

description: A dataset containing 88222 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Forcipulatida"
 ]
}

 The dataset includes 88222 records from 326 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000343-190307172214381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.