cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.pvg2xk
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Mesalina martini (Boulenger, 1897)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 15 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006839-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.63535
title: Occurrence of mammalia relicts at site Burghöhle Dietfurt
DOI: 10.15468/dl.qgsrut
title: Occurrence Download

description: A dataset containing 901 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "HasCoordinate is true",
 "TaxonKey is Mecocerculus minor (Taczanowski, 1879)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 901 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006841-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.672512
title: (Table 3) Relative abundances of planktic foraminifera in middle Miocene sediments of ODP Hole 130-806B from the Ontong Java Plateau, Pacific Ocean
DOI: 10.15468/dl.okl7wn
title: Occurrence Download

description: A dataset containing 132730 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Argentina",
 "Country is Chile",
 "Country is Peru",
 "Country is Bolivia (Plurinational State of)",
 "Country is Uruguay",
 "Country is Ecuador",
 "Country is Brazil",
 "Country is Colombia",
 "Country is Paraguay",
 "Country is Venezuela (Bolivarian Republic of)",
 "Country is Trinidad and Tobago",
 "Country is Guyana",
 "Country is Suriname"
 ]
 },
 "TaxonKey is Pygochelidon cyanoleuca (Vieillot, 1817)"
 ]
}

 The dataset includes 132730 records from 112 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006836-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12804644
title: Experimental and simulation data from Stransky et al. "Ionization by XFEL radiation produces distinct structure in liquid water"

description: This deposition contains two separate gzipped tarballs:



preprocessed_diffraction_data.tar.gzpre-processed diffraction data, specifically I(q) traces for each X-ray pulse along with associated metadata

XMDYN_simulations.tar.gzsimulation trajectories produced by the XMDYN code that describe water ionization following an intense X-ray pulse


In more detail, the preprocessed_diffraction_data.tar.gz contains 36 HDF5 files, each corresponding to a single LCLS run. Each HDF5 contains the following data arrays:

ebeam                    Group
event_time               Dataset {8674/Inf}
evr                      Group
fiducials                Dataset {8674/Inf}
gas_detector             Group
phase_cav                Group
probe_energy             Dataset {8674/Inf}
probe_mag                Dataset {8674/Inf}
pump_energy              Dataset {8674/Inf}
pump_mag                 Dataset {8674/Inf}
radial_profile           Dataset {8674/Inf, 500}
radial_profile_qvalues   Dataset {500/8192}

The X contains trajectories for 7 different simulations, each in a separate directory. These top level directories are named according to simulation parameters:

sim<BOX_SIZE>A_<probe_delay[fs]/singl>_<fraction_of_nominal_fluence>

 

Box sizes are in [Å], probe delay is in [fs] or there is only single pulse, 1.00 is the nominal fluence.

 

Each of these directories contain subdirectories recording snapshots every 5 fs.

The subdirectory name is the snapshot time in attoseconds.

The simulation starts at 0 fs, the pump pulse is centered at the time 30 fs.

That means that if there is a probe pulse with delay of 110 fs, it is centered

at 140 fs.

 

The snapshot directories contain 6 text files:



econf.dat : list of all atomic configurations observed in the simulation snapshot, each line starts with the atomic Z, followed by the electron configuration

T.dat : the electronic configuration for each particle in the simulation, in the form of a list of indices. The n-th element of the list indicates the electronic configuration of the n-th particle in the simulation by specifying a line in econf.dat. For instance, if the 10th element is "0", it indicates the 10th simulated particle has the electronic configuration written on the first line of econf.dat

Z.dat : sequence of atomic numbers for all simulated atoms.

q.dat : charge of atoms in elementary charge units (redundant data).

r.dat : cartesian position in [m], each atom position on one line.

v.dat : velocity components in [m/s], each atom on one line.
DOI: 10.5281/zenodo.12804645
title: Experimental and simulation data from Stransky et al. "Ionization by XFEL radiation produces distinct structure in liquid water"

description: This deposition contains two separate gzipped tarballs:



preprocessed_diffraction_data.tar.gzpre-processed diffraction data, specifically I(q) traces for each X-ray pulse along with associated metadata

XMDYN_simulations.tar.gzsimulation trajectories produced by the XMDYN code that describe water ionization following an intense X-ray pulse


In more detail, the preprocessed_diffraction_data.tar.gz contains 36 HDF5 files, each corresponding to a single LCLS run. Each HDF5 contains the following data arrays:

ebeam                    Group
event_time               Dataset {8674/Inf}
evr                      Group
fiducials                Dataset {8674/Inf}
gas_detector             Group
phase_cav                Group
probe_energy             Dataset {8674/Inf}
probe_mag                Dataset {8674/Inf}
pump_energy              Dataset {8674/Inf}
pump_mag                 Dataset {8674/Inf}
radial_profile           Dataset {8674/Inf, 500}
radial_profile_qvalues   Dataset {500/8192}

The X contains trajectories for 7 different simulations, each in a separate directory. These top level directories are named according to simulation parameters:

sim<BOX_SIZE>A_<probe_delay[fs]/singl>_<fraction_of_nominal_fluence>

 

Box sizes are in [Å], probe delay is in [fs] or there is only single pulse, 1.00 is the nominal fluence.

 

Each of these directories contain subdirectories recording snapshots every 5 fs.

The subdirectory name is the snapshot time in attoseconds.

The simulation starts at 0 fs, the pump pulse is centered at the time 30 fs.

That means that if there is a probe pulse with delay of 110 fs, it is centered

at 140 fs.

 

The snapshot directories contain 6 text files:



econf.dat : list of all atomic configurations observed in the simulation snapshot, each line starts with the atomic Z, followed by the electron configuration

T.dat : the electronic configuration for each particle in the simulation, in the form of a list of indices. The n-th element of the list indicates the electronic configuration of the n-th particle in the simulation by specifying a line in econf.dat. For instance, if the 10th element is "0", it indicates the 10th simulated particle has the electronic configuration written on the first line of econf.dat

Z.dat : sequence of atomic numbers for all simulated atoms.

q.dat : charge of atoms in elementary charge units (redundant data).

r.dat : cartesian position in [m], each atom position on one line.

v.dat : velocity components in [m/s], each atom on one line.
DOI: 10.15468/gmex2a
title: VMNH SUP Paleontology Vertebrates and Paleobotony

description: The collections at the Virginia Museum of Natural History continue to grow, in keeping with the mission and purposes of the Museum: "to interpret Virginia's natural heritage within a global context in ways that are relevant to all the citizens of the Commonwealth, . . . to preserve elements of natural history, to serve as a permanent repository for specimens, especially those of Virginia origin, and to make the natural history material and its data accessible to researchers and the public." The collections provide the basis for both in-house research and research that extends nationally and internationally. There are more than more than More than 5,000 items and 955 unprocessed lots in the Vertebrate Fossils collection.
DOI: 10.15468/iaaimu
title: Macrozoobenthos composition, abundance and biomass in the Arctic Ocean along a transect between Svalbard and the Makarov Basin 1991

description: Dataset of macrofauna sampled between Northern Svalbard and the Makarov Basin, as a basis for understanding aspects of the benthic ecology of the Arctic Ocean.
DOI: 10.15470/knqev7
title: Fishes in MZNA-VERT: interactions between signal crayfish and fish communities. PhD project, Iv?n Vedia

description: Crayfish is one of the most known invasive species in the rivers of the north of Spain. However, its interactions with other non-crustacean species is not well studied. This thesis analyses the habitat selection, the trophic ecology and the interactions of crayfish with fish species (Vedia I. 2016). To study these questions, fish surveys were perfomed in different rivers of northern Navarra (Spain). The records are presented in this dataset.
DOI: 10.1594/pangaea.77451
title: Relative abundance of dead benthic foraminifera of sediment core M5/2_93MC

description: Dead foraminifera.
DOI: 10.1594/pangaea.64381
title: Occurrence of mammalia relicts at site l´Abri du Pont d´Ambon
DOI: 10.6084/m9.figshare.21922536
title: Cohesin prevents cross-domain gene co-activation

description: The contrast between the disruption of genome topology upon cohesin loss and the lack of downstream gene expression changes instigates intense debates regarding the structure-function relationship between genome and gene regulation. Here, by analyzing transcriptome and chromatin accessibility at the single-cell level, we discover that, instead of dictating population-wide gene expression levels, cohesin supplies a general function to neutralize stochastic co-expression tendency of cis-linked genes in single cells. Notably, cohesin loss induces widespread gene co-activation and chromatin co-opening tens of million bases apart in cis. Spatial genome and protein imaging reveals that cohesin prevents gene co-bursting along the chromosome and blocks dynamic fusion of transcriptional hubs. Single molecule imaging shows that cohesin confines the exploration of diverse enhancer and core promoter binding transcriptional regulators. Together, these results support that cohesin arranges nuclear topology to control gene co-expression in single cells.
DOI: 10.6084/m9.figshare.21922536.v1
title: Cohesin prevents cross-domain gene co-activation

description: The contrast between the disruption of genome topology upon cohesin loss and the lack of downstream gene expression changes instigates intense debates regarding the structure-function relationship between genome and gene regulation. Here, by analyzing transcriptome and chromatin accessibility at the single-cell level, we discover that, instead of dictating population-wide gene expression levels, cohesin supplies a general function to neutralize stochastic co-expression tendency of cis-linked genes in single cells. Notably, cohesin loss induces widespread gene co-activation and chromatin co-opening tens of million bases apart in cis. Spatial genome and protein imaging reveals that cohesin prevents gene co-bursting along the chromosome and blocks dynamic fusion of transcriptional hubs. Single molecule imaging shows that cohesin confines the exploration of diverse enhancer and core promoter binding transcriptional regulators. Together, these results support that cohesin arranges nuclear topology to control gene co-expression in single cells.
DOI: 10.1594/pangaea.64614
title: Occurrence of mammalia relicts at site Pestera Hotilor
DOI: 10.1594/pangaea.63570
title: Occurrence of mammalia relicts at site Malerfels_I
DOI: 10.1594/pangaea.68607
title: Abundance of microzooplankton measured on water bottle samples during METEOR cruise M17/1
DOI: 10.15468/ja3p8k
title: Free-living marine Nematodes from San Antonio and Cormoranes sandy beaches (Rio Negro, Argentina), 2006.

description: The aim of this database is collecting all the registered data of free-living marine Nematodes species from San Antonio and Camarones sandy beaches during March 2006.
DOI: 10.1594/pangaea.64555
title: Occurrence of mammalia relicts at site Oblazowa 2
DOI: 10.15470/msoj1m
title: Fishes in MZNA-VERT: ecological assessment of the Aragon river in Sang?esa (Spain)

description: The Iberian fish fauna is affected by numerous human activities, and one of the most important is river pollution. Industry wastewater, such paper mills residues may affect the quality of rivers so the study of the fish populations is necessary to assess the possible ecologic impacts. This study analyses the fish populations of Aragon River in the city of Sang?esa (Navarra, Spain) to assess if its ecological quality is affected by its paper mill.
DOI: 10.1594/pangaea.64589
title: Occurrence of mammalia relicts at site Trou Jadot
DOI: 10.1594/pangaea.63894
title: Occurrence of mammalia relicts at site Roter Berg bei Saalfeld
DOI: 10.1594/pangaea.64672
title: Occurrence of mammalia relicts at site Schweizerbild
DOI: 10.1594/pangaea.64679
title: Occurrence of mammalia relicts at site Felslindlhöhle
DOI: 10.15468/dl.aathqc
title: Occurrence Download

description: A dataset containing 556 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "HasCoordinate is true",
 "TaxonKey is Andigena nigrirostris (Waterhouse, 1839)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 556 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006842-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.25341508
title: Jurassic fossil juvenile reveals protracted life history in early mammals

description: Dataset associated with Panciroli et al. (2024), Jurassic fossil juvenile reveals prolonged life history in early mammals. These data are related to the body mass scaling analysis, outlined in further detail in Panciroli et al. (2024: Supplementary). Data includes limb measurements
DOI: 10.6084/m9.figshare.25341508.v1
title: Jurassic fossil juvenile reveals protracted life history in early mammals

description: Dataset associated with Panciroli et al. (2024), Jurassic fossil juvenile reveals prolonged life history in early mammals. These data are related to the body mass scaling analysis, outlined in further detail in Panciroli et al. (2024: Supplementary). Data includes limb measurements
DOI: 10.1594/pangaea.240021
title: Planktic foraminifera abundance of Hole 22-212

description: Relative abundance: D = dominant, A = abundant, C = common, F = few, R = rare, T = trace, P = present (numerical values are abundance in percent)
DOI: 10.15468/mka0hi
title: CERMES Barbados Lionfish Derby Data

description: Since its first connfirmed sighting in November 2011, it is believed that the lionfish population has steadily increased.One of the methods utlised in Barbados to control the Alien invasive lionfish is that of an annual derby. On December 5th and 6th, 2015, teams of divers (both free divers and SCUBA divers) took to the local waters to hunt for and kill lionfish. Caught lionfish were landed at a scoring station to be counted and allow for the collection of basic biological data (such as lengths, weights, sex and maturity). In addition to biological data, teams (observers) also provide information on dive sites (locations) and associated geographic information (i.e. GPS coordinates) where available. This event was a Reef Environmental Education Foundation (REEF) sanctioned derby event (see http://www.reef.org/lionfish/events).
DOI: 10.1594/pangaea.63885
title: Occurrence of mammalia relicts at site Subalyuk
DOI: 10.1594/pangaea.64676
title: Occurrence of mammalia relicts at site Fuchsenloch
DOI: 10.15470/0qsajx
title: Fishes in MZNA-VERT: freshwater communities in the Larraun river (Spain). PhD project, Javier Oscoz & Master project, A. Cos.

description: Rivers suffer from a wide range of human impacts that need to be studied (Oscoz, 2003). The ecologic quality of the Larraun river was analysed between 1996 and 1998 to assess the impact caused by the building of a new road and industrial activities: water quality, habitat, macroinvertebrates and fish community. The river presented organic pollution near towns and high nitrite levels. Data about fish biometry, age and feeding are given in the study. Some years later, the river was sampled to analyse the evolution of the fish populations after the building of the road.
DOI: 10.15468/xadrki
title: Colección de Paleovertebrados del IANIGLA-CCT CONICET Mendoza: IANIGLA-PV

description: 332 registros que corresponden a la Colección de Paleovertebrados del IANIGLA-CCT CONICET Mendoza (IANIGLA-PV).
DOI: 10.1594/pangaea.63891
title: Occurrence of mammalia relicts at site Remetehegy
DOI: 10.1594/pangaea.64608
title: Occurrence of mammalia relicts at site Gura Cheii-Rasnov
DOI: 10.15468/dl.he2ha2
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Costa Rica",
 "TaxonKey is Leptinotarsa decemlineata (Say, 1824)"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035474-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.64585
title: Occurrence of mammalia relicts at site Gamssulzenhöhle
DOI: 10.15468/wveict
title: Zooplankton Bering Strait Tiglax 1991

description: Zooplankton of the Bering Strait. 1991
DOI: 10.6084/m9.figshare.22770731
title: # Supplementary Data for the Paper "Sexual size dimorphism in mammals is associated with changes in the size of gene families related to brain development"

description: # Supplementary Data for the Paper "Sexual size dimorphism in mammals is associated with changes in the size of gene families related to brain development"

**Author:** Benjamin Padilla-Morales 
**Affiliation:** University of Bath 
**Email:** benjamin.padilla.morales@bath.edu

---

## Overview

This repository contains supplementary tables for the article "Sexual size dimorphism is associated with gene family contractions in brain development in mammals" The study investigates gene family size expansions and contractions in relation to brain development and sexual size dimorphism in mammals, employing a comparative genomics approach. Subsequently, we perform a Gene Ontology (GO) enrichment analysis on the gene families experiencing expansion and contraction to uncover the functional significance of associated genes. Additionally, we conduct a gene expression analysis of genes linked to these families to determine their over expression in brain tissue, showing the potential influence of sexual selection on the mammalian brain.


---

## Contents

- **Supplementary Figures:** Supplementary figures with corresponding descriptions.
- **Supplementary data 1:** Output from gene family expansion/contraction analysis for sexual size dimorphism, along with their corresponding statistical significance per gene family.
- **Supplementary data 2:** Average gene expression levels of brain areas and other tissues for adults and fetuses.
- **Supplementary data 3:** Entrez Gene ID to GO category per gene with foldchange results and p-values 
- **Supplementary data 4:** List of species used in the analysis with phenotypical data, including sources.
- **Supplementary data 5:** List of sequences with respective species used for the orthology mapping analysis and links to ftp with download code.
- **Supplementary data 6:** Output from gene family expansion/contraction analysis including zero variance gene families for sexual size dimorphism. 
- **Supplementary data 7:** List of species with encephalization index used in this research, along with references.
- **Supplementary table 1:** List of terms, abbreviations, and descriptions of brain structures used for sex-biased gene expression in temporal brain analysis.

For any questions or inquiries, please contact Benjamin Padilla-Morales at the provided email address.

---
DOI: 10.6084/m9.figshare.22770731.v1
title: # Supplementary Data for the Paper "Sexual size dimorphism in mammals is associated with changes in the size of gene families related to brain development"

description: # Supplementary Data for the Paper "Sexual size dimorphism in mammals is associated with changes in the size of gene families related to brain development"

**Author:** Benjamin Padilla-Morales 
**Affiliation:** University of Bath 
**Email:** benjamin.padilla.morales@bath.edu

---

## Overview

This repository contains supplementary tables for the article "Sexual size dimorphism is associated with gene family contractions in brain development in mammals" The study investigates gene family size expansions and contractions in relation to brain development and sexual size dimorphism in mammals, employing a comparative genomics approach. Subsequently, we perform a Gene Ontology (GO) enrichment analysis on the gene families experiencing expansion and contraction to uncover the functional significance of associated genes. Additionally, we conduct a gene expression analysis of genes linked to these families to determine their over expression in brain tissue, showing the potential influence of sexual selection on the mammalian brain.


---

## Contents

- **Supplementary Figures:** Supplementary figures with corresponding descriptions.
- **Supplementary data 1:** Output from gene family expansion/contraction analysis for sexual size dimorphism, along with their corresponding statistical significance per gene family.
- **Supplementary data 2:** Average gene expression levels of brain areas and other tissues for adults and fetuses.
- **Supplementary data 3:** Entrez Gene ID to GO category per gene with foldchange results and p-values 
- **Supplementary data 4:** List of species used in the analysis with phenotypical data, including sources.
- **Supplementary data 5:** List of sequences with respective species used for the orthology mapping analysis and links to ftp with download code.
- **Supplementary data 6:** Output from gene family expansion/contraction analysis including zero variance gene families for sexual size dimorphism. 
- **Supplementary data 7:** List of species with encephalization index used in this research, along with references.
- **Supplementary table 1:** List of terms, abbreviations, and descriptions of brain structures used for sex-biased gene expression in temporal brain analysis.

For any questions or inquiries, please contact Benjamin Padilla-Morales at the provided email address.

---
DOI: 10.15468/8lwnal
title: CardObs : Observations naturalistes issues de l'outil CardObs-Données naturalistes (hors araignées) de Claire JACQUET

description: Observations tout groupes sauf araignées
DOI: 10.15468/dl.zljfqx
title: Occurrence Download

description: A dataset containing 27845878 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Actinopterygii"
 ]
}

 The dataset includes 27845878 records from 2295 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006828-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.