cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh1051920.10fu
title: SH1051920.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1051921.10fu
title: SH1051921.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15468/dl.yajfmq
title: Occurrence Download

description: A dataset containing 2016 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Neustanthus phaseoloides (Roxb.) Benth.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 2016 records from 144 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011078-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ekxej8
title: Occurrence Download

description: A dataset containing 831 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Echinochloa stagnina (Retz.) P.Beauv.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 831 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011077-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pe49qw
title: Occurrence Download

description: A dataset containing 514 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Prosthechea vitellina (Lindl.) W.E.Higgins"
 ]
}

 The dataset includes 514 records from 64 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013718-230828120925497/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ch8vgu
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((72 25,105 25,105 40,72 40,72 25))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ophiocordyceps sinensis (Berk.) G.H.Sung, J.M.Sung, Hywel-Jones & Spatafora",
 "Year 1980-2022"
 ]
}

 The dataset includes 22 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005191-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-3258
title: Primiritel' = [Reconciler], vol. 7, no. 5-6 (May-June 1935)

description: [description english/roman)] 12 issues per year; For a history of Reconciler, see https://cdm15799.contentdm.oclc.org/cdm/compoundobject/collection/p15799coll14/id/2561/rec/12
DOI: 10.15468/dl.mmmva7
title: Occurrence Download

description: A dataset containing 335 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Carex caudata (Kük.) Pereda & Laínz"
 ]
}

 The dataset includes 335 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014546-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-ouc11189959
title: Primiritel' = [Reconciler], vol. 10, no. 5-6 (May-June 1938)

description: [description english/roman)] 12 issues per year; For a history of Reconciler, see https://cdm15799.contentdm.oclc.org/cdm/compoundobject/collection/p15799coll14/id/2561/rec/12
DOI: 10.15468/dl.8s2ed6
title: Occurrence Download

description: A dataset containing 11306 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Puma concolor (Linnaeus, 1771))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 11306 records from 221 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007100-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vzjyvr
title: Occurrence Download

description: A dataset containing 2201690 species occurrences available in GBIF matching the query:
(Query is too complex. Can be viewed on the landing page)

 The dataset includes 2201690 records from 1233 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018561-230828120925497/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xqdr3j
title: Occurrence Download

description: A dataset listing the 957 species recorded in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Passiflora L."
 ]
}

 The dataset's 957 records were derived from 987 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000648-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xkadp2
title: Occurrence Download

description: A dataset containing 10402 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Acaena ×ovina A.Cunn."
 ]
}

 The dataset includes 10402 records from 72 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004240-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.99xsav
title: Occurrence Download

description: A dataset containing 7987 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Specimen)"
 ]
 }
 },
 "TaxonKey is Kobus kob (Erxleben, 1777)"
 ]
}

 The dataset includes 7987 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000797-250225214225278/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60893/figshare.apl.28417778
title: Supplementary Material

description: Details on the equivalent circuit model, the extracted fitting parameters, and additional measurements, including figures.
DOI: 10.60893/figshare.apl.28417778.v1
title: Supplementary Material

description: Details on the equivalent circuit model, the extracted fitting parameters, and additional measurements, including figures.
DOI: 10.6084/m9.figshare.28477148
title: Elevational constraints on flight efficiency shape global gradients in avian wing morphology

description: Data and code to reproduce the analyses and figures presented in the manuscript ''Elevational constraints on flight efficiency shape global gradients in avian wing morphology'' (Current Biology).<b>Dataset 1.xlsx</b> contains the full dataset and the metadata of all variables. The .csv versions of files for use in R scripts are provided in folder<b> R data</b>.The 100 randomly selected phylogenetic trees necessary for reproducing all model results are also provided as <b>100 random trees.rds</b>.The R scripts for reproducing PGLS model results are provided as <b>1. PGLS global models.R </b>(related to Figure 3) and <b>2. PGLS elevation band models.R</b> (related to Figure 4).Code for generating figures and supplementary tables can be found in file <b>3. Figures and tables.R</b>.<br><br>
DOI: 10.6084/m9.figshare.28497698
title: Six-hour hypoxia induced protein degradation in <i>M. gastrocnemius</i> of 24-day-old mice by activating FOXO1 and suppressing AKT-mTORC1.Supplementary Tables

description: Long-term hypoxia has been associated with skeletal muscle atrophy, including increased protein degradation over protein synthesis. This contrasts sharply with muscle hypertrophy and net protein synthesis occurring in developing skeletal muscle of young mice. Here, we aimed to understand the impact of acute, physiologically plausible environmental hypoxia on muscle proteostasis of the <i>M. gastrocnemius </i>of young mice. Fasted prepubertal, 24-day-old male B6JRccHsd(B6J)-<i>Nnt</i><sup><em>+</em></sup>/Wuhap mice with similar body weight and lean mass were exposed to normobaric hypoxia (12% O<sub>2</sub>) or normoxia (20.9% O<sub>2</sub>) for 6 hours. The transcriptome (n=12) and protein (n=6) responses of the <i>M. gastrocnemius</i> were analyzed. A hypoxic response of <i>M. gastrocnemius</i> was confirmed by increased expression of HIF1 (<i>Ankrd37</i> and <i>Ddit4</i>) and forkhead box-O (FOXO) 1 (<i>Depp1</i> and <i>Ddit4</i>) target genes. RNA-Seq analysis revealed that hypoxia activated FOXO signaling, which was confirmed by increased FOXO1 protein levels and decreased p-AKT/AKT ratio. Detailed mapping of the FOXO1 pathway suggests a strong FOXO1-mediated hypoxic effect on protein degradation and synthesis. A central role of <i>Atf4 </i>is suggested by the hypoxic-dependent positive correlations with FOXO1, FBXO32, <i>Depp1, Eif4ebp1</i>, and <i>Ddit4</i>. Further analyses showed increased FBXO32, which positively correlated with FOXO1, and decreased p-S6K/S6K and p-4E-BP1/4E-BP1 ratios. Our results showed for the first time that a 6-hour exposure to 12% O<sub>2</sub> normobaric hypoxia in 24-day-old mice activates FOXO1 signaling in <i>M. gastrocnemius</i>,<i> </i>resulting in decreased protein synthesis and increased protein degradation most likely via reduced energy availability, which may be relevant for infant air or high altitude traveling.
DOI: 10.5281/zenodo.14902129
title: Evaluation of weighted Voronoi decompositions of physicochemical ensembles

description: Foam Data Key:

 

The data are organized into two main trees with the same structure, 1000 balls and 100 balls. Within these folders lies six subfolders:

 

1. PBC Overlap 0.0r

2. NonPBC Overlap 0.0r

3. PBC Overlap 0.5r

4. NonPBC Overlap 0.5r

5. PBC Overlap 1.0r

6. NonPBC Overlap 1.0r

 

 

 

Within each subfolder lies the data for each setting across different CV and Density values. These range as follows:

 

CV Values (11)      = [0.05, 0.10, 0.20, 0.30, 0.40, 0.50, 0.60, 0.70, 0.80, 0.90, 1.00]

Density Values (10) = [0.05, 0.10, 0.15, 0.20, 0.25, 0.30, 0.35, 0.40, 0.45, 0.50]

 

Each combination has 20 different iterations bringing the total number of subfolders to 11 x 10 x 20 = 2200. (Note: in ensembles with no overlap, some combinations of low CV and high density are missing due to their difficulty to generate).

 

 

 

The subfolders are named with the settings used to create the ensembles they house. These naming settings are, in order, as follows:

 

1. Mean - The average ball size in the grouping of balls

2. CV - The coefficient of variation of the set of balls

3. Number of Balls - The number of balls in the ensemble (note that if the ensemble has periodic boundary conditions, the number of balls in the actual ball file will be 27x this number)

4. Density - How tightly packed the balls are. Density = Volume of balls / Volume of the box that contains them

5. Number - File number for repeated runs with the same settings

 

 

 

Example:

 

1.0_0.2_1000_0.5_3 = Mean: 1.0, CV: 0.2, # of Balls: 1000, Density: 0.5, Iteration: 3

 

 

 

Each subfolder has the following files in the following structure:

 

> aw

> aw_verts.txt - The vertices from the additively weighted Voronoi diagram. 

> aw_logs.csv - The complete logs of the additively weighted Voronoi diagram

> pow

> pow_verts.txt - The vertices from the power Voronoi diagram. 

> pow_logs.csv - The complete logs of the power Voronoi diagram

> balls.pdb - A pdb file with the location, radius, and grouping of the balls in the foam. This works as a viewable file in molecular visualization software like PyMOL. 

> balls.txt - A text file with the locations and radii of the balls for more precise calculation than the pdb.

> retaining_box.off - This is an object file that shows the box that the balls were constructed using. The volume os the box is used in the density calculation. Note: depending on if the ensemble has a periodic boundary, the balls in the central grouping may hang outside of the box, but in either case their centers will lie inside the box. 

> set_balls.pml - This file is a PyMOL script file that sets the radii of the balls in viewer.
DOI: 10.5281/zenodo.14902130
title: Evaluation of weighted Voronoi decompositions of physicochemical ensembles

description: Foam Data Key:

 

The data are organized into two main trees with the same structure, 1000 balls and 100 balls. Within these folders lies six subfolders:

 

1. PBC Overlap 0.0r

2. NonPBC Overlap 0.0r

3. PBC Overlap 0.5r

4. NonPBC Overlap 0.5r

5. PBC Overlap 1.0r

6. NonPBC Overlap 1.0r

 

 

 

Within each subfolder lies the data for each setting across different CV and Density values. These range as follows:

 

CV Values (11)      = [0.05, 0.10, 0.20, 0.30, 0.40, 0.50, 0.60, 0.70, 0.80, 0.90, 1.00]

Density Values (10) = [0.05, 0.10, 0.15, 0.20, 0.25, 0.30, 0.35, 0.40, 0.45, 0.50]

 

Each combination has 20 different iterations bringing the total number of subfolders to 11 x 10 x 20 = 2200. (Note: in ensembles with no overlap, some combinations of low CV and high density are missing due to their difficulty to generate).

 

 

 

The subfolders are named with the settings used to create the ensembles they house. These naming settings are, in order, as follows:

 

1. Mean - The average ball size in the grouping of balls

2. CV - The coefficient of variation of the set of balls

3. Number of Balls - The number of balls in the ensemble (note that if the ensemble has periodic boundary conditions, the number of balls in the actual ball file will be 27x this number)

4. Density - How tightly packed the balls are. Density = Volume of balls / Volume of the box that contains them

5. Number - File number for repeated runs with the same settings

 

 

 

Example:

 

1.0_0.2_1000_0.5_3 = Mean: 1.0, CV: 0.2, # of Balls: 1000, Density: 0.5, Iteration: 3

 

 

 

Each subfolder has the following files in the following structure:

 

> aw

> aw_verts.txt - The vertices from the additively weighted Voronoi diagram. 

> aw_logs.csv - The complete logs of the additively weighted Voronoi diagram

> pow

> pow_verts.txt - The vertices from the power Voronoi diagram. 

> pow_logs.csv - The complete logs of the power Voronoi diagram

> balls.pdb - A pdb file with the location, radius, and grouping of the balls in the foam. This works as a viewable file in molecular visualization software like PyMOL. 

> balls.txt - A text file with the locations and radii of the balls for more precise calculation than the pdb.

> retaining_box.off - This is an object file that shows the box that the balls were constructed using. The volume os the box is used in the density calculation. Note: depending on if the ensemble has a periodic boundary, the balls in the central grouping may hang outside of the box, but in either case their centers will lie inside the box. 

> set_balls.pml - This file is a PyMOL script file that sets the radii of the balls in viewer.
DOI: 10.15468/dl.7yvff6
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Panthera pardus saxicolor Pocock, 1927"
 ]
}

 The dataset includes 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000019-250226125047203/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60893/figshare.apl.28423976
title: Supplementary Materials

description: Supplementary Materials
DOI: 10.60893/figshare.apl.28423976.v1
title: Supplementary Materials

description: Supplementary Materials
DOI: 10.60893/figshare.apm.28319321
title: Supplementay Materials

description: Supplementary Material (PDF) and all the data behind the graphs (xlsx)
DOI: 10.60893/figshare.apm.28319321.v1
title: Supplementay Materials

description: Supplementary Material (PDF) and all the data behind the graphs (xlsx)
DOI: 10.5281/zenodo.14925729
title: Supplementary information, PhD thesis "Bottleneck legacies and expansion consequences: the Italian wolf genomic make-up and the potential effect of anthropogenic hybridization on its evolutionary pathway"

description: Supplementary information regarding the chapters of my PhD thesis not published yet.

I uploaded only large Excel Tables which would negatively impact thesis readability.

 

Supplemental information for CHAPTER 3

Supplementary Table 1 – Whole-genome dataset. Yellow = related individual removed from the dataset; orange =  non-admixed Italian wolf; red = admixed Italian wolf; blue = non-admixed European wolf; purple = non-admixed dog; green = outgroup.

Supplementary Table 3 – List of genes associated with behavioral traits in dogs and captive wolves, tested using the ‘Behavioral genes shuffling’ approach.

Supplementary Table 5 – Gene ontology network results using STRING on genes within introgressed and validated regions in admixed Italian wolves (i.e., gene PREX2), and all the Italian wolves (the other genes). Green = functional enrichment for the candidate gene.

 

Supplemental information for CHAPTER 4

Supplementary Table 1 – The three datasets used in this study. DATASET1 = whole-genome data; DATASET2 = 170k SNPs data; DATASET3 = DNA samples analyzed for specific sociability loci. Yellow = dog whole-genomes intersected with 170k SNPs.

Supplementary Table 2 – Gene ontology network results using STRING on behavioral genes containing highly differentiated SNPs with effective (MOD-DEL and HIGH) or potential (MOD-NA) deleteriousness in DATASET1.

Supplementary Table 3 – Gene ontology network results using STRING on behavioral genes containing SNPs with significant FST differences between HYB and WIT in DATASET1.

Supplementary Table 4 – Table of sociability-related markers. Internal primers designed on ‘forward’ sequence are colored in green, while internal primers designed on ‘reverse’ sequence are colored in blue. ‘REF/ALT’ are the reference and alternative alleles, ‘Tm’ is the melting temperature, ‘GC%’ is the percentage of guanine and cytosine on the primer sequence.
DOI: 10.5281/zenodo.14925730
title: Supplementary information, PhD thesis "Bottleneck legacies and expansion consequences: the Italian wolf genomic make-up and the potential effect of anthropogenic hybridization on its evolutionary pathway"

description: Supplementary information regarding the chapters of my PhD thesis not published yet.

I uploaded only large Excel Tables which would negatively impact thesis readability.

 

Supplemental information for CHAPTER 3

Supplementary Table 1 – Whole-genome dataset. Yellow = related individual removed from the dataset; orange =  non-admixed Italian wolf; red = admixed Italian wolf; blue = non-admixed European wolf; purple = non-admixed dog; green = outgroup.

Supplementary Table 3 – List of genes associated with behavioral traits in dogs and captive wolves, tested using the ‘Behavioral genes shuffling’ approach.

Supplementary Table 5 – Gene ontology network results using STRING on genes within introgressed and validated regions in admixed Italian wolves (i.e., gene PREX2), and all the Italian wolves (the other genes). Green = functional enrichment for the candidate gene.

 

Supplemental information for CHAPTER 4

Supplementary Table 1 – The three datasets used in this study. DATASET1 = whole-genome data; DATASET2 = 170k SNPs data; DATASET3 = DNA samples analyzed for specific sociability loci. Yellow = dog whole-genomes intersected with 170k SNPs.

Supplementary Table 2 – Gene ontology network results using STRING on behavioral genes containing highly differentiated SNPs with effective (MOD-DEL and HIGH) or potential (MOD-NA) deleteriousness in DATASET1.

Supplementary Table 3 – Gene ontology network results using STRING on behavioral genes containing SNPs with significant FST differences between HYB and WIT in DATASET1.

Supplementary Table 4 – Table of sociability-related markers. Internal primers designed on ‘forward’ sequence are colored in green, while internal primers designed on ‘reverse’ sequence are colored in blue. ‘REF/ALT’ are the reference and alternative alleles, ‘Tm’ is the melting temperature, ‘GC%’ is the percentage of guanine and cytosine on the primer sequence.
DOI: 10.15468/dl.bw2gn3
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Russowia sogdiana (Bunge) B.Fedtsch."
 ]
}

 The dataset includes 16 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000018-250226125047203/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.