cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28632596.v2
title: Supplementary Material for: A Randomized Controlled Crossover Trial to Determine the Effects of Three Nostril Regulated Breathing Practices on Attention and Mood

description: Background: Previous studies on nostril regulated breathing have contrasting findings attributed to lack of controls or not taking into account baseline nostril patency. This randomized crossover study on the effects of three nostril regulated yoga breathing practices and two controls on mood states and attention attempted to address these issues.
Materials and methods: Forty-five participants between 20 and 45 years (group mean age ± SD; 24.3±3.8 years; M;F 23:22) were assessed in five sessions in random order on five separate days. Nostril patency recorded pre-interventions in 225 sessions showed right nostril dominant at rest (RNDR) in 136 and left nostril dominant at rest (LNDR) in 89 sessions. The sessions were: (i) SAV or right uninostril breathing, (ii) CAV or left unnostril breathing, (iii) (AV or alternate nostril yoga breathing, (iv) breath awareness (BAW), and (v) quiet seated rest (QS). The practices were for 15 min each. Nostril patency was recorded pre, Brief mood introspection scale (BMIS), Global Vigor and Affect Scale (GVA) and Six letter cancellation test (SLCT) were recorded pre and post each session. Data analysis used general linear mixed model analysis, with fixed effects of states (pre and post), sessions and baseline nostril dominance (right or left).
Results: A significant interaction of sessions, states and nostril dominance at baseline was observed for total global affect (GA) (F9,396.194=2.871, p=0.003) which increased after SAV, CAV, AV and QS in participants right nostril dominant at rest (NDR) (padj&lt;0.05 in all cases). A significant main effect of states was observed followed by significant post-hoc pair wise comparison in right NDR for (i) pleasant mood after SAV, CAV, AV and QS, (ii) positive mood after SAV and AV, and (iii) global vigor after SAV, CAV, AV and QS, and (iv) a decrease in negative mood after CAV and AV. While the volunteers who had left NDR showed a significant increase in (i) PU after CAV, AV, and QR, (ii) PT after CAV, and (iii) GV after CAV and QS.
Conclusion: Nostril dominance pre intervention appears to influence the effects of nostril regulated yoga breathing practices.
DOI: 10.5281/zenodo.14054840
title: CALIPERS: Cell cycle-aware live imaging for phenotyping experiments and regeneration studies

description: Abstract:

We introduce CALIPERS, a Fluorescence Ubiquitin Cell Cycle Indicator enabling cell cycle-aware phenotyping based on multiplexed live-cell imaging. We validate CALIPERS in three- and four-color reporter lines (HaCaT) and human induced pluripotent stem cells (WTC-11), co-expressing genetically encoded structural and functional fluorescent sensors. To exemplify the broad applications of CALIPERS, we show cell cycle-aware phenotyping in live-cell imaging applications ranging from proliferation and migration to cardiac-specific maturation and drug testing.

Code submission: https://github.com/alessandro-bertero/FUCCIplex.git

Dataset description:



This dataset includes all data and the additional files to recreate the sc-RNAseq analysis in our manuscript. The Rmd files include the Seurat QC pipeline to preprocess the counts data from cellranger (QC_Seurat_gitgub_polished.RmD) and the monocle pipeline to re-create the clusters and pseudotime analysis (monocle_github_polished.Rmd).

Data obtained from Cellranger 7.2 pipeline are also available here including all the 3 files, usually placed in the path "outs/count/filtered_feature_bc_matrix" by cellrancer. This includes: barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz (alternatively the h5 file filtered_feature_bc_matrix.h5 can be loaded directly in Seurat v5).

We also added few RData files to recreate our graphs and follow our pipeline smoothly. 240111_seurat_before_clean.RData, 240111_seurat_clean.RData and 240111_seurat_processed.RData are the files created by the codes in QC_Seurat_gitgub_polished.RmD pipeline. Then, 240118_monocle_cds_clustered_proteincoding_PSEUDOTIME_clean_gene_info.RData is the file set created by the monocle_github_polished.Rmd pipeline.


We also suggest to use this pipeline within a docker container by pulling our docker image with R studio:

docker pull hedgelab/rstudio-hedgelab:latest
DOI: 10.5281/zenodo.14054841
title: CALIPERS: Cell cycle-aware live imaging for phenotyping experiments and regeneration studies

description: Abstract:

We introduce CALIPERS, a Fluorescence Ubiquitin Cell Cycle Indicator enabling cell cycle-aware phenotyping based on multiplexed live-cell imaging. We validate CALIPERS in three- and four-color reporter lines (HaCaT) and human induced pluripotent stem cells (WTC-11), co-expressing genetically encoded structural and functional fluorescent sensors. To exemplify the broad applications of CALIPERS, we show cell cycle-aware phenotyping in live-cell imaging applications ranging from proliferation and migration to cardiac-specific maturation and drug testing.

Code submission: https://github.com/alessandro-bertero/FUCCIplex.git

Dataset description:



This dataset includes all data and the additional files to recreate the sc-RNAseq analysis in our manuscript. The Rmd files include the Seurat QC pipeline to preprocess the counts data from cellranger (QC_Seurat_gitgub_polished.RmD) and the monocle pipeline to re-create the clusters and pseudotime analysis (monocle_github_polished.Rmd).

Data obtained from Cellranger 7.2 pipeline are also available here including all the 3 files, usually placed in the path "outs/count/filtered_feature_bc_matrix" by cellrancer. This includes: barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz (alternatively the h5 file filtered_feature_bc_matrix.h5 can be loaded directly in Seurat v5).

We also added few RData files to recreate our graphs and follow our pipeline smoothly. 240111_seurat_before_clean.RData, 240111_seurat_clean.RData and 240111_seurat_processed.RData are the files created by the codes in QC_Seurat_gitgub_polished.RmD pipeline. Then, 240118_monocle_cds_clustered_proteincoding_PSEUDOTIME_clean_gene_info.RData is the file set created by the monocle_github_polished.Rmd pipeline.


We also suggest to use this pipeline within a docker container by pulling our docker image with R studio:

docker pull hedgelab/rstudio-hedgelab:latest
DOI: 10.15468/dl.stf6qr
title: Occurrence Download

description: A dataset containing 94 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation)",
 "Country is China",
 "GadmGid is one of (CHN.16.5.11_1, CHN.16.5.10_1, CHN.16.5.8_1, CHN.16.5.7_1, CHN.16.6.6_1, CHN.16.6.1_1, CHN.16.10.9_1, CHN.16.10.4_1, CHN.16.10.2_1, CHN.16.10.3_1)",
 "OccurrenceStatus is Present",
 "TaxonKey is Ciconia nigra (Linnaeus, 1758)",
 "Year 2004-2025"
 ]
}

 The dataset includes 94 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020125-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13895461
title: The Solanaceae msa information and GERP score of SNP sites
DOI: 10.5281/zenodo.13895462
title: The Solanaceae msa information and GERP score of SNP sites
DOI: 10.15468/dl.u9kg3h
title: Occurrence Download

description: A dataset containing 36195 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Malva alcea L."
 ]
}

 The dataset includes 36195 records from 492 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020124-250310093411724/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.28638476
title: data for manuscript Vaccines (luciferase).xlsx

description: In vitro luciferase activity measurements
DOI: 10.15468/dl.8bu26h
title: Occurrence Download

description: A dataset containing 569 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation)",
 "Country is China",
 "GadmGid is one of (CHN.16.5.11_1, CHN.16.5.10_1, CHN.16.5.8_1, CHN.16.5.7_1, CHN.16.6.6_1, CHN.16.6.1_1, CHN.16.10.9_1, CHN.16.10.4_1, CHN.16.10.2_1, CHN.16.10.3_1)",
 "OccurrenceStatus is Present",
 "TaxonKey is Ciconia boyciana Swinhoe, 1873",
 "Year 2004-2025"
 ]
}

 The dataset includes 569 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020126-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xs6p7w
title: Occurrence Download

description: A dataset containing 127209 records in GBIF matching the query:
SELECT speciesKey, kingdom, phylum, class, 'order', family, genus, species, decimalLongitude, decimalLatitude, 'year' FROM occurrence WHERE speciesKey = 1651430

 The dataset's 127209 records were derived from 195 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020122-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yz8rgn
title: Occurrence Download

description: A dataset containing 444 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Smilax lanceifolia Roxb.",
 "Year 1970-2000"
 ]
}

 The dataset includes 444 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020127-250310093411724/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.26419432
title: Exploration-Exploitation Trade-off in Psychiatric Disorders: A Systematic Review

description: This systematic review examines the exploration-exploitation trade-off in psychiatric disorders. The researchers conducted a comprehensive literature search, identifying 49 eligible studies that investigated how various mental health conditions affect the balance between exploiting known options and exploring uncertain alternatives in decision-making tasks.The review categorized psychiatric disorders into three groups based on their impact on exploration-exploitation dynamics:1. Addictive disorders showing imbalanced drives and dysfunctional balancing2. Emotional/cognitive disturbances with context-dependent effects3. Neurodevelopmental disorders displaying excessive yet ineffective explorationThe study utilized various experimental paradigms, including n-armed bandit tasks, foraging tasks, probabilistic reversal learning, and the Iowa Gambling Task. These tasks allowed researchers to assess different aspects of the exploration-exploitation trade-off, such as stay-leave behavior, exploration-exploitation patterns, and shifting/switching abilities.By synthesizing findings across multiple disorders and experimental paradigms, this review provides insights into how psychiatric conditions disrupt the delicate balance between exploration and exploitation in decision-making. The results could inform the development of targeted interventions to restore adaptive decision-making in individuals with mental health disorders.
DOI: 10.5281/zenodo.13826125
title: MyoD1 localization at the nuclear periphery is mediated by association of WFS1 with active enhancers - Image Dataset

description: The set of raw images used in this study published on Nature Communications:

https://www.nature.com/articles/s41467-025-57758-x

are available as 4 subsets below:

https://osf.io/w5n43/

https://osf.io/bfxdw/

https://osf.io/rkguq/

 

https://osf.io/q6b4j/

 

The reason of this Zenodo entry is to combine these subsets into a single DOI link.

The total size adds up to 200GB and it is not possible to host such a large dataset on Zenodo, and it is only possible as maximum of 50GB pieces on Open Science Framework.

 

Summary of the study:

Spatial organization of the mammalian genome influences gene expression and cell identity. While association of genes with the nuclear periphery is commonly linked to transcriptional repression, also active, expressed genes can localize at the nuclear periphery. The transcriptionally active MyoD1 gene, a master regulator of myogenesis, exhibits peripheral localization in proliferating myoblasts, yet the underlying mechanisms remain elusive. Using a newly generated reporter cell line, we demonstrate here that peripheral association of the MyoD1 locus is independent of mechanisms involved in heterochromatin anchoring. We identify a set of nuclear envelope transmembrane proteins, particularly WFS1, that actively tether MyoD1 to the nuclear periphery. WFS1 primarily associates with active distal enhancer elements upstream of MyoD1, and with a subset of enhancers enriched in active histone marks genome-wide, which are linked to expressed myogenic genes. Overall, our data identify a novel mechanism involved in tethering active genes to the nuclear periphery.

 

This research was funded in whole or in part by the Austrian Science Fund (FWF) [P29713-B28, P32512-B and P36503-B] to Roland Foisner and a doctorate program funded by the Austrian Science Fund (FWF) [W1261-B28].
DOI: 10.5281/zenodo.13826126
title: MyoD1 localization at the nuclear periphery is mediated by association of WFS1 with active enhancers - Image Dataset

description: The set of raw images used in this study published on Nature Communications:

https://www.nature.com/articles/s41467-025-57758-x

are available as 4 subsets below:

https://osf.io/w5n43/

https://osf.io/bfxdw/

https://osf.io/rkguq/

 

https://osf.io/q6b4j/

 

The reason of this Zenodo entry is to combine these subsets into a single DOI link.

The total size adds up to 200GB and it is not possible to host such a large dataset on Zenodo, and it is only possible as maximum of 50GB pieces on Open Science Framework.

 

Summary of the study:

Spatial organization of the mammalian genome influences gene expression and cell identity. While association of genes with the nuclear periphery is commonly linked to transcriptional repression, also active, expressed genes can localize at the nuclear periphery. The transcriptionally active MyoD1 gene, a master regulator of myogenesis, exhibits peripheral localization in proliferating myoblasts, yet the underlying mechanisms remain elusive. Using a newly generated reporter cell line, we demonstrate here that peripheral association of the MyoD1 locus is independent of mechanisms involved in heterochromatin anchoring. We identify a set of nuclear envelope transmembrane proteins, particularly WFS1, that actively tether MyoD1 to the nuclear periphery. WFS1 primarily associates with active distal enhancer elements upstream of MyoD1, and with a subset of enhancers enriched in active histone marks genome-wide, which are linked to expressed myogenic genes. Overall, our data identify a novel mechanism involved in tethering active genes to the nuclear periphery.

 

This research was funded in whole or in part by the Austrian Science Fund (FWF) [P29713-B28, P32512-B and P36503-B] to Roland Foisner and a doctorate program funded by the Austrian Science Fund (FWF) [W1261-B28].
DOI: 10.6084/m9.figshare.28638464
title: NLID

description: This data presents the means and standard deviations of the changes observed in each dimension of the NLID (New Learning and Instructional Design) framework before and after the intervention, as well as the change in delay time for practical implementation. The differences between pre-test and post-test scores were examined using paired sample T-tests to determine whether the observed changes were statistically significant. This analysis allows us to evaluate the effectiveness of the intervention across multiple dimensions and assess whether it contributed to reducing delays in implementation.
DOI: 10.15468/dl.nbcswn
title: Occurrence Download

description: A dataset containing 423 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation)",
 "Country is China",
 "GadmGid is one of (CHN.16.5.11_1, CHN.16.5.10_1, CHN.16.5.8_1, CHN.16.5.7_1, CHN.16.6.6_1, CHN.16.6.1_1, CHN.16.10.9_1, CHN.16.10.4_1, CHN.16.10.2_1, CHN.16.10.3_1)",
 "OccurrenceStatus is Present",
 "TaxonKey is Platalea leucorodia Linnaeus, 1758",
 "Year 2004-2025"
 ]
}

 The dataset includes 423 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020128-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/4fnzknj8sn
title: Experimental results obtained from a parabolic trough collector installed in Coatzacoalcos, Mexico

description: This database contains seven days of experimental testing of a prototype parabolic solar collector installed in Coatzacoalcos, Veracruz, Mexico. Each file contains the following variables: time, inlet temperature, outlet temperature, ambient temperature, global radiation, diffuse radiation, wind direction, wind speed, and volume flow rate. The experimental tests cover the months of August and September.
DOI: 10.17632/4fnzknj8sn.1
title: Experimental results obtained from a parabolic trough collector installed in Coatzacoalcos, Mexico

description: This database contains seven days of experimental testing of a prototype parabolic solar collector installed in Coatzacoalcos, Veracruz, Mexico. Each file contains the following variables: time, inlet temperature, outlet temperature, ambient temperature, global radiation, diffuse radiation, wind direction, wind speed, and volume flow rate. The experimental tests cover the months of August and September.
DOI: 10.15468/dl.f3rt56
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sida subspicata",
 "Country is Japan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005001-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/jtw-ln8-1hl
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/yfb-yt5-2g2
title: Catopsilia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/z0p-0xm-yvq
title: Telicota augias (Linnaeus, 1763)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ct1-t0m-w9e
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4r7-10h-0x8
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xdq-azz-bqf
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.17026/dans-xxq-4753
title: PAN-00132115 - fishing hook metal

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00132115&lt;/p&gt;
description: Modified: 2023-05-22T08:37:39+02:00
DOI: 10.3535/6ca-xkd-fda
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/g02-bfd-ve0
title: Parantica aspasia (Fabricius, 1787)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/fc6-ke8-54q
title: Graphium

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.17026/dans-xxq-47xr
title: Plangebied ‘t Zand 46 in De Meern, gemeente Utrecht; archeologisch vooronderzoek: een bureauonderzoek en verkennend booronderzoek

description: &lt;p&gt;Het bureau- en aanvullend booronderzoek heeft aangetoond dat in het plangebied, met name op het zuidelijke deel, ter hoogte van de bouwkavels 4 – 8, sprake is van (resten van) Romeinse cultuurlagen. Deze cultuurlagen bevinden zich relatief ondiep onder het huidige oppervlak. Door deze geringe diepteligging worden ze bij vrijwel elke met de beoogde herinrichting van het ge bied met woningen gepaard gaande bodemingreep bedreigd. Om de woningbouw op archeologie vriendelijke wijze te realiseren is het mogelijk om het gebied op te hogen waarmee bereikt wordt dat de benodigde bodemingrepen in boven de archeologische niveaus plaatsvinden. Randvoor waarden hierbij zijn dat er wordt zorggedragen voor een voldoende dikke ophoging waarmee risico’s op aantasting van de archeologische niveaus bij de bouw van de woningen, aanleg van kabels en leidingen en aanleg en onderhoud van tuinen voorkomen worden. Bij het aanbrengen van een ophoging dient zorggedragen te worden voor de aanleg van afdoende drainage om stagnerend regenwater op de archeologische lagen te voorkomen. Het strekt tot voorkeur om niet te bouwen op heipalen aangezien de heipalen verstorend werken en door de aanwezigheid van de heipalen de mogelijkheden voor eventueel toekomstig onderzoek bemoeilijkt worden. De ditke van de benodigde ophoging is afhankelijk van de uiteindelijke bouwplannen. Aangezien deze nog niet vast staan is het prematuur om hier uitspraken over doen. Uiteindelijk beslist de bevoegde overheid, in deze mevrouw Roorda, Rijksdienst voor het Cultu reel Erfgoed of en zo ja onder welke voorwaarden de plannen doorgang kunnen vinden. De hier gegeven adviezen vormen daartoe een basis. Het is daarom aan te raden de bevinden en advie zen aan de Rijksdienst voor het Cultureel Erfgoed voor te leggen. Indien u dat wenst, kunnen wij u in dit overleg assisteren.&lt;/p&gt;
DOI: 10.3535/58y-bq1-983
title: Kallima sylvia (Cramer, 1776)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/yqk-0nc-bal
title: Catopsilia scylla (Linnaeus, 1763)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/gcg-8r1-j2m
title: Hebomoia glaucippe (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.17026/dans-xxq-4ykz
title: PAN-00064260 - leaf-shaped spear-/lance head (Roman)

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00064260&lt;/p&gt;
description: Modified: 2020-08-24T19:33:59+02:00
DOI: 10.3535/1yk-7n0-xxy
title: Catopsilia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/bf6-ns0-d30
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kn1-k9j-vsz
title: Graphium

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/w0n-ehw-ydq
title: Vindula erota (Fabricius, 1793)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.17026/dans-xxq-4zfe
title: PAN-00068128 - button with solid convex head and flat base, loop-shaped shank, decorated

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00068128&lt;/p&gt;
description: Modified: 2020-06-18T11:17:48+02:00
DOI: 10.3535/78q-v2a-p5f
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.