cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/5hw-pjt-k3v
title: Trifolium spadiceum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/5hw-wqp-b67
title: Chenopodium suecicum Murr

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/5hw-z2k-tvp
title: Diphasiastrum Holub

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/5hx-ahc-r8v
title: Poa glauca Vahl

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/5hx-fmf-1y7
title: Equisetum palustre L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/5hx-qgw-n8k
title: Potentilla crantzii (Crantz) Beck ex Fritsch

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/5hx-skp-j1t
title: Atocion rupestre (L.) Oxelman

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/5hx-vd1-rgx
title: Trifolium resupinatum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/5hx-xjh-dt8
title: Potamogeton pusillus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/5hy-17l-4tw
title: Poa compressa L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/5hy-3aq-a4z
title: Diphasiastrum complanatum x ssp. complanatum × ssp. montellii

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/5hw-ldf-mg5
title: Lotus corniculatus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/5hy-0gp-hbm
title: Eriophorum gracile Roth

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/5hy-8lz-lm7
title: Fragaria vesca L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/5hy-9wz-ee0
title: Arabidopsis × suecica (Fr.) Norrl.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/5hy-d88-8v2
title: Carex digitata L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/5hy-fns-rby
title: Drosera intermedia Hayne

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/5hy-jg4-8kz
title: Carex tenuiflora Wahlenb.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/5hy-m3d-49k
title: Sparganium emersum Rehmann

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/5hy-mz1-ztp
title: Parnassia palustris L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.15468/dl.s744a9
title: Occurrence Download

description: A dataset containing 1817 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Naja melanoleuca Hallowell, 1857"
 ]
}

 The dataset includes 1817 records from 82 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000282-250117103327516/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zmhtg4
title: Occurrence Download

description: A dataset containing 1873 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mustela nigripes (Audubon & Bachman, 1851)"
 ]
}

 The dataset includes 1873 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000284-250117103327516/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/s5k7wk8w3p.1
title: LINF_280027000

description: DPCD-like protein; Leishmania infantum (strain JPCM5)
DOI: 10.17632/fvcrhgk67h.1
title: LINF_280025500

description: BCP1 family protein; Leishmania infantum (strain JPCM5)
DOI: 10.5281/zenodo.14143081
title: Model Comparison Benchmark Datasets, Results, and Peptide MD Trajectory

description: Contents of this database include:



aib9.out.zip: zipped file containing raw output of the Aib9 OpenMM MD simulation

aib9_openmm.zip: zipped folder containing all input files for the Aib9 OpenMM MD simulation, as well as the generated trajectory

data_input.zip: zipped folder containing input datasets for the GMM and Aib9 numerical experiments

data_output.zip: zipped folder containing output data and experimental results for three generative models (NS, CFM, DDPM) on the input datasets, included for posterity (file names do not synchronize with most recent repository naming conventions)


The files are automatically retrieved and unzipped via the data_accessor notebook in the GitHub repository.
DOI: 10.5281/zenodo.14143082
title: Model Comparison Benchmark Datasets, Results, and Peptide MD Trajectory

description: Contents of this database include:



aib9.out.zip: zipped file containing raw output of the Aib9 OpenMM MD simulation

aib9_openmm.zip: zipped folder containing all input files for the Aib9 OpenMM MD simulation, as well as the generated trajectory

data_input.zip: zipped folder containing input datasets for the GMM and Aib9 numerical experiments

data_output.zip: zipped folder containing output data and experimental results for three generative models (NS, CFM, DDPM) on the input datasets


Please note:

At this stage datasets are published here for completeness. A more user-friendly integrated Zenodo/GitHub pipeline will be released soon for easy benchmarking of generative models.
DOI: 10.5281/zenodo.14679134
title: Model Comparison Benchmark Datasets, Results, and Peptide MD Trajectory

description: Contents of this database include:



aib9.out.zip: zipped file containing raw output of the Aib9 OpenMM MD simulation

aib9_openmm.zip: zipped folder containing all input files for the Aib9 OpenMM MD simulation, as well as the generated trajectory

data_input.zip: zipped folder containing input datasets for the GMM and Aib9 numerical experiments

data_output.zip: zipped folder containing output data and experimental results for three generative models (NS, CFM, DDPM) on the input datasets, included for posterity (file names do not synchronize with most recent repository naming conventions)


The files are automatically retrieved and unzipped via the data_accessor notebook in the GitHub repository.
DOI: 10.15468/dl.m3wb6a
title: Occurrence Download

description: A dataset containing 44195 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Bacillariophyta"
 ]
}

 The dataset includes 44195 records from 313 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000285-250117103327516/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14172084
title: CRISPuRe-Seq: pooled RNP barcode screening reveals regulation of RNA polymerase III transcription by the Integrated Stress Response via mTOR

description: CombinedPaperData.zip contains the data required for generating figures, including original gel images for western blots.

SupplementaryData.xlsx contains all of the Supplemental Data directly referred to in the manuscript.

Plasmid maps.zip contains plasmid maps for constructs used in the manuscript in genbank format.

Scripts.zip contains the scripts used for screen processing with a text file explaining their usage.

Look_Up_Table.zip contains the look-up-table for decoding barcode and sgRNA pairings.
DOI: 10.17632/72dkxdrjmw.2
title: Receptor-Interacting Protein Kinase 2 (RIPK2) Profoundly Contributes to Post-Stroke Neuroinflammation and Behavioral Deficits with Microglia as Unique Perpetrators

description: Background: Receptor-interacting protein kinase 2 (RIPK2) is a serine/threonine kinase whose activity propagates inflammatory signaling through its association with pattern recognition receptors (PRRs) and subsequent TAK-1, NF-κB, and MAPK pathway activation. The hypoxic and low energy conditions elicited by an ischemic event in the brain lead to rapid cell death of neurons whose blood supply is interrupted. Dead and dying cells release a host of damage-associated molecular patterns (DAMPs) that activate PRRs and initiate an inflammatory immune response. We hypothesize that RIPK2 plays a damaging role in the progression of stroke injury by enhancing the neuroinflammatory response to stroke and that global genetic deletion or microglia-specific conditional deletion of Ripk2 will be protective following ischemic stroke. 
Methods: Adult (3-6 months) male mice were subjected to 45min of transient middle cerebral artery occlusion (tMCAO) followed by 24h, 48h, or 28 days of reperfusion. Aged male and female mice (18-24mo) were subjected to permanent middle cerebral artery occlusion and sacrificed 48h later. Infarct volumes were calculated using TTC staining (24-48h) or Cresyl violet staining (28d). Sensorimotor tests (weight grip, vertical grid, and open field) were performed at indicated timepoints. Blood-brain barrier (BBB) damage, tight junction proteins, matrix metalloproteinase-9 (MMP-9), and neuroinflammatory markers were assessed via Western blotting, ELISA, immunohistochemistry, and RT-qPCR. Differential gene expression profiles were generated through bulk RNA sequencing and nanoString®. 
Results: Global genetic deletion of Ripk2 resulted in decreased infarct sizes and reduced markers of neuroinflammation 24h after stroke compared to wild-type controls. Ripk2 global deletion also improved both acute and long-term behavioral outcomes with powerful effects on reducing infarct volume and mortality at 28d post-stroke. Conditional deletion of microglial Ripk2 (KO) partially recapitulated our results in global Ripk2 deficient mice, showing reductive effects on infarct volume and improved behavioral outcomes within 48h of injury. Finally, we identified a differential gene expression profile in microglia derived from global Ripk2 knockout mice, as well as a differential genetic profile in the ipsilateral cortex of μKO animals during acute stroke injury. 
Conclusion: These results reveal a hitherto unknown role for RIPK2 in the pathogenesis of ischemic stroke injury, with microglia playing a distinct role. This study identifies RIPK2 as a potent propagator of neuroinflammatory signaling, highlighting its potential as a therapeutic target for post-stroke intervention.
DOI: 10.17632/72dkxdrjmw.1
title: Receptor-Interacting Protein Kinase 2 (RIPK2) Profoundly Contributes to Post-Stroke Neuroinflammation and Behavioral Deficits with Microglia as Unique Perpetrators

description: Background: Receptor-interacting protein kinase 2 (RIPK2) is a serine/threonine kinase whose activity propagates inflammatory signaling through its association with pattern recognition receptors (PRRs) and subsequent TAK-1, NF-κB, and MAPK pathway activation. The hypoxic and low energy conditions elicited by an ischemic event in the brain lead to rapid cell death of neurons whose blood supply is interrupted. Dead and dying cells release a host of damage-associated molecular patterns (DAMPs) that activate PRRs and initiate an inflammatory immune response. We hypothesize that RIPK2 plays a damaging role in the progression of stroke injury by enhancing the neuroinflammatory response to stroke and that global genetic deletion or microglia-specific conditional deletion of Ripk2 will be protective following ischemic stroke. 
Methods: Adult (3-6 months) male mice were subjected to 45min of transient middle cerebral artery occlusion (tMCAO) followed by 24h, 48h, or 28 days of reperfusion. Aged male and female mice (18-24mo) were subjected to permanent middle cerebral artery occlusion and sacrificed 48h later. Infarct volumes were calculated using TTC staining (24-48h) or Cresyl violet staining (28d). Sensorimotor tests (weight grip, vertical grid, and open field) were performed at indicated timepoints. Blood-brain barrier (BBB) damage, tight junction proteins, matrix metalloproteinase-9 (MMP-9), and neuroinflammatory markers were assessed via Western blotting, ELISA, immunohistochemistry, and RT-qPCR. Differential gene expression profiles were generated through bulk RNA sequencing and nanoString®. 
Results: Global genetic deletion of Ripk2 resulted in decreased infarct sizes and reduced markers of neuroinflammation 24h after stroke compared to wild-type controls. Ripk2 global deletion also improved both acute and long-term behavioral outcomes with powerful effects on reducing infarct volume and mortality at 28d post-stroke. Conditional deletion of microglial Ripk2 (KO) partially recapitulated our results in global Ripk2 deficient mice, showing reductive effects on infarct volume and improved behavioral outcomes within 48h of injury. Finally, we identified a differential gene expression profile in microglia derived from global Ripk2 knockout mice, as well as a differential genetic profile in the ipsilateral cortex of μKO animals during acute stroke injury. 
Conclusion: These results reveal a hitherto unknown role for RIPK2 in the pathogenesis of ischemic stroke injury, with microglia playing a distinct role. This study identifies RIPK2 as a potent propagator of neuroinflammatory signaling, highlighting its potential as a therapeutic target for post-stroke intervention.
DOI: 10.17632/72dkxdrjmw.3
title: Receptor-Interacting Protein Kinase 2 (RIPK2) Profoundly Contributes to Post-Stroke Neuroinflammation and Behavioral Deficits with Microglia as Unique Perpetrators

description: Background: Receptor-interacting protein kinase 2 (RIPK2) is a serine/threonine kinase whose activity propagates inflammatory signaling through its association with pattern recognition receptors (PRRs) and subsequent TAK-1, NF-κB, and MAPK pathway activation. The hypoxic and low energy conditions elicited by an ischemic event in the brain lead to rapid cell death of neurons whose blood supply is interrupted. Dead and dying cells release a host of damage-associated molecular patterns (DAMPs) that activate PRRs and initiate an inflammatory immune response. We hypothesize that RIPK2 plays a damaging role in the progression of stroke injury by enhancing the neuroinflammatory response to stroke and that global genetic deletion or microglia-specific conditional deletion of Ripk2 will be protective following ischemic stroke. 
Methods: Adult (3-6 months) male mice were subjected to 45min of transient middle cerebral artery occlusion (tMCAO) followed by 24h, 48h, or 28 days of reperfusion. Aged male and female mice (18-24mo) were subjected to permanent middle cerebral artery occlusion and sacrificed 48h later. Infarct volumes were calculated using TTC staining (24-48h) or Cresyl violet staining (28d). Sensorimotor tests (weight grip, vertical grid, and open field) were performed at indicated timepoints. Blood-brain barrier (BBB) damage, tight junction proteins, matrix metalloproteinase-9 (MMP-9), and neuroinflammatory markers were assessed via Western blotting, ELISA, immunohistochemistry, and RT-qPCR. Differential gene expression profiles were generated through bulk RNA sequencing and nanoString®. 
Results: Global genetic deletion of Ripk2 resulted in decreased infarct sizes and reduced markers of neuroinflammation 24h after stroke compared to wild-type controls. Ripk2 global deletion also improved both acute and long-term behavioral outcomes with powerful effects on reducing infarct volume and mortality at 28d post-stroke. Conditional deletion of microglial Ripk2 (KO) partially recapitulated our results in global Ripk2 deficient mice, showing reductive effects on infarct volume and improved behavioral outcomes within 48h of injury. Finally, we identified a differential gene expression profile in microglia derived from global Ripk2 knockout mice, as well as a differential genetic profile in the ipsilateral cortex of μKO animals during acute stroke injury. 
Conclusion: These results reveal a hitherto unknown role for RIPK2 in the pathogenesis of ischemic stroke injury, with microglia playing a distinct role. This study identifies RIPK2 as a potent propagator of neuroinflammatory signaling, highlighting its potential as a therapeutic target for post-stroke intervention.
DOI: 10.17632/pg56v4mdb8.1
title: LINF_280028000

description: Dynein light chain; Leishmania infantum (strain JPCM5)
DOI: 10.17632/6v8mywch3d.1
title: LINF_280027900

description: cullin 2; Leishmania infantum (strain JPCM5)
DOI: 10.17632/z33c6m25h3
title: LDHU3_19.1230

description: tRNA pseudouridine synthase A-like protein | mt-SAF11; Leishmania donovani (HU3 strain)
DOI: 10.17632/z33c6m25h3.1
title: LDHU3_19.1230

description: tRNA pseudouridine synthase A-like protein | mt-SAF11; Leishmania donovani (HU3 strain)
DOI: 10.17632/gytwpf42jt.1
title: LINF_280027300

description: Threonylcarbamoyl-AMP synthase; Leishmania infantum (strain JPCM5)
DOI: 10.17632/pyz7j78bg6.1
title: Data for: Japan's Dual Labor Market and its Macroeconomic Characteristics

description: The Excel file "working_hours_monthly_data.xlsx" examines the compositional effects of full- and part-time employment on Japanese weekly working hours in both short and long terms. The Excel file "transition_probabilities.xlsx" contains transition probabilities between any two states of the following working conditions for all samples and subsamples grouped by gender and age: regular employment, non-regular employment, self-employed and others, unemployment, and not being in the labor force. These transition probabilities are calculated using monthly data from the Japanese Labour Force Survey (https://www.stat.go.jp/english/data/roudou/index.html) from February 2013 to December 2022 and adjusted for margin-error bias and seasonality. The CSV file "transition_probabilities_aggregate.csv" contains the transition probabilities for all workers, and the m-file "decompose_variance_aggregate.m" decomposes the changes in the non-regular worker ratio and unemployment rate into the contribution of each labor flow using data in this CSV file.
DOI: 10.17632/pyz7j78bg6.4
title: Data for: Japan's Dual Labor Market and its Macroeconomic Characteristics

description: The Excel file "working_hours_2002Q1_2022Q4.xlsx" examines the compositional effects of standard and non-standard employment on the average hours per worker over the business cycles. The Excel file "transition_probabilities.xlsx" contains transition probabilities between any two states of the following working conditions for the aggregate sample and sub-samples grouped by gender and age: standard employment, non-standard employment, self-employed and others, unemployment, and not being in the labor force. These transition probabilities are calculated using monthly data from the Japanese Labour Force Survey (https://www.stat.go.jp/english/data/roudou/index.html) from February 2013 to December 2022 and adjusted for margin-error bias and seasonality. The CSV file "transition_probabilities_aggregate.csv" contains the transition probabilities for the aggregate, and the m-file "decompose_variance_aggregate.m" uses this CSV file to decompose the changes in each labor market indicator into the contribution of each labor flow.
DOI: 10.17632/frv3g4z8n4.1
title: Experimental data of lignin recovery from coconut husk using response surface methodology (RSM) through thermal pretreatment process

description: This investigation examines the impact of low nitric acid concentration, temperature, and residue time on the recovery of lignin from coconut husk through a thermal pretreatment process under optimal conditions. Additionally, the RSM response surface methodology is employed to determine the optimal conditions for lignin recovery. The results of the statistical analysis of independent variables, including temperature, time, and nitric acid concentration, indicate that these parameters had a substantial effect on the recovery of lignin. The ANOVA analysis indicates that all independent parameters and the model were statistically significant at the 95% confidence level. The current study's results demonstrated that the highest lignin recovery yield was 85.31%. This was achieved by processing coconut under optimal conditions, which included a low nitric acid concentration of 0.010 M and a temperature of 200 °C for 30 minutes. Furthermore, the thermal pretreatment procedure resulted in the complete conversion of the crystalline cellulose present in the coconut husk to an amorphous form, as demonstrated by the scanning electron microscope (SEM) analysis. Meanwhile, the crystallinity index of solid residue following thermal pretreatment demonstrated a substantial increase of 76.65% in comparison to that of native coconut husk (64.12%). Nevertheless, the lignin that is recovered is utilized as a precursor for the production of high-value products. Consequently, it is crucial to implement a thermal pretreatment process in order to enhance the efficiency of the chemical conversion process.
DOI: 10.17632/83vxxdxxrt.1
title: Canadian Cultural Institutions and Climate Action

description: The data was collected in 2022 through a survey sent out to over 700 Canadian museums to assess the state of sustainability policies and practices in Canadian cultural institutions. The survey created a larger picture of what actions the Canadian museum sector is taking with regards to climate action and environmental sustainability. The results from the survey were used to develop an original research study as part of my master's thesis requirements.
DOI: 10.17632/n6w2b6j2vg.1
title: Code for next generation sequencing data analysis of the Gene Expression Omnibus dataset GSE210779

description: This only contains the original code used to analyze the NGS data for the dataset. The associated manuscript will be published in Cell Reports.
DOI: 10.17632/k7zf8893x2.1
title: Safety and immunogenicity of SARS-CoV-2 self-amplifying RNA vaccine expressing anchored RBD: a randomised, observer-blind, phase 1 study, Akahata et al.

description: VLPCOV-01 is a lipid nanoparticle-encapsulated self-amplifying RNA (saRNA) vaccine that expresses a membrane-anchored receptor-binding domain (RBD) derived from the SARS-CoV-2 spike protein. A phase 1 study of VLPCOV-01 is conducted (jRCT2051210164). Participants who had completed two doses of the BNT162b2 mRNA vaccine previously are randomised to receive one intramuscular vaccination of 0·3, 1·0, or 3·0 µg VLPCOV-01, 30 µg BNT162b2, or placebo. No serious adverse events have been reported. VLPCOV-01 induces robust IgG titres against RBD protein that are maintained up to 26 weeks in non-elderly participants, with geometric means ranging from 5037 (95% CI 1,272–19,940) at 0·3 µg to 12,873 (95% CI 937–17,686) at 3 µg, in comparison to 3,166 (95% CI 1,619–6,191) with 30 µg BNT162b2. Neutralising antibody titres against all variants of SARS-CoV-2 tested are induced. VLPCOV-01 is immunogenic following low dose administration. These findings support the potential for saRNA as a vaccine platform.