cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/lts-m2v-vta
title: †Lepidocyclina Gümbel, 1870

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/b0e-cxe-h38
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/q8q-d9h-l4b
title: †Hippurites Lamarck, 1801

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5ng-djf-m1q
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pjd-lpd-j35
title: Orbulina universa d'Orbigny, 1839

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.b759tt
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ailanthus altissima",
 "Country is Moldova, Republic of",
 "HasCoordinate is true"
 ]
}

 The dataset includes 37 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022174-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/2d6-hwl-tdb
title: †Fusulinidae Möller, 1878

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/abt-eep-zc3
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/65j-rf9-14y
title: †Sagrina limbata (Terquem, 1882)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/f6e-tcs-kda
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9d1-v89-el0
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/y9e-yad-863
title: Orbulina universa d'Orbigny, 1839

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.ejvr78
title: Occurrence Download

description: A dataset containing 55 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ailanthus altissima",
 "Country is Montenegro",
 "HasCoordinate is true"
 ]
}

 The dataset includes 55 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022175-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/32r-m46-t02
title: Arcestes

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hf2-4v3-h0v
title: †Arnaudiella grossouvrei Douvillé, 1907

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/zm8-bxa-emh
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kr8-8jx-lz8
title: Sphincterochila Ancey, 1887

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lk5-fjg-eb2
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.wakhfy
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ailanthus altissima",
 "Country is Morocco",
 "HasCoordinate is true"
 ]
}

 The dataset includes 15 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022176-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/aym-3p7-393
title: †Escharina meandrina (Canu & Lecointre, 1928)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/gyc-5yg-lsk
title: †Strophalosia King, 1846

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/w1e-srw-5t5
title: Bolivina reticulata Hantken, 1875

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jax-ycr-ray
title: Echinoidea Schumacher, 1817

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/p4s-x3n-z4j
title: †Archaeocidaris McCoy, 1844

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1vw-wbb-6r2
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/f6c-ysc-lqy
title: Lingula Bruguière, 1791

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.5281/zenodo.16899781
title: Neulite Kernel and sample datasets for "Microscopic-Level Mouse Whole Cortex Simulation Composed of 9 Million Biophysical Neurons and 26 Billion Synapses on the Supercomputer Fugaku"
DOI: 10.60893/figshare.apm.28821839
title: Supplement

description: Supplement methods and figures
DOI: 10.5281/zenodo.15309724
title: Dual-specific autophosphorylation of kinase IKK2 enables phosphorylation of substrate I-kappaBalpha through a phosphoenzyme intermediate

description: This repository contains data and findings from the study titled "Dual-specific autophosphorylation of kinase IKK2 enables phosphorylation of substrate IkBa through a phosphoenzyme intermediate". It includes the following datasets:

Molecular Dynamics Simulation Data:

GROMACS input files (topology files, coordinate files, parameter files)Energy minimization and equilibration configuration filesProduction MD run parametersAnalysis data including RMSD, RMSF, energy, dynamic cross-correlation matrix (DCCM) resultsMD simulation of three phosphorylated form of IKK2 available withim simulation_apo_200ns folderMD simulation of ADP/ATP complex with three phosphorylated form of IKK2 available withim simulation_complex_10ns folderMM-PBSA of all phosphorylated form of IKK2 complexed with ADP/ATP available within mmpbsa folder

Scripts and Analysis Code:

Python scripts used for data analysis and plot visualizations available within script folder. 

 

Below is the abstract of the corresponding manuscript:

"Rapid and high-fidelity phosphorylation of serine residues at positions 32 and 36 of IkBa by IKK2, a prototypical Ser/Thr kinase, is critical for canonical NF-kB activation. Here, we report that IKK2 not only phosphorylates substrate serine residues and autophosphorylates its own activation loop, but also autophosphorylates at a tyrosine residue proximal to the active site  and is, therefore, a dual-specificity kinase. We observed that mutation of Y169, an autophosphorylatable tyrosine located at the DFG+1 (DLG in IKK1) position, to phenylalanine renders IKK2 incapable of catalyzing phosphorylation at S32 within its IkBa substrate. We also observed that mutation of the phylogenetically conserved ATP-contacting residue K44 in IKK2 to methionine converts IKK2 to an enzyme that no longer catalyzes specific phosphorylation of IkBa at S32 or S36, but rather directs phosphorylation of IkBa at other residues. Lastly, we report evidence of a phospho-relay from autophosphorylated IKK2 to IkBa in the presence of ADP. These observations suggest an unusual evolution of IKK2, in which autophosphorylation of tyrosine(s) in the activation loop, and the conserved ATP-contacting K44 residue provide its signal-responsive substrate specificity and ensure fidelity during NF-kB activation."
DOI: 10.5281/zenodo.15309725
title: Dual-specific autophosphorylation of kinase IKK2 enables phosphorylation of substrate I-kappaBalpha through a phosphoenzyme intermediate

description: This repository contains data and findings from the study titled "Dual-specific autophosphorylation of kinase IKK2 enables phosphorylation of substrate IkBa through a phosphoenzyme intermediate". It includes the following datasets:

Molecular Dynamics Simulation Data:

GROMACS input files (topology files, coordinate files, parameter files)Energy minimization and equilibration configuration filesProduction MD run parametersAnalysis data including RMSD, RMSF, energy, dynamic cross-correlation matrix (DCCM) resultsMD simulation of three phosphorylated form of IKK2 available withim simulation_apo_200ns folderMD simulation of ADP/ATP complex with three phosphorylated form of IKK2 available withim simulation_complex_10ns folderMM-PBSA of all phosphorylated form of IKK2 complexed with ADP/ATP available within mmpbsa folder

Scripts and Analysis Code:

Python scripts used for data analysis and plot visualizations available within script folder. 

 

Below is the abstract of the corresponding manuscript:

"Rapid and high-fidelity phosphorylation of serine residues at positions 32 and 36 of IkBa by IKK2, a prototypical Ser/Thr kinase, is critical for canonical NF-kB activation. Here, we report that IKK2 not only phosphorylates substrate serine residues and autophosphorylates its own activation loop, but also autophosphorylates at a tyrosine residue proximal to the active site  and is, therefore, a dual-specificity kinase. We observed that mutation of Y169, an autophosphorylatable tyrosine located at the DFG+1 (DLG in IKK1) position, to phenylalanine renders IKK2 incapable of catalyzing phosphorylation at S32 within its IkBa substrate. We also observed that mutation of the phylogenetically conserved ATP-contacting residue K44 in IKK2 to methionine converts IKK2 to an enzyme that no longer catalyzes specific phosphorylation of IkBa at S32 or S36, but rather directs phosphorylation of IkBa at other residues. Lastly, we report evidence of a phospho-relay from autophosphorylated IKK2 to IkBa in the presence of ADP. These observations suggest an unusual evolution of IKK2, in which autophosphorylation of tyrosine(s) in the activation loop, and the conserved ATP-contacting K44 residue provide its signal-responsive substrate specificity and ensure fidelity during NF-kB activation."
DOI: 10.15468/dl.aqxbnd
title: Occurrence Download

description: A dataset containing 1224 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 Salvia argentea L."
 ]
}

 The dataset includes 1224 records from 72 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011311-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h5rv84
title: Occurrence Download

description: A dataset containing 12094 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((13.8 51.2,13.95 51.2,13.95 51.4,13.8 51.4,13.8 51.2))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 12094 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011309-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qc8j9h
title: Occurrence Download

description: A dataset containing 1447 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Canadian National Collection (CNC) of Insects, Arachnids and Nematodes",
 "GadmGid is CAN.12_1"
 ]
}

 The dataset includes 1447 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082217-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc110604428
title: Persepolis Fortification Aramaic Text 519, PFAT 519

description: [Text Description:] Administrative text with seals ❧ [Text or Publication Number Note:] PFAT 519 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Aramaic ❧ [Physical Object Description:] Clay tablet with ink inscription. Seal impressions obverse, upper edge, reverse, bottom edge, flat edge. ❧ [Physical Object Note:] Damage on round edge.
DOI: 10.25549/inscriptifact-ouc110604115
title: Persepolis Fortification Aramaic Text 509, PFAT 509

description: [Text Description:] Administrative text with seals PFS 0078 ❧ [Text or Publication Number Note:] PFAT 509, Bowman 509 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Aramaic ❧ [Physical Object Description:] Clay tablet with ink inscription. Seal impression PFS 0078 obverse, reverse, flat edge.
DOI: 10.25549/inscriptifact-ouc110604420
title: Persepolis Fortification Aramaic Text 518, PFAT 518

description: [Text Description:] Administrative text with illegible seals ❧ [Text or Publication Number Note:] PFAT 518 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Aramaic ❧ [Physical Object Description:] Clay tablet with ink inscription. Seal impressions obverse, upper edge, reverse, bottom edge, flat edge? ❧ [Physical Object Note:] Damage on round edge.
DOI: 10.25549/inscriptifact-ouc110604104
title: Persepolis Fortification Aramaic Text 509, PFAT 509

description: [Text Description:] Administrative text with seals PFS 0078 ❧ [Text or Publication Number Note:] PFAT 509, Bowman 509 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Aramaic ❧ [Physical Object Description:] Clay tablet with ink inscription. Seal impression PFS 0078 obverse, reverse, flat edge.
DOI: 10.25549/inscriptifact-ouc110604413
title: Persepolis Fortification Aramaic Text 518, PFAT 518

description: [Text Description:] Administrative text with illegible seals ❧ [Text or Publication Number Note:] PFAT 518 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Aramaic ❧ [Physical Object Description:] Clay tablet with ink inscription. Seal impressions obverse, upper edge, reverse, bottom edge, flat edge? ❧ [Physical Object Note:] Damage on round edge.
DOI: 10.25549/inscriptifact-ouc110604102
title: Persepolis Fortification Aramaic Text 510, PFAT 510

description: [Text Description:] Administrative text with seals PFATS 0468 ❧ [Text or Publication Number Note:] PFAT 510, Bowman 510 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Aramaic ❧ [Physical Object Description:] Clay tablet with ink inscription. Seal impression PFATS 0468 obverse, reverse. ❧ [Physical Object Note:] Damage on round edge.
DOI: 10.25549/inscriptifact-ouc1sto1608318
title: InscriptiFact -- an image database of inscriptions and artifacts

description: The InscriptiFact Collection is designed to allow access via the Internet to high-resolution images of ancient inscriptions and artifacts, primarily from the Near Eastern and Mediterranean Worlds. The targeted inscriptions constitute some of the world’s earliest written records, which are mostly housed in a number of international museums and libraries, as well as field projects where inscriptions still remain in situ. Included, for example, are, selected Dead Sea Scrolls; cuneiform tablets from Mesopotamia, Persia, Canaan and Egypt; early Jewish papyri from Egypt; lapidary inscriptions, primarily from Jordan, Lebanon and Cyprus; inscriptions on a variety of hard media (e.g., ostraca, copper, semi-precious stones, jar handles) mostly written in early Canaanite, Phoenician, Hebrew, Aramaic, Ammonite and Edomite; and much more. These ancient texts are foundational documents that serve as a point of reference for Judaism, Christianity, Islam and the cultures out of which they emerged. The name "InscriptiFact" is intended to convey the concept of a scholarly archive based on "facts" about "inscriptions" and "artifacts." West Semitic Research Project (WSRP) under the auspices of the University of Southern California (USC) is broadly acknowledged as a leader in the application of photographic and digital technologies to capture and analyze data of ancient texts. The West Semitic Research image archive now contains approximately 1,500,000 images. Important! Search terms with more than one word or number need to be enclosed in quotation marks.Guide to Searching InscriptiFact
DOI: 10.25549/inscriptifact-ouc110600052
title: Persepolis Fortification Anepigraphic Tablet 0916.101, PFAnep 0916.101

description: [Text Description:] Administrative text with seals PFUTS 0118 ❧ [Text or Publication Number Note:] PFAnep 0916.101, PFUT 0916-101 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Non-Text ❧ [Physical Object Description:] Clay tablet with seal impression PFUTS 0118 on obverse, reverse, bottom edge, left edge.
DOI: 10.25549/inscriptifact-ouc110604085
title: Persepolis Fortification Aramaic Text 509, PFAT 509

description: [Text Description:] Administrative text with seals PFS 0078 ❧ [Text or Publication Number Note:] PFAT 509, Bowman 509 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Aramaic ❧ [Physical Object Description:] Clay tablet with ink inscription. Seal impression PFS 0078 obverse, reverse, flat edge.
DOI: 10.25549/inscriptifact-ouc110601520
title: Persepolis Fortification Aramaic Text 437, PFAT 437

description: [Text Description:] Administrative text with seals PFS 0075 ❧ [Text or Publication Number Note:] PFAT 437, Bowman 437 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Aramaic ❧ [Physical Object Description:] Clay tablet with ink inscription. Seal impression PFS 0075 on obverse, upper edge, reverse, bottom edge, flat edge.
DOI: 10.25549/inscriptifact-ouc110600039
title: Persepolis Fortification Anepigraphic Tablet 0893.201, PFAnep 0893.201

description: [Text Description:] Administrative text with seals ❧ [Text or Publication Number Note:] PFAnep 0893.201, PFUT 0893-201 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Non-Text ❧ [Physical Object Description:] Clay tablet with ink traces, seal impressions on obverse, reverse, upper edge? ❧ [Physical Object Note:] Cracks and damage on obverse reverse, upper right reverse almost broken off.
DOI: 10.25549/inscriptifact-ouc110601516
title: Persepolis Fortification Aramaic Text 436, PFAT 436

description: [Text Description:] Administrative text with seals PFATS 0414 ❧ [Text or Publication Number Note:] PFAT 436, Bowman 436 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Aramaic ❧ [Physical Object Description:] Clay tablet with ink inscription. Seal impression PFATS 0414 on obverse, upper edge, reverse, bottom edge. ❧ [Physical Object Note:] Damage on flat edge, round edge.
DOI: 10.25549/inscriptifact-ouc110600036
title: Persepolis Fortification Anepigraphic Tablet 0893.201, PFAnep 0893.201

description: [Text Description:] Administrative text with seals ❧ [Text or Publication Number Note:] PFAnep 0893.201, PFUT 0893-201 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Non-Text ❧ [Physical Object Description:] Clay tablet with ink traces, seal impressions on obverse, reverse, upper edge? ❧ [Physical Object Note:] Cracks and damage on obverse reverse, upper right reverse almost broken off.