cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18797095
title: Distinct Long Non-coding RNA Regulatory Architectures Encode Lineage Stability and Epithelial Plasticity

description:  






Filename



Scientific content



Status





lncrna_lineage_hematopoietic_pc1.csv



1,410 probe sets driving PC1 (haematopoietic axis). Ranked by |PCA loading|. Loading range: +0.005563 to +0.005774. Shannon entropy: 10.4614 bits. All positive loadings are on the haematopoietic-enriched axis.



✓ Ready





lncrna_lineage_brain_pc2.csv



1,410 probe sets driving PC2 (brain/neural axis). Loading range: +0.007709 to +0.010418. Shannon entropy: 10.4589 bits. Mixed probe types: TC=1,041, PSR=289, JUC=7.



✓ Ready





lncrna_lineage_breast_pc3.csv



1,410 probe sets driving the PC3 positive pole (breast epithelial axis). Loading range: +0.009501 to +0.013979. Shannon entropy: 10.4570 bits. Widest |loading| range of all four lineages.



✓ Ready





lncrna_lineage_endometrium_pc3.csv



1,410 probe sets driving the PC3 negative pole (endometrial axis). Loading range: −0.010876 to −0.005712. Shannon entropy: 10.4503 bits. Negative loadings = endometrium occupies opposite PC3 pole to breast.



✓ Ready





summary_statistics.csv



Aggregate statistics for all 4 lineages: loading ranges, means, SD, Shannon entropy, and probe-type counts. Machine-readable summary used for Table 1 / Results paragraph.



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overlap_matrix.csv



4×4 pairwise intersection matrix. Confirms Brain∩Endometrium=33, all other pairwise=0, and all four=0. Direct evidence for lineage-specificity of regulatory programmes.



✓ Ready





brain_endometrium_shared_probes.csv



Complete listing of all 33 probe sets shared between Brain (PC2) and Endometrium (PC3), with PC2 loading, PC3 loading, and rank in each list.



✓ Ready





README.txt



Plain-text description of the entire dataset. Zenodo displays this as the record description. Contains column definitions, method notes, LncExpDB annotation status, source dataset accessions, and citation blocks.



✓ Ready





 



ℹ️  The ENST_transcript_id, RefSeq_accession, gene_symbol, and lncexpdb_validated columns in the four lineage CSV files are currently blank. This is correctly noted in the README.txt. You can update the Zenodo record with annotated versions after completing the LncExpDB lookup step — Zenodo supports versioned updates without losing the DOI.
DOI: 10.25549/maw-ouc113888374
title: Shamanic flight

description: The figure is in good condition. The figure is flat on the underbelly and has its hands outward with the plums flat. There are four small holes in the top of the head. There are two holes on the ears and the mouth has an opening. At the bottom of the figure there is a large opening. No presence of significant cracks or scratches. The figure is structurally safe. There are black markings on the eyes, center of the upper chest, and ankles of the feet. The shaman wears a large bell pendant necklace, ear discs, a loincloth and four holes in the top of his head.
DOI: 10.5281/zenodo.18797094
title: Distinct Long Non-coding RNA Regulatory Architectures Encode Lineage Stability and Epithelial Plasticity

description:  






Filename



Scientific content



Status





lncrna_lineage_hematopoietic_pc1.csv



1,410 probe sets driving PC1 (haematopoietic axis). Ranked by |PCA loading|. Loading range: +0.005563 to +0.005774. Shannon entropy: 10.4614 bits. All positive loadings are on the haematopoietic-enriched axis.



✓ Ready





lncrna_lineage_brain_pc2.csv



1,410 probe sets driving PC2 (brain/neural axis). Loading range: +0.007709 to +0.010418. Shannon entropy: 10.4589 bits. Mixed probe types: TC=1,041, PSR=289, JUC=7.



✓ Ready





lncrna_lineage_breast_pc3.csv



1,410 probe sets driving the PC3 positive pole (breast epithelial axis). Loading range: +0.009501 to +0.013979. Shannon entropy: 10.4570 bits. Widest |loading| range of all four lineages.



✓ Ready





lncrna_lineage_endometrium_pc3.csv



1,410 probe sets driving the PC3 negative pole (endometrial axis). Loading range: −0.010876 to −0.005712. Shannon entropy: 10.4503 bits. Negative loadings = endometrium occupies opposite PC3 pole to breast.



✓ Ready





summary_statistics.csv



Aggregate statistics for all 4 lineages: loading ranges, means, SD, Shannon entropy, and probe-type counts. Machine-readable summary used for Table 1 / Results paragraph.



✓ Ready





overlap_matrix.csv



4×4 pairwise intersection matrix. Confirms Brain∩Endometrium=33, all other pairwise=0, and all four=0. Direct evidence for lineage-specificity of regulatory programmes.



✓ Ready





brain_endometrium_shared_probes.csv



Complete listing of all 33 probe sets shared between Brain (PC2) and Endometrium (PC3), with PC2 loading, PC3 loading, and rank in each list.



✓ Ready





README.txt



Plain-text description of the entire dataset. Zenodo displays this as the record description. Contains column definitions, method notes, LncExpDB annotation status, source dataset accessions, and citation blocks.



✓ Ready





 



ℹ️  The ENST_transcript_id, RefSeq_accession, gene_symbol, and lncexpdb_validated columns in the four lineage CSV files are currently blank. This is correctly noted in the README.txt. You can update the Zenodo record with annotated versions after completing the LncExpDB lookup step — Zenodo supports versioned updates without losing the DOI.
DOI: 10.25549/maw-ouc113888319
title: Shamanic flight

description: The figure is in good condition. The figure is flat on the underbelly and has its hands outward with the plums flat. There are four small holes in the top of the head. There are two holes on the ears and the mouth has an opening. At the bottom of the figure there is a large opening. No presence of significant cracks or scratches. The figure is structurally safe. There are black markings on the eyes, center of the upper chest, and ankles of the feet. The shaman wears a large bell pendant necklace, ear discs, a loincloth and four holes in the top of his head.
DOI: 10.25549/maw-ouc113888373
title: Nopiloa articulated figure

description: The Nopiloa culture produced elaborate press mold figures. This figure appears to be a male elite. He wears a tasseled headdress, large disc earrings, a pendant necklace, bracelets, and a dual strapped body covering with an elaborate raptor design. The purpose of this articulated figure is not known. The figure is in poor condition. There is a significant amount of wear, but no significant cracks. There is lots of fading and small scratches on the surfaces of the figure. The ears have holes. The arms and legs are attached to the torso of the figure's body by pins. Overall, the figure is fragile and not structurally safe.
DOI: 10.25549/maw-ouc113888364
title: Large huastec zoomorphic pouring vessel

description: A zoomorphic vessel resembling a rodent-like creature with an elaborately painted body. The strap handle facilitates handling and the tail spout allows for control pouring. In Mesoamerica the number three refers to the three realms; the heavens or the sky, the earth or the living world, and the underworld or the land of the dead.
DOI: 10.25549/maw-ouc113888362
title: Huastec zoomorphic vessel : bat

description: A stylized bat has been superimposed on a double-bodied figural vessel. Lug handles, pierced ears, and a snout have been appliqued. The surface has been painted with geometric designs in chocolate-brown and red-brown slip on a cream ground.
DOI: 10.25549/maw-ouc113889229
title: Standing male figure holding a dog and a bowl

description: A standing Colima male holds a dog and an empty bowl. He wears a turban headdress, ear ornaments, and an elaborate pair of textile pants. The dog served as a pet, an alarm, a good source of protein and a guide to the underworld.
DOI: 10.15468/dl.4yynsm
title: Occurrence Download

description: A dataset containing 195 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "OccurrenceStatus is Present",
 "TaxonKey is Myxini"
 ]
}

 The dataset includes 195 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001345-260226173443078/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/maw-ouc113889231
title: Standing male figure wearing a turban headdress

description: Another way to modify a person's body alters the surface of their skin. Body painting, tattooing and scarification changes the body's skin temporarily or permanently. Mesoamerican skin when cut forms a swollen scar. This cutting is done with a design in mind. Juat after the skin is cut, a mineral was rubbed into the wound to enhance the scar. This male figure with shoulder scarification is a good example.
DOI: 10.25549/maw-ouc113889234
title: Seated figure holding a round object

description: A seated male figure holding a large ball suggests he is a ball player. The ball, made from latex and the juice of the morning glory vine, was very dense and heavy. A solid rubber ball could vary in size from four inches to twelve inches and in weight from a pound to seven and a half pounds.
DOI: 10.25549/maw-ouc113889310
title: Seated mother holding a child

description: Seated female presents her child.
DOI: 10.25549/maw-ouc113889309
title: Seated mother holding a child

description: Seated female presents her child.
DOI: 10.15151/esrf-es-2234936511
title: CHRONOS (continuation)

description: The CHRONOS BAG at ESRF is a specialized access mode designed for long-term in situ synchrotron experiments. Its mission is to capture slow processes in real time by enabling continuous X-ray imaging over extended periods. The principle relies on automated, scheduled scans that allow researchers to track dynamic changes in materials under controlled conditions with implications for numerous scientific and industrial fields. In geosciences, it enhances our understanding of fault mechanics, fluid-rock interactions, and carbon sequestration. In material science, it provides insights into creep, fatigue, and phase changes. By bridging timescales and automating data collection, CHRONOS advances synchrotron techniques and opens new possibilities for studying time-dependent natural and manufactured systems.
DOI: 10.15151/esrf-es-2290411021
title: Austrian Crystallographic Diffraction Consortium

description: The Austrian Crystallographic Diffraction Consortium (ACDC) BAG aims at supporting several macromolecular structural biology groups across Austria (in total
20 research groups at 9 institutions in 4 cities). We employ mainly the technique of X-ray crystallography to characterize macromolecular biological complexes,
but also solution scattering approaches are frequently used to characterize dynamic assemblies. Approval of this BAG will be essential for researchers in all
our groups to carry out their structural studies on various health-related and basic research-oriented topics, which are targeted at characterizing large molecular
assemblies or proteins currently under-represented in the PDB, including membrane proteins. Corresponding high-resolution diffraction data are only obtainable
through the use of synchrotron radiation sources. Thus regular synchrotron access is highly desirable to maintain a competitive advantage in our individual
research fields
DOI: 10.25549/maw-ouc113889250
title: Seated mother holding a child

description: Seated female presents her child.
DOI: 10.34808/wg26-tv29
title: Input Files for REUS Free Energy Calculations of Loop Folding, G-tract Binding, and Propeller Loop Shift in G-Quadruplexes

description: This data set contains complete input files required to perform replica exchange umbrella sampling (REUS) simulations of three processes in G-quadruplex systems: (i) folding of isolated loops containing one to four thymine residues into defined loop geometries, (ii) binding of an unconnected G-tract to a preassembled G-core, and (iii) positional shift of a two-guanine G-tract between the upper and lower binding sites within a three-tetrad G-core scaffold in propeller loop geometries.
In the loop-folding simulations, the reaction coordinate is defined as the mean pairwise distance between atoms involved in the formation of Hoogsteen hydrogen bonds between the 3’-end loop-connected G-tract and its two neighboring G-tracts in the G-core. In the unconnected G-tract binding simulations, the same type of reaction coordinate monitors formation of Hoogsteen hydrogen bonds between the binding G-tract and the G-core, with separate systems corresponding to distinct glycosidic bond angle conformations. In the propeller loop shift simulations, the reaction coordinate is defined as the difference between the mean pairwise distances of hydrogen bond–forming atoms of the two-guanine G-tract to guanine bases in the upper versus lower binding site.
For each REUS window, the data set provides: (i) an initial structure extracted from nonequilibrium simulations spanning the relevant reaction-coordinate range, (ii) a PLUMED input file defining the reaction coordinate and umbrella bias together with structural restraints used to preserve the integrity of the G-core and the position of channel K+ ion(s), (iii) reference structure file(s) where required for RMSD-based definitions, and (iv) a compiled GROMACS .tpr file containing the full system topology and molecular dynamics parameters. All systems are fully solvated and include the preassembled G-core scaffold, the relevant loop or G-tract component, and K+ and Cl– ions at physiological concentration (150 mM).
The data set therefore enables reconstruction of free energy profiles for loop folding, G-tract binding, and propeller loop positional shift using consistent REUS protocols across all systems.
DOI: 10.15151/esrf-es-2290392876
title: Development of novel small molecules to target cellular pathways

description: Small molecules represent powerful tools to dissect physiological and pathological states of signaling pathways, yet require characterization through X-ray crystallography. This proposal encompasses the investigation of new classes of small molecules that target difficult proteins and non-typical binding sites. This includes the development of supramolecular compounds or cyclic peptides to address “non-druggable" proteins. The main collaborative research fields are tackling Ras protein signaling with structure-guided ligand design, developing inhibitors of the Ras-binding protein PDEd, screening of a novel sp3-enriched fragment library or targeting genetic regulators. Cellular signaling will also be addressed through the structural analysis of deubiquitinating enzymes or regulators of the kinetochore. Finally, we plan to crystallize membrane proteins including GPCRs in order to understand their biological function, characterize their ligand specificity and develop novel regulators.
DOI: 10.15151/esrf-es-2359223465
title: Structural Biology at EMBL Grenoble, IBS-CIBB, IAB and ILL

description: This proposal clusters macromolecular crystallography (MX) and biological small angle X-ray scattering (bioSAXS) projects at the EMBL Grenoble, IBS-CIBB, IAB and ILL. It combines groups working on different topics with a major focus on cell signaling proteins, ubiquitination pathways, nucleic acid-protein complexes, sarcomere development, host-pathogen interactions and drug discovery. The BAG group has been quite productive this last year/reporting period, as summarized in the report, with many results still being further analysed and follow-up experiments planned. Most notably, the BAG has produced 7 PDB depositions, 1 SASDB deposition and 10 publications in peer reviewed journals. The proposers have long-standing experience in the use, as well as the development of beam lines for MX and bioSAXS, and have participated in successive successful BAG applications over the years, mostly at the ESRF. The BAG responsible is again Andrew McCarthy (EMBL Grenoble) for this application round.
DOI: 10.25549/maw-ouc113889327
title: Seated horned figure holding a child

description: A seated male shaman presents a child. There are three horns on the shaman's headdress. His shoulders bear the marks or modules of scarification. The act of cutting the wound can be done in a short time, but the healing process can take up to a year.
DOI: 10.15151/esrf-es-2359102582
title: Structural studies of insulin and lysozyme microcrystals

description: Structural studies of insulin and lysozyme microcrystals
DOI: 10.25549/maw-ouc113889255
title: Seated couple : male with hand on shoulder

description: A male sits with his right knee drawn to his body and he rests his right elbow on it. He touches his left shoulder with his right hand. He has traces of black pigment on his eyes, mouth, upper arms, clothing, and right leg.
DOI: 10.25549/maw-ouc113889251
title: Seated couple : male with hand on shoulder

description: A male sits with his right knee drawn to his body and he rests his right elbow on it. He touches his left shoulder with his right hand. He has traces of black pigment on his eyes, mouth, upper arms, clothing, and right leg.
DOI: 10.15151/esrf-es-2313087384
title: Real-time studies of the dynamic evolution of multi-length scale structures of recycled Al alloys in controlled solidification processes - J

description: This is a continuation of the research work of PID27735 (experiments done on 13-20 Sep.24 at ID11 and ID 19 of the ESRF). We have demonstrated that, by adding 0.5% V into the Al-Fe-Mn recycled alloys with carefully controlled cooling rates, significant phase refining effects and morphology change in the multiple element Fe-containing intermetallic phases have been achieved, resulting a superior combination of strength and ductility in the as-cast condition. Based on these new findings, in this proposal, we will investigate further and systematically the combined beneficial effects of further tailoring the composition, optimising the cooling conditions and implementing pulse magnetic field for controlling and changing the Fe-phases’ size and morphologies, starting right from the phase nucleation stage. To achieve this, we will use (1) 3D XRD plus tomography simultaneously at ID11 of the ESRF, (2) ultrafast tomography plus pulse magnetic field at the ID19 of the ESRF to track the phase n
DOI: 10.25549/maw-ouc113888900
title: Seated couple : female with hands on her cheek

description: The male sits with his right knee drawn to his body and he rests his right elbow on it. He is unusual, because his chin has a beard. The female sits with crossed legs, her hand to a cut on her cheek. Incised marks on her chest suggest a form of scarification. Both figures have traces of black pigment.
DOI: 10.25549/pcra-ouc11399bwfx
title: Maiak = [Lighthouse], vol. 13, no. 8 (1935)

description: Monthly
DOI: 10.5281/zenodo.18797554
title: Phase Shift & Temporal Variance Audit — Solar-Economic Alignment (1841–2013)

description: This dataset is part of the Bicameral Solar Engine project, a multi-scalar deterministic framework that maps the relationship between solar harmonic cycles and terrestrial systems including climate, economics, and biological populations. All datasets share a common methodology: raw signals are detrended using an 11-year centered moving average, normalized into Z-scores. This record contains the Phase Shift and Temporal Variance Audit (1841–2013), quantifying the transmission buffer between theoretical solar gear-turn boundaries and observed GDP pivot points across three historical eras.
DOI: 10.5281/zenodo.18797553
title: Phase Shift & Temporal Variance Audit — Solar-Economic Alignment (1841–2013)

description: This dataset is part of the Bicameral Solar Engine project, a multi-scalar deterministic framework that maps the relationship between solar harmonic cycles and terrestrial systems including climate, economics, and biological populations. All datasets share a common methodology: raw signals are detrended using an 11-year centered moving average, normalized into Z-scores. This record contains the Phase Shift and Temporal Variance Audit (1841–2013), quantifying the transmission buffer between theoretical solar gear-turn boundaries and observed GDP pivot points across three historical eras.
DOI: 10.15151/esrf-es-2354437486
title: Lattice Distortions in Protein Superstructures

description: Lattice Distortions in Protein Superstructures
DOI: 10.25549/pcra-ouc11399bwgj
title: Maiak = [Lighthouse], vol. 14, no. 9 (1936)

description: Monthly
DOI: 10.15468/dl.5u6vej
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "DistanceFromCentroidInMeters is greater than or equal to 2000",
 "Geometry POLYGON ((105.610544 14.999999, 179.999961 14.999999, 179.999961 65.08290100000001, 105.610544 65.08290100000001, 105.610544 14.999999))",
 "TaxonKey is Epinephelus posteli"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001346-260226173443078/datasets/export for details.
DOI: 10.15468/dl.d9y4cb
title: Occurrence Download

description: A dataset containing 3380 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Xiphorhynchus obsoletus",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2026",
 "Country is Colombia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3380 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001347-260226173443078/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-ouc11399bwg5
title: Maiak = [Lighthouse], vol. 14, no. 11-12 (1936)

description: Monthly
DOI: 10.25549/pcra-ouc11399cclj
title: Put' = Voie = [The way], no. 20 (February 1930)

description: Irregular frequency
DOI: 10.25549/pcra-ouc11399cclv
title: Put' = Voie = [The way], no. 29 (August 1931)

description: Irregular frequency
DOI: 10.25549/maw-ouc113889807
title: Small tripodal vessel with hollow rattle feet : incised procession of priests singing or chanting

description: This Teotihuacan cylinder is quite unique as a storytelling vessel, which relates a journey past mountains, waterfalls and streams. The journey is shown by means of footprints. The elite figures, known by their elaborate hats, process past natural wonders under the protection of an astronomical phenomenon.
DOI: 10.25549/maw-ouc113889801
title: Small tripodal vessel with hollow rattle feet : incised procession of priests singing or chanting

description: This Teotihuacan cylinder is quite unique as a storytelling vessel, which relates a journey past mountains, waterfalls and streams. The journey is shown by means of footprints. The elite figures, known by their elaborate hats, process past natural wonders under the protection of an astronomical phenomenon.
DOI: 10.15468/dl.h2nq7y
title: Occurrence Download

description: A dataset containing 169 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Centropus steerii"
 ]
}

 The dataset includes 169 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001349-260226173443078/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/maw-ouc113889800
title: Small tripodal vessel with hollow rattle feet : incised procession of priests singing or chanting

description: This Teotihuacan cylinder is quite unique as a storytelling vessel, which relates a journey past mountains, waterfalls and streams. The journey is shown by means of footprints. The elite figures, known by their elaborate hats, process past natural wonders under the protection of an astronomical phenomenon.