cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18318396
title: Input data and cached results for, "MSA-based pLMs encode evolutionary distance but don't reliably exploit it"

description: Input Data

- response_regulator_inputs: Raw Pfam alignments (PF00072, PF00196, PF00486, PF04397) and PDB representative sequences for responseregulator analysis- msa_difficulty: Pythia 2.0 MSA difficulty scores (msa_difficulty.csv)- casp15_input: CASP15 MSAs and target PDB structures (msas/, targets/)

Intermediate Results

- response_regulators_seq_weights: MSA Pairformer sequence weights for response regulator queries (inference_results.pt)- uniclust30_msas: Diversity-filtered MSAs from OpenProteinSet (1024 sequences each)- uniclust30_trees: FastTree phylogenies for each MSA (.fasttree.newick, .fasttree.log)- uniclust30_seq_weights: MSA Pairformer sequence weights for all UniClust30 MSAs (seq_weights.pt)- uniclust30_iqtrees: IQ-TREE phylogenies for 10 smallest MSAs (.iqtree.newick, .iqtree.log)- uniclust30_seq_weights_depth_200: Sequence weights for depth-200 filtered MSAs (seq_weights_depth_200.pt)- contact_prediction: Beta-carbon contact predictions with/without sequence weighting (cb_contacts.pt, cb_contacts_uniform.pt, pdbs/)- casp15_contact_prediction: Beta-carbon contact predictions for CASP15 targets (casp15_cb_contacts.pt,casp15_cb_contacts_uniform.pt)- layer_shuffling: Layer ablation study with shuffled sequence weights (single/, cumulative/)

Pub Info

- No need to manually download, the notebook pub will download necessary materials when executed

- DOI: https://doi.org/10.57844/arcadia-ppdz-asaz

- URL: https://arcadia-science.github.io/2025-phylogenetic-analysis-of-msa-pairformer
DOI: 10.5281/zenodo.18318397
title: Input data and cached results for, "MSA-based pLMs encode evolutionary distance but don't reliably exploit it"

description: Input Data

- response_regulator_inputs: Raw Pfam alignments (PF00072, PF00196, PF00486, PF04397) and PDB representative sequences for responseregulator analysis- msa_difficulty: Pythia 2.0 MSA difficulty scores (msa_difficulty.csv)- casp15_input: CASP15 MSAs and target PDB structures (msas/, targets/)

Intermediate Results

- response_regulators_seq_weights: MSA Pairformer sequence weights for response regulator queries (inference_results.pt)- uniclust30_msas: Diversity-filtered MSAs from OpenProteinSet (1024 sequences each)- uniclust30_trees: FastTree phylogenies for each MSA (.fasttree.newick, .fasttree.log)- uniclust30_seq_weights: MSA Pairformer sequence weights for all UniClust30 MSAs (seq_weights.pt)- uniclust30_iqtrees: IQ-TREE phylogenies for 10 smallest MSAs (.iqtree.newick, .iqtree.log)- uniclust30_seq_weights_depth_200: Sequence weights for depth-200 filtered MSAs (seq_weights_depth_200.pt)- contact_prediction: Beta-carbon contact predictions with/without sequence weighting (cb_contacts.pt, cb_contacts_uniform.pt, pdbs/)- casp15_contact_prediction: Beta-carbon contact predictions for CASP15 targets (casp15_cb_contacts.pt,casp15_cb_contacts_uniform.pt)- layer_shuffling: Layer ablation study with shuffled sequence weights (single/, cumulative/)

Pub Info

- No need to manually download, the notebook pub will download necessary materials when executed

- DOI: https://doi.org/10.57844/arcadia-ppdz-asaz

- URL: https://arcadia-science.github.io/2025-phylogenetic-analysis-of-msa-pairformer
DOI: 10.15468/dl.b3eks2
title: Occurrence Download

description: A dataset containing 134755 records in GBIF matching the query:
SELECT
 '506' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 51.21395264452012
 AND decimalLatitude &lt;= 56.135291543055025
 AND decimalLongitude &gt;= -7.195510188352444
 AND decimalLongitude &lt;= 0.0
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 134755 records were derived from 562 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004232-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13140/rg.2.2.30621.58083
title: Tratado de Clínica Médica: a Medicina Contemporânea Tomo I e II
DOI: 10.15468/dl.wcef52
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Echinorhynchus bothniensis",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004241-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25919/2pkq-0g70
title: Long-term project observations for project P1321 semester 2025OCTS_19

description: The atomic interstellar medium shows tiny-scale optical depth fluctuations on the scale of 0.1~10,000 AU, whose origin and nature are poorly understood. The existence of this Tiny-Scale Atomic Structure (TSAS) has significant implications, potentially calling into question our fundamental understanding of heating, cooling and dynamical processes in the interstellar medium. Yet observations remain sparse. This long-term project plans to search for temporal variations in HI absorption spectra seen against background pulsars to characterise TSAS in the Milky Way interstellar medium (ISM). These observations constitute the largest number of sightlines and densest temporal sampling ever performed in a single experiment, and will test predictions that TSAS is the tail end of a turbulent cascade, constrain its minimum size scale (down to resolutions of ~0.05 AU) and potentially provide the first direct measurements of pressures in "large" TSAS features of &gt; 1000 AU. We make use of the phase-resolved spectral line mode that we have recently implemented on Parkes, which has cut data rates and processing times by factors of ~1000 compared to past studies. This is an expansion of our pilot P1321 to a long term study.
DOI: 10.5061/dryad.j9kd51cpm
title: Santa Cruz and Santa Barbara active transportation infrastructure data

description: This data set contains organized data created based on data from the City
 of Santa Cruz, the City of Santa Barbara, and other public records. The
 data describes the active transportation infrastructure projects that were
 installed in the cities of Santa Cruz and Santa Barbara between 2018 and
 2024. Some project information was interpreted from documents such as
 project alignment maps and project descriptions. Other information was
 directly communicated by city staff. The data contains information about
 the type of infrastructure element and the amount (in feet or count) of
 each element by the following change conditions: new, upgrade, retrofit.
description: The data set was created through the manual review of count data,
 infrastructure data, and other public sources such as websites, as well as
 Google Street View. The infrastructure information has not gone through
 any processing.
description: # Santa Cruz and Santa Barbara Active Transportation Infrastructure Data
 [https://doi.org/10.5061/dryad.j9kd51cpm](https://doi.org/10.5061/dryad.j9kd51cpm) ## Description of the data and file structure The data describes the type and amount of active transportation project infrastructure installed in the City of Santa Cruz and the City of Santa Barbara between 2018 and 2024.  ### Files and variables #### File: import-sb-infrastructure.xlsx **Description:** Data for Santa Barbara ##### Variables * project_id (GUID): a unique identifier used for projects of the California Active Transportation Benefit-Cost Tool ([https://activetravelbenefits.ucdavis.edu/](https://activetravelbenefits.ucdavis.edu/)) * element (string): description of infrastructure type * new (double): count or linear ft of new infrastructure * upgrade (double): count or linear ft of upgraded infrastructure * retrofit (double): count or linear ft of retrofit infrastructure #### File: import-sc-infrastructure.xlsx **Description:** Data for Santa Cruz ##### Variables * project_id (GUID): a unique identifier used for projects of the California Active Transportation Benefit-Cost Tool ([https://activetravelbenefits.ucdavis.edu/](https://activetravelbenefits.ucdavis.edu/)) * element (string): description of infrastructure type * new (double): count or linear ft of new infrastructure * upgrade (double): count or linear ft of upgraded infrastructure * retrofit (double): count or linear ft of retrofit infrastructure ## Code/software Google Sheets, R, or other tools that can read xlsx data. ## Access information Other publicly accessible locations of the data: * NA Data was derived from the following sources: * Personal communication with the City of Santa Cruz and City of Santa Barbara, media reports, Google Street View
DOI: 10.5061/dryad.7pvmcvf48
title: Data from: Chilling induces prompt and synchronised hatching after obligatory diapause in the subtropical cricket <em>Cardiodactylus guttulus</em>

description: Cardiodactylus guttulus is a subtropical cricket endemic to the Ryukyu
 Islands. C. guttulus has a univoltine life cycle with an obligatory
 diapause in embryos during winter. An environmental time cue(s) is
 required to terminate diapause and synchronise the life cycle with the
 seasonal cycle. In several temperate crickets, chilling terminates
 embryonic diapause and induces prompt and synchronised hatching. In the
 present study, by observing the day of hatching after chilling, we
 investigated whether C. guttulus terminates embryonic diapause with
 reference to temperature, as shown in temperate crickets. After chilling
 at 16°C, the hatching rates to day 120 after oviposition increased
 compared to the control maintained at 25°C without chilling. When the
 chilling treatment lasted more than 30 days, hatching occurred
 synchronously, showing that chilling at 16°C for 1 month is sufficient to
 terminate diapause and induce synchronised hatching in C. guttulus. In
 addition, longer exposure to 16°C was associated with shorter days of
 transfer from 16 to 25°C to hatching. This result suggests that
 embryogenesis post-diapause progressed slowly during chilling. These
 characteristics would be adaptive to warm winters in subtropical regions.
description: # Chilling induces prompt and synchronized hatching after obligatory
 diapause in the subtropical cricket *Cardiodactylus guttulus* Dataset DOI:
 [10.5061/dryad.7pvmcvf48](10.5061/dryad.7pvmcvf48) ## Description of the
 data and file structure We examined whether chilling at 16°C terminates
 obligately embryonic diapause of a subtropical cricket, *Cardiodactylus
 guttulus*. The eggs were collected by changing the moist cotton every day,
 and the day of egg collection was defined as day 0. The collected eggs
 were incubated at 25.0 ± 1.0°C for 10 days, transferred to 16.0 ± 1.0°C,
 and incubated for 0(negative control), 15, 30, 4,5, or 60 days. After
 chilling, they were returned to 25.0 ± 1.0°C, and the number of hatched
 eggs was counted every day until day 120. **Hatching_days.csv** | **Column
 name** | **Description** | **Units** | **Data format** | **Missing data
 code** | | :-------------- |
 :----------------------------------------------------------- | :-------- |
 :-------------- | :-------------------- | | Chilling | The number of days
 of chilling. | - | Number | - | | Collection | The date of egg collection
 in the format (year, month, day). | - | Number | - | | Day\_X | The number
 of eggs hatched on day X. | - | Number | - | | Not\_hatched | The number
 of eggs that did not hatch even after day 120. | - | Number | - |
DOI: 10.15468/dl.bpe52w
title: Occurrence Download

description: A dataset containing 94722 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Trachurus trachurus",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 94722 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004215-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6s77vy
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Echinorhynchus brayi",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004243-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18407142
title: UTMF Capstone Composite Archive v1: Immutable Measurement Metadata for Multifractal Analysis

description: This archive provides a single, self-contained composite of immutable measurementmetadata supporting the capstone paper:



A Universal Measurement Geometry for Multifractal Analysis –Empirical Coherence, Hierarchical Structure, and the Fractal Asymmetry Kernel.


(DOi: 10.5281/zenodo.18407377)

The archive contains only measurement-level outputs produced by the UTMFpipeline. It does not store higher-order constructs such as Fractal AsymmetryTheory (FAT), the Fractal Asymmetry Kernel (FAK), Emergence Depth (ED), confinement,or trajectories. All such objects are reconstructed externally and exclusivelyfrom the archived metadata.

What the archive contains

The composite JSON records:





complete MFDFA subset outputs and multifractal spectra h(q)h(q)h(q),




raw and aggregated coherence measures (TCI, MCI, TMCI),




full bootstrap samples and cross-validation statistics,




configuration snapshots and code fingerprints ensuring numerical reproducibility,




time-series snapshots sufficient to recompute or audit coherence measures,




dataset health diagnostics and metadata.



All raw time series are processed exactly once under a fixed UTMF v5.2 protocol.No raw data are reprocessed after archival.

What the archive does not contain

The archive deliberately excludes:





Fractal Asymmetry Theory (FAT) outputs,




Fractal Asymmetry Kernel (FAK) realizations,




Emergence Depth (ED) or hierarchical embeddings,




confinement or trajectory constructions,




physical models, dynamical assumptions, or interpretation layers.



These structures are derived post-hoc as part of the analytical frameworkdescribed in the associated paper.

Provenance

This composite archive merges the following previously published UTMF measurementrecords without modification:





UTMF v5.2 MFDFA Stability Archive v1 (2025-12-30)DOI: 10.5281/zenodo.18090981




FULL_DETAILS UTMF v5.2 (2026-01-03)DOI: 10.5281/zenodo.18149263




FULL_DETAILS UTMF v5.2 (2026-01-12)DOI: 10.5281/zenodo.18226887



Each component remains independently citable.

Intended use

This archive is intended for:





full reproduction of measurement-level results,




independent auditing of multifractal measurement behavior,




recomputation or alternative analysis of coherence measures,




methodological studies of estimator stability and protocol effects,




external reconstruction of higher-order structures under transparent assumptions.



The dataset defines a fixed empirical measurement space against which allsubsequent geometric or interpretive analyses must be tested.

License

Released under the same open license as the original component datasets.
DOI: 10.5281/zenodo.18407143
title: UTMF Capstone Composite Archive v1: Immutable Measurement Metadata for Multifractal Analysis

description: This archive provides a single, self-contained composite of immutable measurementmetadata supporting the capstone paper:



A Universal Measurement Geometry for Multifractal Analysis –Empirical Coherence, Hierarchical Structure, and the Fractal Asymmetry Kernel.


(DOi: 10.5281/zenodo.18407377)

The archive contains only measurement-level outputs produced by the UTMFpipeline. It does not store higher-order constructs such as Fractal AsymmetryTheory (FAT), the Fractal Asymmetry Kernel (FAK), Emergence Depth (ED), confinement,or trajectories. All such objects are reconstructed externally and exclusivelyfrom the archived metadata.

What the archive contains

The composite JSON records:





complete MFDFA subset outputs and multifractal spectra h(q)h(q)h(q),




raw and aggregated coherence measures (TCI, MCI, TMCI),




full bootstrap samples and cross-validation statistics,




configuration snapshots and code fingerprints ensuring numerical reproducibility,




time-series snapshots sufficient to recompute or audit coherence measures,




dataset health diagnostics and metadata.



All raw time series are processed exactly once under a fixed UTMF v5.2 protocol.No raw data are reprocessed after archival.

What the archive does not contain

The archive deliberately excludes:





Fractal Asymmetry Theory (FAT) outputs,




Fractal Asymmetry Kernel (FAK) realizations,




Emergence Depth (ED) or hierarchical embeddings,




confinement or trajectory constructions,




physical models, dynamical assumptions, or interpretation layers.



These structures are derived post-hoc as part of the analytical frameworkdescribed in the associated paper.

Provenance

This composite archive merges the following previously published UTMF measurementrecords without modification:





UTMF v5.2 MFDFA Stability Archive v1 (2025-12-30)DOI: 10.5281/zenodo.18090981




FULL_DETAILS UTMF v5.2 (2026-01-03)DOI: 10.5281/zenodo.18149263




FULL_DETAILS UTMF v5.2 (2026-01-12)DOI: 10.5281/zenodo.18226887



Each component remains independently citable.

Intended use

This archive is intended for:





full reproduction of measurement-level results,




independent auditing of multifractal measurement behavior,




recomputation or alternative analysis of coherence measures,




methodological studies of estimator stability and protocol effects,




external reconstruction of higher-order structures under transparent assumptions.



The dataset defines a fixed empirical measurement space against which allsubsequent geometric or interpretive analyses must be tested.

License

Released under the same open license as the original component datasets.
DOI: 10.15468/dl.b75yxc
title: Occurrence Download

description: A dataset containing 5310 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Acrocomia aculeata, Acrocomia aculeata)"
 ]
}

 The dataset includes 5310 records from 271 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004244-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16900894
title: Dataset for Scale-free Bacteria Collective Motion
DOI: 10.5281/zenodo.16900895
title: Dataset for Scale-free Bacteria Collective Motion
DOI: 10.15468/dl.awycbb
title: Occurrence Download

description: A dataset containing 107 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "TaxonKey is Myrcianthes hallii"
 ]
}

 The dataset includes 107 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025743-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.778272
title: (Appendix) Late Cretaceous calcareous nannofossils of DSDP Holes 80-549 and 80-551

description: he early late Cretaceous (Cenomanian–early Turonian) is thought to have been one of the warmest periods of the Phanerozoic. This period was characterised by tropical sea surface temperatures of up to 36 °C and a pole-to-equator-gradient of less than 10 °C. The subsequent Turonian–Maastrichtian was characterised by a continuous climatic cooling, peaking in the Maastrichtian. This climatic cooling and the resulting palaeoceanographic changes had an impact on planktic primary producer communities including calcareous nannofossils. In order to gain a better understanding of these Cenomanian–Maastrichtian palaeoceanographic changes, calcareous nannofossils have been studied from the proto North Atlantic (Goban Spur, DSDP Sites 549, 551). In order to see potential differences between open oceanic and shelf dwelling nannofossils, the data from Goban Spur have been compared to findings from the European shelf (northern Germany).A total of 77 samples from Goban Spur were studied for calcareous nannofossils revealing abundant (mean 6.2 billion specimens/g sediment) and highly diverse (mean 63 species/sample) nannofossil assemblages. The dominant taxa are Watznaueria spp. (mean 30.7%), Prediscosphaera spp. (mean 18.3%), Zeugrhabdotus spp. (mean 8.3%), Retecapsa spp. (mean 7.2%) and Biscutum spp. (mean 6.6%). The Cenomanian assemblages of both Goban Spur (open ocean) and Wunstorf (shelf) are characterised by elevated abundances of high fertility taxa like Biscutum spp., Zeugrhabdotus spp. and Tranolithus orionatus. Early Turonian to Maastrichtian calcareous nannofossil assemblages of Goban Spur are, however, quite different to those described from European sections. Oceanic taxa like Watznaueria spp., Retecapsa spp. and Cribrosphearella ehrenbergii dominate in Goban Spur whereas the fertility indicators Biscutum spp. and T. orionatus are more abundant in the European shelf assemblages. This shift from a homogeneous distribution of calcareous nannofossils in the Cenomanian towards a heterogeneous one in the Turonian–Maastrichtian implies a change of the ocean circulation. The “eddy ocean” system of the Cenomanian was replaced by an oceanic circulation similar to the modern one in the Turonian–Maastrichtian, caused by the cooling. The increased pole-to-equator-gradients resulted in an oceanic circulation similar to the modern one.
description: Supplement to: Linnert, Christian; Mutterlose, Jörg; Herrle, Jens O (2011): Late Cretaceous (Cenomanian–Maastrichtian) calcareous nannofossils from Goban Spur (DSDP Sites 549, 551): Implications for the palaeoceanography of the proto North Atlantic. Palaeogeography, Palaeoclimatology, Palaeoecology, 15(3+4), 507-528
DOI: 10.1594/pangaea.778223
title: (Table 1) Apparent bedding dips in core-cut sections and apparent azimuth of dip from ODP Hole 128-799B
DOI: 10.1594/pangaea.778224
title: (Table 2) Reported fractures: joints, faults, and veinlets, veins from ODP Hole 128-794D

description: For sample 128-794D-16R-1,32-43 a dip angel of 60-65 deg is reported.
DOI: 10.1594/pangaea.754721
title: Physical oceanography at CTD station PotterCove_2 at Potter Cove, King George Island, West Antarctic Peninsula in 1999
DOI: 10.1594/pangaea.860495
title: Stable carbon and oxygen isotope record of Nuttallides truempyi of IODP Hole 342-U1409C
DOI: 10.1594/pangaea.860497
title: Stable carbon and oxygen isotope record of bulk carbonate of IODP Site 342-U1409
DOI: 10.1594/pangaea.754728
title: Physical oceanography at CTD station PotterCove_2 at Potter Cove, King George Island, West Antarctic Peninsula in 2008
DOI: 10.1594/pangaea.771930
title: (Table S1) Magnetic reversal age calibration of ODP Site 199-1218

description: sediment depth is given in revised meters composite depth (rmcd), the Eocene/Oligocene transition is interpolated.
DOI: 10.1594/pangaea.736908
title: Physical oceanography at CTD station PotterCove_2 at Potter Cove, King George Island, West Antarctic Peninsula in 1996