cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18743775
title: Structure-Based Virtual Screening for Cystathionine β-Synthase Inhibitors: Target-Specific Machine-Learning Scoring Functions Outperform State-of-the-Art Deep-Learning Docking and Co-Folding Methods

description: Cystathionine beta-synthase (CBS) has emerged as an important therapeutic target implicated in cancer and Down syndrome, yet the discovery of selective CBS inhibitors remains challenging due to limited structural diversity of known ligands and the scarcity of target-focused virtual screening (VS) benchmarks. 

In this study, we present the first comprehensive evaluation of CBS-specific machine-learning (ML) models for structure-based VS, supported by a carefully curated and up-to-date data set of experimentally validated CBS inhibitors, true inactives and decoys. Importantly, we benchmarked their performance against a diverse panel of 16 established VS pipelines, including classical docking-based scoring schemes, modern deep-learning (DL) docking tools, and recent co-folding approaches for protein-ligand modeling and affinity prediction.

The CBS-specific ML classifiers substantially outperformed these state-of-the-art (SOTA) methods in early enrichment, highlighting the advantage of target-focused training for VS tasks. Our results further reveal that generic DL docking and co-folding approaches struggle to achieve reliable screening performance when applied to targets that are under-represented in or entirely absent from their training data, as appears to be the case for CBS. This underscores a key limitation of broadly trained foundation-style models in prospective drug discovery campaigns involving less-studied proteins.
DOI: 10.5281/zenodo.7561918
title: Natrolite - Sample 2 NanED Round Robin, Data ESR3

description: General information:
			
			
			
 
			
		
		
			
			
Project
			
			
			
NanED (www.naned.eu)
			
		
		
			
			
ESR Project
			
			
			
ESR3
			
		
		
			
			
 
			
			
			
 
			
		
		
			
			
Instrumental:
			
			
			
 
			
		
		
			
			
Instrument
			
			
			
FEI Titan
			
		
		
			
			
Radiation source
			
			
			
FEG
			
		
		
			
			
Accelerating voltage
			
			
			
300 kV
			
		
		
			
			
Wavelength
			
			
			
0.0197 Å
			
		
		
			
			
Acquisiton Method
			
			
			
Nanodiffraction
			
		
		
			
			
Detector
			
			
			
US1000 – CCD Camera
			
		
		
			
			
Number of pixels in the image
			
			
			
2048 x 2048
			
		
		
			
			
Calibration constant (not corrected for Effective Camera length)
			
			
			
0.00179 Å-1/pixel
			
		
		
			 
			 
		
		
			
			
Sample description:
			
			
			
 
			
		
		
			
			
Name
			
			
			
Natrolite
			
		
		
			
			
Chemical composition
			
			
			
Ca2FexAl3-xSi3O13H
			
		
		
			 
			 
		
		
			
			
Experimental:
			
			
			
 
			
		
		
			
			
Data Type
			
			
			
Electron diffraction data - 3D ED
			
		
		
			
			
Data collection method
			
			
			
Stepwise
			
		
		
			
			
Temperature (K) used during data collection
			
			
			
293 K
			
		
		
			
			
Number of crystals contributing to the data set
			
			
			
1
			
		
		
			
			
Number of experimental frames
			
			
			
626
			
		
		
			
			
tilt range, tilt step
			
			
			
-70° to +70°, 0.2°
			
		
		
			
			
Exposure time per frame
			
			
			
1s
			
		
		
			
			
 
			
			
			
 
			
		
		
			
			
Software:
			
			
			
 
			
		
		
			
			
Software used for the data collection
			
			
			
TIA
			
		
		
			
			
Software used for processing
			
			
			
PETS2
			
		
		
			
			
Software used for solution
			
			
			
Jana
			
		
		
			
			
Software used for refinement
			
			
			
Olex2
description: "This research was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 956099 (NanED – Electron Nanocrystallography – H2020- MSCAITN)"
DOI: 10.5281/zenodo.7561917
title: Natrolite - Sample 2 NanED Round Robin, Data ESR3

description: General information:
			
			
			
 
			
		
		
			
			
Project
			
			
			
NanED (www.naned.eu)
			
		
		
			
			
ESR Project
			
			
			
ESR3
			
		
		
			
			
 
			
			
			
 
			
		
		
			
			
Instrumental:
			
			
			
 
			
		
		
			
			
Instrument
			
			
			
FEI Titan
			
		
		
			
			
Radiation source
			
			
			
FEG
			
		
		
			
			
Accelerating voltage
			
			
			
300 kV
			
		
		
			
			
Wavelength
			
			
			
0.0197 Å
			
		
		
			
			
Acquisiton Method
			
			
			
Nanodiffraction
			
		
		
			
			
Detector
			
			
			
US1000 – CCD Camera
			
		
		
			
			
Number of pixels in the image
			
			
			
2048 x 2048
			
		
		
			
			
Calibration constant (not corrected for Effective Camera length)
			
			
			
0.00179 Å-1/pixel
			
		
		
			 
			 
		
		
			
			
Sample description:
			
			
			
 
			
		
		
			
			
Name
			
			
			
Natrolite
			
		
		
			
			
Chemical composition
			
			
			
Ca2FexAl3-xSi3O13H
			
		
		
			 
			 
		
		
			
			
Experimental:
			
			
			
 
			
		
		
			
			
Data Type
			
			
			
Electron diffraction data - 3D ED
			
		
		
			
			
Data collection method
			
			
			
Stepwise
			
		
		
			
			
Temperature (K) used during data collection
			
			
			
293 K
			
		
		
			
			
Number of crystals contributing to the data set
			
			
			
1
			
		
		
			
			
Number of experimental frames
			
			
			
626
			
		
		
			
			
tilt range, tilt step
			
			
			
-70° to +70°, 0.2°
			
		
		
			
			
Exposure time per frame
			
			
			
1s
			
		
		
			
			
 
			
			
			
 
			
		
		
			
			
Software:
			
			
			
 
			
		
		
			
			
Software used for the data collection
			
			
			
TIA
			
		
		
			
			
Software used for processing
			
			
			
PETS2
			
		
		
			
			
Software used for solution
			
			
			
Jana
			
		
		
			
			
Software used for refinement
			
			
			
Olex2
description: "This research was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 956099 (NanED – Electron Nanocrystallography – H2020- MSCAITN)"
DOI: 10.15468/dl.rewtnc
title: Occurrence Download

description: A dataset containing 4329 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Material sample, Specimen, Occurrence evidence)",
 "Continent is one of (North America, South America)",
 "TaxonKey is Triatoma dimidiata",
 "Year 1970-2026"
 ]
}

 The dataset includes 4329 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000284-260225131425191/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18773996
title: COMPATIBILITY OF ALGEBRAIC AND VISUAL APPROACHES IN SOLVING 3RD AND 4TH ORDER EQUATIONS

description: The article analyzes a methodology for teaching third- and fourth-degree algebraic equations in which algebraic methods are employed as the primary instructional approach, while visual tools are used as auxiliary instruments. Students often encounter difficulties when searching for rational roots and applying Horner’s scheme in solving higher-degree equations. In the study, algebraic methods are considered the main teaching mechanism, whereas GeoGebra is treated as a tool for verifying and reinforcing algebraic solutions. The proposed step-by-step model emphasizes thorough instruction in algebraic methods at the initial stage, followed by visual verification to consolidate the results. Such an approach serves as an effective means of developing students’ functional thinking, enhancing their ability to independently identify errors, and fostering mathematical intuition.
DOI: 10.5281/zenodo.18773997
title: COMPATIBILITY OF ALGEBRAIC AND VISUAL APPROACHES IN SOLVING 3RD AND 4TH ORDER EQUATIONS

description: The article analyzes a methodology for teaching third- and fourth-degree algebraic equations in which algebraic methods are employed as the primary instructional approach, while visual tools are used as auxiliary instruments. Students often encounter difficulties when searching for rational roots and applying Horner’s scheme in solving higher-degree equations. In the study, algebraic methods are considered the main teaching mechanism, whereas GeoGebra is treated as a tool for verifying and reinforcing algebraic solutions. The proposed step-by-step model emphasizes thorough instruction in algebraic methods at the initial stage, followed by visual verification to consolidate the results. Such an approach serves as an effective means of developing students’ functional thinking, enhancing their ability to independently identify errors, and fostering mathematical intuition.
DOI: 10.5281/zenodo.7561805
title: Epidote - Sample 1 NanED Round Robin, Data ESR3

description: General information:
			
			
			
 
			
		
		
			
			
Project
			
			
			
NanED (www.naned.eu)
			
		
		
			
			
ESR Project
			
			
			
ESR3
			
		
		
			
			
 
			
			
			
 
			
		
		
			
			
Instrumental:
			
			
			
 
			
		
		
			
			
Instrument
			
			
			
FEI TECNAI
			
		
		
			
			
Radiation source
			
			
			
FEG
			
		
		
			
			
Accelerating voltage
			
			
			
200 kV
			
		
		
			
			
Wavelength
			
			
			
0.0251 Å
			
		
		
			
			
Acquisiton Method
			
			
			
SAED
			
		
		
			
			
Detector
			
			
			
Eagle – CCD Camera
			
		
		
			
			
Number of pixels in the image
			
			
			
2048 x 2048
			
		
		
			
			
Calibration constant (not corrected for Effective Camera length)
			
			
			
0.00182 Å-1/pixel
			
		
		
			
			
Sample description:
			
			
			
 
			
		
		
			
			
Name
			
			
			
Epidote
			
		
		
			
			
Chemical composition
			
			
			
Ca2FexAl3-xSi3O13H
			
		
		
			 
			 
		
		
			
			
Experimental:
			
			
			
 
			
		
		
			
			
Data Type
			
			
			
Electron diffraction data - 3D ED
			
		
		
			
			
Data collection method
			
			
			
Stepwise
			
		
		
			
			
Temperature (K) used during data collection
			
			
			
293 K
			
		
		
			
			
Number of crystals contributing to the data set
			
			
			
1
			
		
		
			
			
Number of experimental frames
			
			
			
351
			
		
		
			
			
tilt range, tilt step
			
			
			
-35° to +35°, 0.2°
			
		
		
			
			
Exposure time per frame
			
			
			
1s
			
		
		
			
			
 
			
			
			
 
			
		
		
			
			
Software:
			
			
			
 
			
		
		
			
			
Software used for the data collection
			
			
			
TIA
			
		
		
			
			
Software used for processing
			
			
			
PETS2
			
		
		
			
			
Software used for Solution
			
			
			
Jana
			
		
		
			
			
Software used for refinement
			
			
			
Olex2
description: "This research was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 956099 (NanED – Electron Nanocrystallography – H2020- MSCAITN)"
DOI: 10.5281/zenodo.7561804
title: Epidote - Sample 1 NanED Round Robin, Data ESR3

description: General information:
			
			
			
 
			
		
		
			
			
Project
			
			
			
NanED (www.naned.eu)
			
		
		
			
			
ESR Project
			
			
			
ESR3
			
		
		
			
			
 
			
			
			
 
			
		
		
			
			
Instrumental:
			
			
			
 
			
		
		
			
			
Instrument
			
			
			
FEI TECNAI
			
		
		
			
			
Radiation source
			
			
			
FEG
			
		
		
			
			
Accelerating voltage
			
			
			
200 kV
			
		
		
			
			
Wavelength
			
			
			
0.0251 Å
			
		
		
			
			
Acquisiton Method
			
			
			
SAED
			
		
		
			
			
Detector
			
			
			
Eagle – CCD Camera
			
		
		
			
			
Number of pixels in the image
			
			
			
2048 x 2048
			
		
		
			
			
Calibration constant (not corrected for Effective Camera length)
			
			
			
0.00182 Å-1/pixel
			
		
		
			
			
Sample description:
			
			
			
 
			
		
		
			
			
Name
			
			
			
Epidote
			
		
		
			
			
Chemical composition
			
			
			
Ca2FexAl3-xSi3O13H
			
		
		
			 
			 
		
		
			
			
Experimental:
			
			
			
 
			
		
		
			
			
Data Type
			
			
			
Electron diffraction data - 3D ED
			
		
		
			
			
Data collection method
			
			
			
Stepwise
			
		
		
			
			
Temperature (K) used during data collection
			
			
			
293 K
			
		
		
			
			
Number of crystals contributing to the data set
			
			
			
1
			
		
		
			
			
Number of experimental frames
			
			
			
351
			
		
		
			
			
tilt range, tilt step
			
			
			
-35° to +35°, 0.2°
			
		
		
			
			
Exposure time per frame
			
			
			
1s
			
		
		
			
			
 
			
			
			
 
			
		
		
			
			
Software:
			
			
			
 
			
		
		
			
			
Software used for the data collection
			
			
			
TIA
			
		
		
			
			
Software used for processing
			
			
			
PETS2
			
		
		
			
			
Software used for Solution
			
			
			
Jana
			
		
		
			
			
Software used for refinement
			
			
			
Olex2
description: "This research was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 956099 (NanED – Electron Nanocrystallography – H2020- MSCAITN)"
DOI: 10.57783/q0jw-hg36
title: Marketscan Medicare Set A

description: For technical support with Columbia Data Platform please contact: dataplatform@columbia.edu. 

For User Group and Access questions please contact: rit@cumc.columbia.edu. 

For specific technical questions of the Marketscan data, please contact marketscan.support@merative.com, or the Merative Support Community Portal at https://merative.my.site.com/mysupport.
description: The MarketScan® Research Databases aggregate claims & enrollment data from commercial, federal, state and public health plans, linking paid claims to real-world data for healthcare research, economics and treatment outcomes for ~300m patients.
description: The Merative™ MarketScan® Research Databases capture person-specific clinical utilization, expenditures, and enrollment across inpatient, outpatient, prescription drug, and carve-out services. The data come from a selection of large employers, health plans, and government and public organizations. The MarketScan Research Databases link paid claims and encounter data to detailed patient information across sites and types of providers and over time. The annual medical databases include private-sector health data from approximately 350 payers. Historically, more than 20 billion service records are available in the MarketScan databases. These data represent the medical experience of insured employees and their dependents for active employees, early retirees, Consolidated Omnibus Budget Reconciliation Act (COBRA) continuees, and Medicare-eligible retirees with employer-provided Medicare Supplemental and Medicare Advantage plans.
DOI: 10.57783/5xsa-5117
title: Marketscan Medicare Set A

description: For technical support with Columbia Data Platform please contact: dataplatform@columbia.edu. 

For User Group and Access questions please contact: rit@cumc.columbia.edu. 

For specific technical questions of the Marketscan data, please contact marketscan.support@merative.com, or the Merative Support Community Portal at https://merative.my.site.com/mysupport.
description: The MarketScan® Research Databases aggregate claims & enrollment data from commercial, federal, state and public health plans, linking paid claims to real-world data for healthcare research, economics and treatment outcomes for ~300m patients.
description: The Merative™ MarketScan® Research Databases capture person-specific clinical utilization, expenditures, and enrollment across inpatient, outpatient, prescription drug, and carve-out services. The data come from a selection of large employers, health plans, and government and public organizations. The MarketScan Research Databases link paid claims and encounter data to detailed patient information across sites and types of providers and over time. The annual medical databases include private-sector health data from approximately 350 payers. Historically, more than 20 billion service records are available in the MarketScan databases. These data represent the medical experience of insured employees and their dependents for active employees, early retirees, Consolidated Omnibus Budget Reconciliation Act (COBRA) continuees, and Medicare-eligible retirees with employer-provided Medicare Supplemental and Medicare Advantage plans.
DOI: 10.57783/7s5n-8446
title: MarketScan Medicare Dental

description: For technical support with Columbia Data Platform please contact: dataplatform@columbia.edu. 

For User Group and Access questions please contact: rit@cumc.columbia.edu. 

For specific technical questions of the Marketscan data, please contact marketscan.support@merative.com, or the Merative Support Community Portal at https://merative.my.site.com/mysupport.
DOI: 10.17882/112220
title: Particulate Organic Carbon and Nitrogen in the Northwest Atlantic from DFO Atlantic Zone and Atlantic Offshelf Zone Monitoring Programs (AZMP & AZOMP)

description: The dataset is made of particulate organic carbon and nitrogen concentration measured from water sampled collected in the Northwest Atlantic as part of the Atlantic Zone Monitoring Program (AZMP, https://www.dfo-mpo.gc.ca/science/data-donnees/azmp-pmza/index-eng.html) and the Atlantic Offshelf Monitoring Program (AZOMP, https://www.bio.gc.ca/science/monitoring-monitorage/azomp-pmzao/azomp-pmzao-en.php) . samples were  collected within the first 20 m of the ocean surface. 
Samples for particulate organic carbon (POC) and nitrogen (PON) were filtered on pre-baked 25mm GF/F filters (0.7 µm mesh). Filters were baked at 450°C for 24 hours to remove all organic material and stored in a beaker covered with foil paper.  Between 0.2 and 1 L of water were filtered, volume was selected after visual inspection of filter to ensure that enough material was retained for analysis. Duplicates were collected and both filters were folded using tweezers, placed into a single petri dish and stored at -20°C until analysis in the laboratory at the Bedfrod Institute of Oceanography, Dartmouth, Nova Scotia, Canada.
Particulate Organic Carbon (POC) and Nitrogen (PON) mass were measured on a CHN elemental auto-analyser (Collos, 2002) and concentration was determined by dividing the mass of POC and PON by the volume filtered. Several blanks were ran at each beginning of a batch of samples, including two air blanks, a cap blank and a filter blank, as well as two standards. 
Data were collected during about 60 cruises that happened in Spring and Fall on the Scotian Shelf/Gulf of Maine, and in Springin the Labrador Sea. For additional datasets, please refer to the Canadian Integrated Ocean Observations System ERRDAP website (https://cioosatlantic.ca/erddap/index.html) and enter the AZMP orAZOMP search keywords
DOI: 10.17882/112242
title: Meiofaunal Communities from Three Contrasting Habitats at the Lucky Strike Vent Field, Northern Mid-Atlantic Ridge

description: Meiofaunal community composition, with emphasis on nematode genera and their functional traits, collected within an induced-disturbance experiment at the Lucky Strike vent field (Northern Mid-Atlantic Ridge). This study builds on the disturbance experiment initiated in 2017 at the Montségur active edifice (Marticorena et al., 2021) during the Momarsat 2017, 2018, and 2019 cruises conducted within the framework of the MERCES H2020 European project. Twelve stainless-steel quadrats (50 × 50 cm) were deployed at the Montségur edifice in 2017 using the ROV Victor6000. Four quadrats (R0a, R0b, R1, R2) served as reference samples to characterize baseline meiofaunal assemblages and assess natural temporal variability. Eight experimental quadrats were subjected to induced faunal clearance to monitor recolonization dynamics. At the active site, four quadrats were defaunated in 2017 and sampled after one year (C1a, C1b; 2018) and two years (C2a, C2b; 2019) to evaluate recovery trajectories. In 2018, the experimental design was extended to two additional habitats: a sedimented peripheral area (P1, P2) located approximately 30 m from Montségur and a visually inactive sulfide structure (I1, I2) located approximately 400 m north of Montségur. At these habitats, quadrats were defaunated in 2018 and sampled after one year to assess recolonization patterns. Faunal removal and sampling were conducted using the mechanical arm and suction sampler of the ROV Victor6000 (2017–2018) and the Nautile submersible (2019). In contrast to previous studies focusing on macrofauna retained on a 300 µm sieve, this dataset targets the meiofaunal fraction retained on a 32 µm mesh (32 µm–1 mm). Meiofauna were extracted by Ludox centrifugation, sorted into major taxonomic groups, and fixed in 4% formalin. For nematodes, 150 individuals per sample were randomly subsampled, cleared, mounted on permanent slides, and identified to genus level using standard pictorial keys. The dataset includes meiofaunal abundances per quadrat, nematode genus-level composition, and genus-based functional trait assignments (feeding type, body shape, tail morphology, and maturity index based on the c–p scale), together with associated environmental variables. This dataset enables analyses of meiofaunal community structure, functional composition, and post-disturbance recolonization dynamics across active, peripheral, and inactive hydrothermal habitats.
DOI: 10.17882/112300
title: Nordic Seas Deep Convection and Ventilation Variability – Southern Norwegian Sea (32–41 ka b2k) – Paired Planktic and Benthic Radiocarbon Data

description: This dataset comprises paired planktic and benthic radiocarbon (¹⁴C) measurements from marine sediment core MD99-2284 (62°22.48′N, 0°58.81′W; 1496 m water depth), located along the Atlantic inflow to the Norwegian Sea, spanning four Dansgaard–Oeschger (DO) cycles between ~32 and 41 ka (GICC05 b2k timescale).
The age model was constructed using 13 stratigraphic match points previously published in Berben et al. These include nine tie points linking distinct SST changes in MD99-2284 to stadial–interstadial transitions in NGRIP δ¹⁸O, and four cryptotephra horizons that directly align the marine core to the Greenland ice-core record. All match points were assigned their corresponding GICC05 b2k ages (absolute timescale, no radiocarbon calibration required). To quantify chronological uncertainties, we employed a bootstrap approach using Monte Carlo resampling (50,000 realizations) of the 13 tie points with replacement, followed by natural spline interpolation to generate bootstrapped age–depth functions and estimate confidence intervals. The final continuous age model was constructed using a Bayesian age–depth model (Bacon v2.3), applying default priors except for accumulation rate parameters (acc.mean = 5; acc.shape = 0.5).
Radiocarbon ventilation ages are calculated as planktic-atmosphere (P-ATM) and benthic-atmosphere (B-ATM) offsets with full propagation of analytical and reservoir-age uncertainties (2σ).
DOI: 10.5281/zenodo.18774011
title: LINF_340012800

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.5281/zenodo.18774031
title: THE IMPORTANCE OF INDUSTRIAL WASTEWATER TREATMENT USING BASALT-BASED FILTERS

description:  Currently, in order to save metal, more attention is being paid to the issue of replacing it with non-depleted and durable materials in a number of industries. Saving metal involves the widespread introduction of the production of substitutes. One of its substitutes is stoneware, from which more than 800 types of durable and acid-resistant industrial products are made. In addition, stone products are resistant to almost all acids, alkalis and salts and can replace protective materials such as iron, lead, other non-ferrous metals and their alloys. Recently, the demand for UBT (continuous basalt fiber) has increased sharply.
DOI: 10.5281/zenodo.18774012
title: LINF_340012800

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)