cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30720524.v1
title: EV protein Corona dataset + R pipeline

description: Extracellular vesicles (EVs) were isolated from HEK293T cells stably expressing CD63-APEX2 and incubated with mouse plasma to study protein corona formation under inflammatory conditions. Plasma was obtained from C57BL/6J mice treated intraperitoneally with either PBS or LPS (5 mg/kg) 3 hours prior to blood collection.EVs (1 × 10¹¹ particles per condition) were incubated with 100 µL of plasma at 37°C for 30 minutes to allow corona formation. Biotin-phenol (500 µM) and H₂O₂ (1 mM) were then added for 1 minute to initiate APEX2-catalyzed biotinylation of proteins in proximity to the EV surface. The reaction was quenched using a solution of sodium ascorbate (10 mM), Trolox (5 mM), and sodium azide (10 mM).Biotinylated proteins were enriched using streptavidin magnetic beads, digested on-bead with trypsin, and analyzed by LC-MS/MS (Orbitrap Eclipse). Raw data were processed with MaxQuant and filtered to remove contaminants and red blood cell proteins. Differential enrichment analysis was performed using the Limma package in R, with significant hits defined as log₂FC ≥ 1 or ≤ –1 and adjusted <i>p</i> ≤ 0.05. Functional enrichment was conducted using clusterProfiler and ReactomePA.
DOI: 10.3535/8kz-wex-tt7
title: Rosa majalis Herrm.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/f07-hb0-26r
title: Carex limosa L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/8z1-y3q-jyx
title: Convallaria majalis L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/rjm-3vg-e1b
title: Carex pilulifera L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/z0c-l4g-6p7
title: Pulsatilla vernalis (L.) Mill.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/1l1-scx-xv0
title: Carex limosa L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.25921/zrw8-kn24
title: A compilation of inorganic carbon system and other hydrographic and chemical discrete profile measurements obtained during the fifty five Line P cruises in the Northeast Pacific Ocean over the period from 1990 to 2019 (NCEI Accession 0234342)

description: This dataset contains a compilation of inorganic carbon system and other hydrographic and chemical discrete profile measurements obtained during the fifty five Line P cruises in the Northeast Pacific Ocean over the period from 1990-05-10 to 2019-06-19. The data in the dataset include dissolved inorganic carbon (DIC), total alkalinity (TA), water temperature, salinity, dissolved oxygen concentration and nutrients. The majority of the cruises from 1990 to 2015 have been reported elsewhere as individual files (e.g., GLODAP and PACIFICA databases). This dataset is a combination of the available cruises into a single database, and extended the time series to June 2019. A secondary quality control was performed and the quality flags revised. Additionally, the suggested PACIFICA corrections for salinity, oxygen, dissolved inorganic carbon and nutrients were applied. Oxygen units were converted to µmol/kg when reported in ml/L. Nutrient concentrations were converted to µmol/kg from µmol/L.
DOI: 10.15468/dl.4m8zub
title: Occurrence Download

description: A dataset containing 88228 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Acianthera hygrophila, Acianthera pubescens, Aechmea bromeliifolia, Asplenium praemorsum, Billbergia distachia, Billbergia porteana, Brassavola tuberculata, Bulbophyllum chloroglossum, Campylocentrum grisebachii, Campylocentrum micranthum, Campyloneurum angustifolium, Capanemia micromera, Capanemia superflua, Catasetum cernuum, Cattleya cernua, Cattleya lundii, Encyclia patens, Epidendrum densiflorum, Epidendrum latilabre, Epidendrum pseudodifforme, Epiphyllum phyllanthus, Eurystyles actinosophila, Gomesa imperatoris-maximiliani, Gomesa pubes, Gomesa varicosa, Isochilus linearis, Leptotes unicolor, Microgramma lindbergii, Microgramma squamulosa, Miltonia flavescens, Notylia lyrata, Peperomia acuminata, Peperomia circinnata, Peperomia rotundifolia, Peperomia succulenta, Peperomia tetraphylla, Peperomia urocarpa, Peperomia velloziana, Philodendron propinquum, Phlebodium aureum, Pleopeltis hirsutissima, Pleopeltis minima, Pleopeltis pleopeltifolia, Polystachya concreta, Rhipsalis baccifera, Thaumatophyllum bipinnatifidum, Tillandsia pohliana, Tillandsia stricta, Tillandsia tenuifolia, Tillandsia usneoides, Trichocentrum pumilum, Vriesea flava, Vriesea friburgensis, Zygostates lunata)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 88228 records from 778 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007599-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17605/osf.io/syzga
title: Sample Datasets for ABI3 Manuscript Vascular and Neuronal Analysis Pipelines

description: This repository contains sample datasets used to demonstrate and test the analysis pipelines developed for our study on ABI3-dependent vascular and neuronal phenotypes. These data examples are not the full experimental dataset but provide representative input files required to run the image-processing and analysis scripts shared in the accompanying GitHub repository.

The sample data include:

Arterial amyloid-β imaging (Fig. 5):
Example image stacks and intermediate files for running the arterial amyloid-β preprocessing and bounding-boxing scripts.

Neuronal calcium recordings (Fig. 7e–f):
Sample ΔF/F traces and event-detection outputs to illustrate neuronal activity analysis.

Laser Speckle Contrast Imaging (LSCI; Fig. 7k–l):
Small LSCI recordings and vessel masks provided for running the LSCI dilation analysis workflow.

Vessel dilation dynamics (Fig. 7h–i):
Example files for computing time-to-dilation and maximum dilation responses.

These reduced datasets allow users to execute the full computational pipeline, understand the workflow, and reproduce the figure-generation steps without accessing the complete raw dataset.

The full experimental raw data are available upon request or will be made accessible through a separate data release.
DOI: 10.25921/5mer-zp93
title: Cetacean and sea turtle visual observations using line-transect survey methods aboard a NOAA DeHavilland DHC-6 Twin Otter (TO) aircraft in the Gulf of Mexico, during the Gulf of Mexico Marine Assessment Program for Protected Species (GoMMAPPS survey TO18Wi) from 2018-01-18 to 2018-03-14 (NCEI Accession 0242273)

description: As part of the Gulf of Mexico Marine Assessment Program for Protected Species (GoMMAPPS), the Southeast Fisheries Science Center (SEFSC) conducted aerial surveys of the U.S. continental shelf waters (up to the 200-m isobath) in the Gulf of Mexico from 2018-01-18 to 2018-03-14. The survey was designed for a two-team independent visual observer approach with distance sampling to estimate abundance and characterize spatial distribution of marine mammals and sea turtles. This dataset includes marine mammal and sea turtle visual observation data and effort points with surveying conditions that can be used in abundance and density modeling per visual line-transect survey protocols. This dataset also includes marine mammal photographs used to aid in species identification.
DOI: 10.25921/1kvt-mr60
title: Dissolved inorganic carbon, total alkalinity, pH and other variables collected from surface discrete measurements using Coulometer, alkalinity titrator and other instruments from the Philippines from 2012-03-12 to 2015-06-03 (NCEI Accession 0242691)

description: This dataset contains carbonate chemistry data from samples collected across the Philippines as part of the USAID-funded US Coral Triangle Initiative from 2012-03-12 to 2015-06-03. The project monitors changes to coral reef carbonate chemistry over time at coral reef sites within the Philippines by quantifying key chemical parameters that are expected to change with ocean acidification. Incorporating an interdisciplinary approach, this project collects, processes, analyzes, and stewards dissolved inorganic carbon (DIC) and total alkalinity (TA) water sample data to document seawater carbonate chemistry at monitoring sites in coral reef areas of the Philippines region.
DOI: 10.25921/mdc3-3246
title: Cetacean and sea turtle visual observations using line-transect survey methods aboard a NOAA DeHavilland DHC-6 Twin Otter (TO) aircraft in the Gulf of Mexico, during the Gulf of Mexico Marine Assessment Program for Protected Species (GoMMAPPS survey TO17Su) from 6/29/2017 to 8/17/2017 (NCEI Accession 0243469)

description: As part of the Gulf of Mexico Marine Assessment Program for Protected Species (GoMMAPPS), the Southeast Fisheries Science Center (SEFSC) conducted aerial surveys of the U.S. continental shelf waters (up to the 200-m isobath) in the Gulf of Mexico from 6/29/2017 to 8/17/2017. The survey was designed for a two-team independent visual observer approach with distance sampling to estimate abundance and characterize spatial distribution of marine mammals and sea turtles. This dataset includes marine mammal and sea turtle visual observation data and effort points with surveying conditions that can be used in abundance and density modeling per visual line-transect survey protocols. This dataset also includes marine mammal photographs used to aid in species identification.
DOI: 10.25921/01c2-5g70
title: Cetacean visual observations using line-transect survey methods, and environmental parameters collected by CTD and other instruments onboard NOAA Ship Pisces (PC) in the Gulf of Mexico, during the Gulf of Mexico Marine Assessment Program for Protected Species (GoMMAPPS survey PC1805) from 2018-08-12 to 2018-10-05 (NCEI Accession 0244002)

description: As part of the Gulf of Mexico Marine Assessment Program for Protected Species (GoMMAPPS), the Southeast Fisheries Science Center (SEFSC) conducted shipboard surveys of the U.S. oceanic waters of the Gulf of Mexico out to the Exclusive Economic Zone (EEZ) from 2018-08-12 to 2018-10-05. The survey was designed for a two-team independent visual observer approach with distance sampling to estimate the detection probabilities for marine mammal sightings. This dataset includes marine mammal visual observation data and effort points with surveying conditions that can be used in abundance and density modeling per visual line-transect survey protocols. This dataset also includes opportunistic marine mammal photographs and non-marine mammal sightings (occurrences) such as sea turtles. Raw and processed files from conductivity, temperature and depth (CTD) and expendable bathythermograph (XBT) casts performed on a daily basis during the survey are also available.
DOI: 10.25921/padc-s385
title: Using Endmember Models to Estimate Seasonal Carbonate Chemistry and Acidification Sensitivity in Temperate Estuaries from 2015-11-19 to 2018-03-29 (NCEI Accession 0244177)

description: This dataset consists of data collected from the Salish Sea, British Columbia, specifically nearshore locations in Baynes Sound and Okeover Inlet; mostly via small skiffs and hand deployment of Niskin bottles. Some samples were collected from the CCGS Vector between 2015-2018. These data are used in "Using Endmember Models to Estimate Seasonal Carbonate Chemistry and Acidification Sensitivity in Temperate Estuaries" (2021) published in Geophysical Research Letters. Discrete total alkalinity (TA); dissolved inorganic carbon (DIC); dissolved oxygen; salinity; and nutrient samples were taken, 5L Niskin bottles and analyzed at the Institute of Ocean Sciences; Sidney, Canada. CTD profiles were recorded with each cast. A total of 578 DIC and TA pairs were sampled with a 20% replication rate; and the pooled standard deviations (of difference between replicate pairs) were calculated to be 2.1 umol/kg and 3.9 umol/kg respectively.
DOI: 10.15468/dl.knhuh5
title: Occurrence Download

description: A dataset containing 348269 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Reef Life Survey: Global reef fish dataset"
 ]
}

 The dataset includes 348269 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007601-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25921/5fza-nj73
title: Discrete profile measurements of dissolved inorganic carbon (DIC), total alkalinity (TA), salinity, oxygen, nutrients, and temperature during the CCGS John P. Tully cruise 2019.23 (EXPOCODE 18DD20190829) in the Salish Sea and off the west coast of Vancouver Island of the North American Pacific coast from 2019-08-29 to 2019-09-06 (NCEI Accession 0252614)

description: This dataset consists of data collected during the CCGS John P. Tully cruise 2019.23 (EXPOCODE 18DD20190829) in the Salish Sea and off the west coast of Vancouver Island of the North American Pacific coast from 2019-08-29 to 2019-09-06 as part of the La Perouse Water Properties Survey. Discrete dissolved inorganic carbon (DIC), total alkalinity (TA), salinity, and nutrient samples were taken from rosette casts with 10L Niskin bottles and analysed at the Institute of Ocean Sciences. Discrete samples of dissolved oxygen were also collected and analysed onboard the vessel. CTD profiles were recorded with each rosette cast. DIC and TA samples were placed in cold storage for 1-4 weeks before analysis. A total of 61 DIC and TA pairs were sampled with a 22 percent replication rate. Replicates are not averaged in this dataset and appear individually, indicated by decimal sample ID's (e.g. 26.1, 26.2). The pooled standard deviations (of difference between replicate pairs) were calculated to be 6 umol/kg and 5 umol/kg respectively. Replicates with a QC flag = 3 were included in the pooled standard deviation calculation but replicate pairs with at least one QC flag = 4 (n = 1) were excluded.
DOI: 10.5281/zenodo.17710891
title: PAR(2) Framework for Crypt Homeostasis

description: This archive contains the Python source code and discovery results for the Phase-Gated Order-2 Autoregressive (PAR(2)) model. The code reproduces the key finding that the Ccnd1 (Cyclin D1) renewal hazard is significantly phase-gated by the Per2 circadian clock (P-values: 0.0012, 0.0048). The underlying AR(2) structure is confirmed to capture the Fibonacci-based geometry of the crypt.
DOI: 10.5281/zenodo.17710892
title: PAR(2) Framework for Crypt Homeostasis

description: This archive contains the Python source code and discovery results for the Phase-Gated Order-2 Autoregressive (PAR(2)) model. The code reproduces the key finding that the Ccnd1 (Cyclin D1) renewal hazard is significantly phase-gated by the Per2 circadian clock (P-values: 0.0012, 0.0048). The underlying AR(2) structure is confirmed to capture the Fibonacci-based geometry of the crypt.
DOI: 10.25921/fa4v-fj79
title: Dissolved inorganic carbon (DIC), total alkalinity, water temperature, salinity, dissolved oxygen, nutrients, and other measurements collected from profile and discrete sample observations during the R/V Hans Brattstrøm cruise (EXPOCODE 58HB20201110) in the Norwegian Sea, North Atlantic Ocean from 2020-11-10 to 2021-11-16 (NCEI Accession 0253701)

description: This dataset includes discrete profile measurements of dissolved inorganic carbon (DIC), total alkalinity, water temperature, salinity, dissolved oxygen, nutrients, and other measurements collected during the R/V Hans Brattstrøm cruise (EXPOCODE 58HB20201110) in the Norwegian Sea, North Atlantic Ocean from 2020-11-10 to 2021-11-16.
DOI: 10.25921/zp3g-cm29
title: Dissolved inorganic carbon (DIC), total alkalinity, water temperature, salinity, dissolved oxygen, phosphate, silicate, nitrate, nitrite, dissolved organic carbon (DOC), chlorofluorocarbons (CFC-11, CFC-12) and other measurements collected from profile and discrete sample observations during the R/V Pelagia GEOTRACES cruise PE319 (EXPOCODE 64PE20100428) in the North Atlantic Ocean from 2010-04-28 to 2010-05-26 (NCEI Accession 0253809)

description: This dataset includes discrete profile measurements of dissolved inorganic carbon (DIC), total alkalinity, water temperature, salinity, dissolved oxygen, phosphate, silicate, nitrate, nitrite, dissolved organic carbon (DOC), chlorofluorocarbons (CFC-11, CFC-12) and other measurements collected during the R/V Pelagia GEOTRACES cruise PE319 (EXPOCODE 64PE20100428) in the North Atlantic Ocean from 2010-04-28 to 2010-05-26.
DOI: 10.25921/cj9s-fy87
title: Dissolved inorganic carbon (DIC), total alkalinity, water temperature, salinity, dissolved oxygen, phosphate, silicate, nitrate, nitrite, dissolved organic carbon (DOC), chlorofluorocarbons (CFC-11, CFC-12) and other measurements collected from profile and discrete sample observations during the R/V Pelagia GEOTRACES cruise PE321 (EXPOCODE 64PE20100611) in the North and Tropical Atlantic Ocean from 2010-06-11 to 2010-07-08 (NCEI Accession 0253811)

description: This dataset includes discrete profile measurements of dissolved inorganic carbon (DIC), total alkalinity, water temperature, salinity, dissolved oxygen, phosphate, silicate, nitrate, nitrite, dissolved organic carbon (DOC), chlorofluorocarbons (CFC-11, CFC-12) and other measurements collected during the R/V Pelagia GEOTRACES cruise PE321 (EXPOCODE 64PE20100611) in the North and Tropical Atlantic Ocean from 2010-06-11 to 2010-07-08.
DOI: 10.25921/n51y-es20
title: Dissolved inorganic carbon (DIC), total alkalinity, water temperature, salinity, dissolved oxygen, phosphate, silicate, nitrate, nitrite and other measurements collected from profile and discrete sample observations during the RRS Discovery GEOTRACES cruise D357 (EXPOCODE 74EQ20101018) in the South Atlantic Ocean from 2010-10-18 to 2010-11-22 (NCEI Accession 0253812)

description: This dataset includes discrete profile measurements of Dissolved inorganic carbon (DIC), total alkalinity, water temperature, salinity, dissolved oxygen, phosphate, silicate, nitrate, nitrite and other measurements collected during the RRS Discovery GEOTRACES cruise D357 (EXPOCODE 74EQ20101018) in the South Atlantic Ocean from 2010-10-18 to 2010-11-22.
DOI: 10.25921/c8rj-ek12
title: Dissolved inorganic carbon (DIC), total alkalinity, pH on total scale, discrete pCO2, chlorofluorocarbons (CFC11, CFC12), dissolved organic carbon (DOC), water temperature, salinity, dissolved oxygen, nutrients and other hydrographic and chemical variables collected from discrete samples and profile observations during the R/V Thomas G. Thompson cruise on GO-SHIP repeat section A20 (EXPOCODE 325020210316) in the North Atlantic Ocean from 2021-03-16 to 2021-04-16 (NCEI Accession 0258957)

description: This dataset includes discrete profile measurements of Dissolved inorganic carbon (DIC), total alkalinity, pH on total scale, discrete pCO2, chlorofluorocarbons (CFC11, CFC12), dissolved organic carbon (DOC), water temperature, salinity, dissolved oxygen, nutrients and other hydrographic and chemical variables collected from discrete samples and profile observations during the R/V Thomas G. Thompson cruise on GO-SHIP repeat section A20 (EXPOCODE 325020210316) in the North Atlantic Ocean from 2021-03-16 to 2021-04-16. GO-SHIP repeat transoceanic surveys (www.goship.org) provide full water column hydrographic observations with temporal and spatial resolutions adequate to resolve decadal variability in oceanic storage of heat, freshwater, carbon, oxygen, nutrients and transient tracers. Repeat hydrographic physical-biogeochemical measurements nominally along 52° 20’N in the North Atlantic Ocean enables scientists to better tackle important unresolved aspects of the Atlantic Ocean’s response to decadal scale variability and increases in both heat and carbon dioxide as a result of anthropogenic activities. The U.S. GO-SHIP A20 2021 hydrographic section revisited this line for the fourth time, with prior transects occurring in 1997, 2003, and 2012.
DOI: 10.6084/m9.figshare.30705524
title: More with Less: An Empirical Study of Turn-Control Strategies for Efficient Coding Agents

description: LLM-powered coding agents, which operate in iterative loops (turns) to solve software engineering tasks, are becoming increasingly powerful. However, their practical deployment is hindered by significant and unpredictable costs. This challenge arises from a combination of factors: quadratically growing token counts with each turn, the high price of state-of-the-art models, the large number of turns required for real-world tasks, and the tendency of agents to take inefficient or unnecessary actions. While existing research focuses on optimizing individual turns, the strategic control of the total number of turns remains an underexplored area for managing agent performance and cost. To address this gap, we conduct a comprehensive empirical study on the SWE-bench benchmark using three state-of-the-art models (Claude 4 Sonnet, Gemini 2.5 Pro, and GPT 4.1). We systematically evaluate the impact of three distinct turn-control strategies: an unrestricted baseline, a fixed-turn limit with reminders, and a novel dynamic-turn strategy that grants extensions on-demand. Our findings first reveal a fundamental trade-off in the unrestricted setting, where no single model excels across performance, cost, and turn efficiency. We then show that a fixed-turn limit, specifically at the 75th percentile of the baseline, serves as a "sweet spot", substantially reducing costs (by 24%-68%) with minimal impact on solve rates. Most significantly, our proposed dynamic-turn strategy consistently outperforms fixed-limit approaches, achieving comparable or better solve rates while further reducing costs by an additional 12%-24% by intelligently allocating resources only to tasks that need them. This work provides the first systematic analysis of turn-control strategies, offering simple yet effective guidelines for developers to balance cost and efficacy. We demonstrate that dynamic resource allocation is a superior, easy-to-implement approach for deploying powerful yet economically viable coding agents.