cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5066/p14uqe4m
title: RNA yield and sequencing data from Exosomal miRNA isolation in white-tailed deer (Odocoileus virginianus) for diagnostic biomarker discovery

description: This study presents the isolation of exosomes and RNA from 20 samples of white-tailed deer serum using a commercially available kit, incorporating optimizations for RNA yield through two elutions and replicate pooling. The RNA yield from each method is reported, with six samples processed using three techniques. Seven samples underwent RNA sequencing, where total RNA was prepared for miRNA analysis using the NEBNext library preparation protocol. Adaptors were ligated to the sRNA ends, and cDNA libraries were generated through PCR enrichment. Sequencing was performed on the Illumina NovaSeq 6000 platform with 50 bp single-end reads. Data analysis involved filtering raw reads, mapping sequences against the white-tailed deer reference genome, and aligning mapped sRNA to miRBase22 for known miRNA structures. Novel miRNA predictions were made using miREvo and mirdeep2. Six samples yielded at least 1 million reads, with a Pearson’s correlation coefficient (⍴) greater than 0.7, while one sample was excluded due to insufficient sequencing depth.
DOI: 10.5066/p13tkwby
title: Greater white-fronted goose Anser albifrons habitat use in Louisiana in winter, 2016-2019 (ver. 2.0, December 2025)

description: Greater White-fronted Geese Anser albifrons breed in Arctic habitats in North America and winter in the California Central Valley, Mexico and southern United States. Louisiana historically provided winter habitat to a large portion of the Greater White-fronted Goose population in North America. We used global positioning system (GPS) neck collars to monitor 78 Greater White-fronted Geese in Louisiana each winter from 2016–2019. Tracking devices were set to record GPS locations every 30 minutes, but fix intervals were occasionally lengthened due to reduced battery voltage. Nominal accuracy of GPS locations was 6 m. We defined a habitat unit as a polygonal feature that had distinct boundaries (e.g., roads, levees, fence rows, tree lines, etc.) with consistent land use. Habitat units were often crop fields but were occasionally wetlands. We visited all used habitat units to record land cover, vegetation height, and water depth to examine winter habitat use. We digitized each used habitat unit and assigned it to one of four regions in Louisiana, which largely reflected broad land use trends: central, coastal, north, and southwest. We also categorized each location by diel period (night, dawn, day, dusk) and hunting season (during or not during). Records in the dataset represent the number of Greater White-fronted Goose locations in each habitat unit according to each recorded covariate. Thus, each habitat unit may appear multiple times in the dataset because Greater-White-fronted Geese used that habitat unit at different times of the day or year.

First release: April 2025

Revised: December 2025 (ver. 2.0)
DOI: 10.5066/p1yeeu3l
title: 2002 Survey of Diamondback Terrapins in the Chesapeake Bay

description: The survey was conducted to assess the distribution of terrapins in the Chesapeake Bay, based on evidence related to nesting. We conducted a survey of the beaches during the nesting season in the summer of 2002. We walked along the shoreline of over 1350 beach segments looking for evidence signifying the presence of terrapins based on nesting activity. These results represent a single-season snapshot of conditions during the surveys and at the locations visited during that season; it should not be assumed that this is representative of terrapin nest locations and numbers today.
DOI: 10.5066/p1rkcvoj
title: Horizon Scan for Vertebrates in Trade

description: This is a dataset summarizing filtering criteria and rapid risk assessments for ~25,000 species undertaken during a data-driven horizon scan of imported fish, amphibians, reptiles, birds, and mammals. The files represented in this dataset are the following:
1) 'species_filtering_metadata_table.xlsx' is the tabular summary of all intake list species names and the reason for inclusion/exclusion.
2) 'review_scores.xlsx' is the tabular summary of taxa expert risk assessment scores for species included after filtering.
These data will be relayed to the U.S. Fish & Wildlife Service for further assessment and prioritization related to import regulation.
DOI: 10.5066/p13rwqzg
title: Data for salinity regressions and total dissolved solids calculations in groundwater in the United States (ver. 1.1, January 2026)

description: Groundwater salinity impacts water quality and limits usability for drinking, irrigation, and industrial purposes where salinity is high. Salinity is a measure of the mass of dissolved salts in a given volume of solution and is closely related to the concentration of Total Dissolved Solids (TDS) as well as the ability of water to conduct electricity, or specific conductance (SC) (McCleskey and others, 2025). The relationship between salinity, TDS, and SC are controlled by the major ion composition of groundwater, or hydrochemical facies. Hydrochemical facies represent the chemical reactions between groundwater and the surrounding geology and correlate with depth (Stackelberg and others, 2025). Thus, understanding the hydrochemical facies and salinity of groundwater is crucial for effective water resource management.

This data release documents groundwater data and calculations (scripted workflow written in Python) that uses the hydrochemical facies of groundwater, in conjunction with measurements of specific conductance, to accurately estimate the salinity of groundwater for the continental United States (CONUS). Additionally, TDS can be calculated several ways. TDS can be measured directly following U.S. Geological Survey (USGS) residual on evaporation method 70300 or by utilizing a summation of constituents (TDSsoc) USGS method 70301. The TDSsoc method sums the concentrations, in milligrams per liter (mg/L) for the following major ion constituents: Ca, Mg, Na, K, Cl, SO4, NO3, CO3, and SiO2. The data sources include dissolved solids data from a brackish groundwater assessment (Qi and others, 2017), produced waters geochemical data, (Blondes and others, 2023), state groundwater-quality data from the Safe Drinking Water Information System (SDWIS) contained within the workflow, and preprocessed groundwater-quality data retrieved from the National Water Quality Portal (WQP), also contained within the workflow.

An additional R script utilizes the output from the Python workflow and cleans, filters, and prepares data for geochemical modeling, ensuring that only high-quality, relevant samples are included for further analysis and facilitates the execution and output handling of PHREEQC and Pitzer calculations. 

First released July 2025
Revised January 2026 (ver. 1.1)
DOI: 10.5066/p134pxap
title: Records of vessel-Florida manatee collision outcomes and empirical boat speeds in Florida waters, 1978 - 2014

description: The dataset contains observational records detailing collisions between boats and Florida manatees (Trichechus manatus latirostris). Data include boat speeds, collision locations, and manatee injury outcomes, and are intended for ecological analysis and conservation purposes.
DOI: 10.5066/p13w8k3y
title: Morphometric and reproductive data from blue catfish (Ictalurus furcatus) collected in tributaries of the Chesapeake Bay, Maryland and Delaware 2020-2022

description: In this study, blue catfish were sampled from tidal reaches of the Chesapeake Bay in Maryland (Nanticoke River, Broad Creek, Marshyhope Creek, and Patuxent River) from March - October and at some sites, during specific times of the year. All fish were analyzed with histology to assess reproductive stage (immature, pre-spawn, and post-spawn) and plasma was collected for multiple endpoints including 17β-estradiol (E2), calcium, and total protein. The histology results showed that the number of vitellogenic, pre-spawn females began to increase in April with the greatest number of individuals observed in May, which gradually declined through July. In males, the greatest number of pre-spawn individuals was observed in April and gradually declined through June. Additionally, female E2 levels showed a trend similar to the histology results, indicating that this plasma endpoint was beneficial for assessing reproductive changes over time. Collectively, these results showed typical spawning patterns observed in blue catfish and future work will need to be done across different watersheds to provide additional data for management purposes.
DOI: 10.5066/p13x6mkt
title: Loss of acclimation response of brook trout acclimated to three thermal regimes for 2-years and then moved to a common colder temperature

description: This dataset contains records of body sizes and critical thermal maximum test results of brook trout reared for 2 years under three different temperature regimes (+0 °C (the average daily water temperature of a nearby long-term study site), as well as +2 °C and +4 °C above that daily average), moved to a common colder temperature (~15 °C), and thermal tolerance measured using a critical thermal maximum test where thermal ramp rate was 2 °C per hour three, seven, 14, 21, 28, and 42 days later.
DOI: 10.5066/p13qb9zb
title: Data for relationships of pyrethroids, amphipods, wetland quality, and land use in Minnesota from 2019-2020

description: We investigated relationships among amphipod abundances (specifically, Gammarus lacustris and Hyalella azteca), land uses, and pyrethroid insecticide contamination in wetlands of Minnesota in years 2019 and 2020. Our study design targeted a large gradient of amphipod abundances and accounted for water quality, hydrology, and habitat metrics that commonly influence invertebrates. We found a significant, negative relationship between pyrethroid concentrations and the abundance of the two amphipod species. Pyrethroids were detected at relatively low concentrations (<2.5 ng/g sediment) in 44% of study wetlands and occurred most frequently in intensively cropped watersheds with low vegetative filter strip coverage. Wetlands on state and federal wildlife reserves had similar occurrence of pyrethroids to croplands.
DOI: 10.5066/p1ohpg2j
title: Summary from posterior distributions of multistate movement model for silver carp in the upper Mississippi River from 2014 to 2021

description: This data contains the mean and standard deviations for movement rates for silver carp in the upper Mississippi River 2014 and 2021. The data are summaries of the posterior distribution from a Bayesian multistate model described in Stanton et al. 2024 (https://doi.org/10.7717/peerj.17834).

References:

Stanton JC, Brey MK, Coulter AA, Stewart DR, Knights B. 2024. Bayesian multistate models for measuring invasive carp movement and evaluating telemetry array performance. PeerJ 12:e17834 https://doi.org/10.7717/peerj.17834
DOI: 10.5066/p14qwjf2
title: Upper Mississippi River System Vital Rate Data - Bluegill (Lepomis macrochirus) 2018-2020

description: This dataset includes bluegill age data from five study reaches of the Mississippi River and one study reach from the Illinois River as presented in the manuscript Big River Bluegill: Combining vital rates and long-term monitoring to understand population dynamics in large rivers.

Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
DOI: 10.5066/p1hh3x5w
title: Application of a prior-based model discrimination framework using synthetic MODFLOW 6 groundwater models

description: A synthetic one-dimensional groundwater flow model was developed using MODFLOW 6 as a test application of the prior-based model discrimination method described in the associated publication (https://doi.org/10.1029/2025WR040323). The model represents a steady-state unconfined aquifer where water flows horizontally between two constant head boundaries (a lake at the lefthand side and river at the righthand side) and precipitation recharges the aquifer. Process module uncertainty is considered in the representations of groundwater recharge, geologic structure, and snowmelt that controls the river stage constant head boundary. Two process modules are considered to represent each of the three uncertain system processes. This yielded eight candidate configurations of the groundwater model. This USGS data release contains all of the input and output files and ancillary Python scripts for the simulations and results described in the associated publication (https://doi.org/10.1029/2025WR040323).
DOI: 10.5066/p1gpwgbv
title: Impacts of bird predation on the detection of acoustic telemetry tags in fish

description: Note: this data release has been superseded by version 2.0, available here: https://doi.org/10.5066/P14P7RT6.

This data release contains the methodology and results of two field experiments performed in 2024 to better understand how predation impacts detection efficiency of acoustic tags. The first experiment was a static approach focusing on how different tag types, tag power, depth distance to passive receivers, and predation would affect detection efficiency. It utilized both tagged yellow perch (Perca flavescens) as well as double-crested cormorants (Phalacrocorax auritus) that had "consumed" a tagged yellow perch. The second experiment was designed to simulate cormorant diving activity and determined how that behavior and tags with different nominal signal delays affected detection efficiency.
DOI: 10.5066/p1qzvlju
title: Towards an integrated theory of body size distributions, life history and functional traits, and environmental flows in freshwater ecosystems

description: Efforts to quantify and explain individual size distributions (ISD) are prominent in ecological research and potentially for applications to management which increasingly consider ecosystem-scale objectives. We use a nation-wide database of individual size measurements for United States stream fishes paired with species’ traits and test for direct and indirect effects of traits, flow, and land use on the slope of the interspecific ISD. Modeling results show that traits have strong, direct effects on ISD whereas flow and land use primarily indirectly affect ISD via mediation by functional traits. ISDs flatten (i.e., greater abundances of larger-bodied individuals) when environmental conditions favor higher trophic levels, thermal tolerances, and periodic life histories, but steepen (i.e., greater abundances of smaller-bodied individuals) when environments benefit opportunistic life histories. Our framework that incorporates direct and indirect of traits, flow alteration, and land-use on ISD could be expanded to incorporate additional variables that interact with flow regimes (e.g., temperature, physical habitat) to understand and predict how multiple environmental stressors affect ecosystem functions.
DOI: 10.5066/p1qgvhs5
title: Data for Analysis of Factors Affecting Success of Dorsally Mounted Trackers in 37 Species of Shorebirds

description: This dataset includes details of 2,745 tracking devices (hereafter "trackers") deployed on shorebirds, including traits of the tags, traits of the shorebirds, and locations of the field sites. The dataset was used in the accompanying paper to evaluate how factors affected "success" of each tag package (tracker + attachment to the bird), where "success" was defined as whether the tag package reached its expected tracking duration. Failure could have been caused by several factors relating to the tracker, its attachment, and the bird's survival and site fidelity. See Weiser et al. (2025) for further details on how the data were collected and used.
DOI: 10.5066/p1pszzs3
title: Diet, morphometric and demographic data for cisco (Coregonus artedi) collected in the winter and spring of 2022-2023 in Lake Michigan and connected waters

description: These data describe demographic, diet contents and associated weights, fullness index, morphometrics (body shape), and meristic (total number of gill rakers) measurements of cisco (Coregonus artedi) collected in Lake Michigan along the eastern shoreline, the Pine River/ Lake Charlevoix Channel, and from three drowned river mouth lakes (Portage Lake, Muskegon Lake, Lake Charlevoix) from May 2021 - April 2023.
DOI: 10.5066/p139etsk
title: 2022-2023 Phragmites australis Cut-to-drown Field Experiment Data in the Great Lakes Region

description: This dataset represents field data from a multi-year experiment testing the cut-to-drown management strategy in patches of Phragmites australis at two sites in the Great Lakes coastal zone. We established research plots where Phragmites was cut under the water to test that treatment's effectiveness as a control strategy. The experiment took place in 2022 and 2023. Over the multi-year study, we assessed effectiveness by collecting stem densities, rhizome carbohydrates, and viability of rhizome fragments to produce new stems. This dataset includes all field data collected to analyze treatment effectiveness at our sites.
DOI: 10.5066/p1492cka
title: Quantification of event sediment dynamics from 2007 to 2023 for statistical analyses and Machine Learning application in the Delaware and Illinois River Basins

description: This Data Release contains four child items that represent sequential data processing and modeling steps. {Child Item 1} Data Preparation contains data inputs and processing steps for select sites in the Delaware and Illinois River Basins (DRB/IRB). This child item includes five sub folders: site info, streamflow and turbidity time-series, climatological information, basin shape statistics, and basin characteristics and attributes. {Child Item 2} Streamflow Event Delineation and Analysis contains scripts that process data from Child Item 1 to delineate hydrological events, calculates hysteresis indices among other variables, generate hysteresis loops, hydrographs, and climographs, and produce event summary files classifying events into 5, 7, or 9 Hysteresis Index - Concentration Index (HI-CI) classes. {Child Item 3} Statistical Analysis contains Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA) scripts to analyze regional and event variables related to hysteresis. {Child Item 4} Machine Learning Application contains machine learning scripts using XGBoost classification models to train and test prediction of 5, 7, or 9 HI-CI classes.
DOI: 10.5066/p14mbbrm
title: Landsat 8-9 Operational Land Imager (OLI) Level 2 Provisional Aquatic Reflectance Products, Collection 2 

description: The U.S. Geological Survey (USGS) provides Level-2 Provisional Aquatic Reflectance (AR) Products through EROS Science Processing Architecture (ESPA) On-Demand Interface for the Collection 2 Landsat 8-9 archive. This dataset includes n=742 provisional AR products for the visible and near-infrared (VNIR) bands for the Operational Land Imager (OLI) sensor at 30 meters resolution coincident with same-day in situ radiometric measurements from coastal validation platforms (AERONET-OC) and community driven records (GLORIA). This dataset is intended to be used as a reference during future Collection reprocessing events and to track any algorithmic changes to the provisional aquatic reflectance image processing pipeline.
DOI: 10.15468/dl.mpx7fq
title: Occurrence Download

description: A dataset containing 2097 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pseudechinolaena polystachya",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 2097 records from 161 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000224-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17423336
title: QA Dataset for SaaS Editorial Content

description: This public repository contains the question-answering (QA) dataset we created for the research work that we submit for review at International Journal of Artificial Intelligence (IJ-AI). The research work is titled "From fixed-size to structure-aware: evaluating document chunking approaches for retrieval-augmented generation in SaaS editorial content", by LAVAREC and DU. The dataset contains 2,419 QA pairs in SaaS editorial content, suitable for evaluating large language models (LLMs).
description: Retrieval-augmented generation systems promise grounded answers from large language models (LLM), yet performance depends critically on how source documents are segmented before indexing. This study investigates how pre-index chunking strategies affect both retrieval accuracy and answer quality in domain-specific scenarios. We curated a corpus of software-as-a-service editorial content and constructed a high-quality evaluation dataset containing 2,419 question-answer pairs generated through automated prompting and quality control. We compared four chunking approaches including fixed-size, structure-aware recursive, semantic, and LLM-based methods. Our evaluation protocol assessed retrieval through document localization, semantic similarity, and context relevance, while generation quality was evaluated using chain-of-thought criteria driven by LLM judges. Results demonstrate that recursive chunking consistently outperforms other approaches across all metrics. Smaller chunks improve document localization, while moderately larger chunks enhance semantic alignment and generation scores. LLM-based chunking variants show competitive performance but do not exceed top recursive configurations on the dataset. These findings indicate that preserving document structure through recursive chunking is beneficial for practical RAG implementations, providing actionable guidance for chunk size selection while highlighting token budget constraints in current long-context models.
DOI: 10.5281/zenodo.17423337
title: QA Dataset for SaaS Editorial Content

description: This public repository contains the question-answering (QA) dataset we created for the research work that we submit for review at International Journal of Artificial Intelligence (IJ-AI). The research work is titled "From fixed-size to structure-aware: evaluating document chunking approaches for retrieval-augmented generation in SaaS editorial content", by LAVAREC and DU. The dataset contains 2,419 QA pairs in SaaS editorial content, suitable for evaluating large language models (LLMs).
description: Retrieval-augmented generation systems promise grounded answers from large language models (LLM), yet performance depends critically on how source documents are segmented before indexing. This study investigates how pre-index chunking strategies affect both retrieval accuracy and answer quality in domain-specific scenarios. We curated a corpus of software-as-a-service editorial content and constructed a high-quality evaluation dataset containing 2,419 question-answer pairs generated through automated prompting and quality control. We compared four chunking approaches including fixed-size, structure-aware recursive, semantic, and LLM-based methods. Our evaluation protocol assessed retrieval through document localization, semantic similarity, and context relevance, while generation quality was evaluated using chain-of-thought criteria driven by LLM judges. Results demonstrate that recursive chunking consistently outperforms other approaches across all metrics. Smaller chunks improve document localization, while moderately larger chunks enhance semantic alignment and generation scores. LLM-based chunking variants show competitive performance but do not exceed top recursive configurations on the dataset. These findings indicate that preserving document structure through recursive chunking is beneficial for practical RAG implementations, providing actionable guidance for chunk size selection while highlighting token budget constraints in current long-context models.