cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.x3ffbg7vc
title: Data from: A genetic polymorphism underlying alternative reproductive tactics in Eurycea salamanders

description: Alternative reproductive tactics are discrete, intrasexual differences in
 reproductive behavior within a population. In some cases,  these
 complex phenotypes are determined by autosomal supergenes or sex
 chromosomes—both of which exhibit reduced recombination and thus enable
 the linked inheritance of co-adapted alleles from multiple loci. Most
 alternative reproductive tactics in amphibians are plastic (and
 reversible), environmentally determined, and lacking morphological
 differentiation, but a striking exception is found in the two-lined
 salamander (Eurycea bislineata) species complex. In some populations, two
 distinct male phenotypes coexist: “searching” males have mental glands,
 protruding premaxillary teeth, and elongate cirri used in terrestrial
 courtship, while “guarding” males lack these traits and instead have
 hypertrophied jaw musculature used in mate-guarding at aquatic nesting
 sites. These tactics differ in many morphological and behavioral
 phenotypes, but their proximate cause has not yet been described. Here, we
 generated genome-wide SNP data from &gt;130 Eurycea cf. wilderae
 collected from Highlands Biological Station. We provide evidence for a XY
 sex determination and for a Y-linked polymorphism underlying alternative
 reproductive tactics in this population. We then develop and validate a
 PCR-based genotyping assay and apply this to characterize the sex ratio
 and relative frequency of tactics from a sample of larvae. Our results add
 to the growing body of literature exploring the importance of supergenes
 and sex chromosomes in complex intraspecific polymorphisms, and we
 highlight opportunities for future work to continue exploring the genomic
 architecture of these traits.
description: # A genetic polymorphism underlying alternative reproductive tactics in
 Eurycea salamanders
 [https://doi.org/10.5061/dryad.x3ffbg7vc](https://doi.org/10.5061/dryad.x3ffbg7vc) ## Description of the data and file structure To study alternative reproductive tactics, we generated genome-wide SNP data from 2RAD library preparations for &gt;130 *Eurycea *cf. *wilderae *collected from Highlands Biological Station. We conducted analyses to identify sex-linked and tactic-linked markers, estimate genome-wide genetic differentiation, and (from a genotyping assay) evaluate sex ratios and relative frequencies of alternative reproductive tactics.  ### Files and variables #### File: Kalki\_Pierson\_metadata.csv **Description:** Metadata (i.e., sex and male tactic) for all samples. ##### Variables * sample: Sample name, matching VCF file. * sex_tactic: Sex and/or tactic (options = female, searching, guarding) * sex: Sex (options = female, male) #### File: highlands\_final.vcf **Description:** VCF output file from ipyrad assembly of 2RAD data. ## Code/software We include an R script to replicate all analyses in our manuscript.
DOI: 10.15468/dl.frv3cp
title: Occurrence Download

description: A dataset containing 1405 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Computarización de la colección de moluscos holoplanctónicos del Golfo de California y Golfo de Tehuantepec"
 ]
}

 The dataset includes 1405 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004160-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/ypsd84
title: Colisión de aves contra ventanas en Costa Rica

description: Este dataset contiene registros de aves que han colisionado contra ventanas o puertas de vidrio en Costa Rica, recogidos mediante ciencia ciudadana, aportes de biólogos y museos. Incluye datos de especie, fecha, localización (coordenadas), estado vital (vivo/muerto), residencia (residente/migratorio) y otras observaciones (por ejemplo fotos, observador). Los datos abarcan múltiples años y provienen de diferentes regiones del país, con la intención de documentar y analizar la incidencia de colisiones de aves contra ventanas.
DOI: 10.5281/zenodo.18293098
title: Functional Calmodulin States are Selected from an Electrostatically Tuned Free Energy Landscape

description: Contents





Conventional MD trajectories: Duplicate 1 μs conventional molecular dynamics (cMD) simulations for all systems.




Metadynamics output files: PMF files and collective variable trajectory files used to reconstruct the free-energy surfaces of calmodulin under different ionic strength and calcium-binding conditions.




Conformer-based analyses: Unbiased cMD simulations initiated from conformers selected from metadynamics free-energy minima, together with the corresponding analysis outputs, including:





Dihedral–distance analysis files




Salt-bridge analysis files




Radial distribution function (RDF) analysis files




Associated trajectory files
DOI: 10.5281/zenodo.18293097
title: Functional Calmodulin States are Selected from an Electrostatically Tuned Free Energy Landscape

description: Contents





Conventional MD trajectories: Duplicate 1 μs conventional molecular dynamics (cMD) simulations for all systems.




Metadynamics output files: PMF files and collective variable trajectory files used to reconstruct the free-energy surfaces of calmodulin under different ionic strength and calcium-binding conditions.




Conformer-based analyses: Unbiased cMD simulations initiated from conformers selected from metadynamics free-energy minima, together with the corresponding analysis outputs, including:





Dihedral–distance analysis files




Salt-bridge analysis files




Radial distribution function (RDF) analysis files




Associated trajectory files
DOI: 10.5061/dryad.pk0p2ngz8
title: AERPAW helikite spectrum measurements at Lake Wheeler site in August 2024

description: This dataset captures spectrum measurements collected during the AERPAW
 helikite flight at Lake Wheeler in August 2024. The helikite ascended to
 an altitude of 300 m, maintained this altitude for approximately six
 hours, and then descended. Using the USRP B205mini, continuous spectrum
 sweeps up to 6 GHz were performed, with power measurements logged across
 various frequency bands. The dataset includes post-processed results using
 Matlab, focusing on spectrum occupancy across different bands and
 examining the impact of altitude on spectrum sensing outcomes.ele
description: # Dataset README Spectrum monitoring dataset by a helikite in a rural
 area, which is measured by AERPAW. The dataset is formatted by
 SigMF. Please find instructions in the readme. MATLAB post-processing code
 for the dataset is attached. ## Contents 1. **SigMF formatted power
 spectrum raw dataset**: Located in the folder `pow_spec`. 2. **SigMF
 formatted GPS logs**: Located in the folder `GPS_logs`. 3. **SigMF
 formatted spectrum monitoring logs**: Located in the folder `GPS_logs`. 4.
 **SigMF to MATLAB format conversion Python code**: The script
 `sigMF2mat_PW.py` converts SigMF formatted power spectrum data to MATLAB
 format. 5. **SigMF to CSV format conversion Python code**: The script
 `sigMF2csv_GPS.py` converts SigMF formatted GPS logs to CSV format. ##
 Running the Code 1. Run `sigMF2mat_PW.py` to convert the power spectrum
 data into MATLAB format. The output files will be saved in the folder
 `./pow_spec/matfile`. 2. Run `sigMF2csv_GPS.py` to convert the GPS logs
 into CSV format. The output files will be saved in the folder
 `./GPS_logs/csvfile`. ## Raw Data Description 1. **Power Spectrum**: Each
 MATLAB file contains `freqs` (in MHz) and `powers` (in dBm). The filenames
 correspond to timestamps representing the data collection time. 2. **GPS
 Logs**: The generated CSV files contain four columns: * Column 1:
 Longitude * Column 2: Latitude * Column 3: Altitude (in meters) * Column
 4: Timestamp (seconds since epoch time) 3. **Spectrum Monitoring Logs**:
 The generated CSV file contains a single column representing the
 timestamps of center frequency shifts during spectrum sweeps. ## SigMF
 Format This dataset is compliant with **SigMF v1.2** standards.\ More
 information on SigMF can be found here: [SigMF v1.x
 Documentation](https://github.com/gnuradio/SigMF/). ## MATLAB
 Post-Processing After converting the power spectrum data to MATLAB format
 and the logs to CSV format, run the `Post_processing_main.m` script to
 analyze the dataset.
DOI: 10.5061/dryad.pvmcvdnvw
title: Data from: Wood jam characteristics influence but do not fully explain wood jam morphologic functions

description: In-stream wood jams alter their surrounding channel morphology, thus
 setting riverscape morphology and ecosystem function. While wood jams
 clearly scour pools, retain sediment, and influence bank erosion, there is
 a lack of observational evidence of how wood jam characteristics
 themselves control morphologic effects. Here, I analyzed field
 observations of hundreds of wood jams to test the hypothesis that wood jam
 characteristics can predict local morphologic effects such as sediment
 retention, bar forcing, and pool scour. I found mixed support for this
 hypothesis: while jam characteristics such as porosity, channel blockage
 ratio, thalweg occupation, and having rootwads and multiple trunks
 significantly predicted morphologic effect occurrence and magnitude, they
 only explained a small portion of the variance in those morphologic
 effects. While wood jam characteristics are relevant in controlling their
 overall morphologic functions, those functions are both inherently
 variable and likely affected by numerous other factors, such as
 reach-scale topography, the sediment transport capacity to supply ratio,
 and interactions with surrounding wood and vegetation. Wood function
 restoration may be more effective if it targets reach-scale objectives
 across dynamic wood jam assemblages, instead of individual jams.
description: ## Data from: Wood jam characteristics influence but do not fully explain
 wood jam morphologic functions This dataset describes wood jam
 characteristics and morphologic effects across 6 study sites in the
 western United States. ## Description of the Data and file structure Data
 are shown in the wood_morph_dataset.csv file. Metadata are shown in the
 wood_morph_dataset_metadata.csv. The Metadata describe each variable in
 detail. Missing data are marked as "NA" cells.
DOI: 10.5061/dryad.dbrv15fbq
title: Broadband realtime measurement of optical Einstein–Podolsky–Rosen states using optical parametric amplifiers

description: Entanglement is a key resource for various quantum technologies. Besides
 the purity of entanglement, the available bandwidth also plays a crucial
 role in quantum information processing with light, as it directly
 determines the clock speed of processing. While many efforts have been
 made to enhance the bandwidth of optical entanglement resources, they have
 generally been limited to a few tens of MHz at best. In this work, we
 report the real-time measurement of EPR states over a broad bandwidth of
 60 GHz, achieved using a fast homodyne detection technique supplemented by
 phase-sensitive amplification. The quantum correlation level exceeds 4.5
 dB at its peak, which is sufficient for applications of several quantum
 technologies. This research marks a significant milestone in the
 advancement of high-speed optical quantum information processing.
description: This dataset contains the raw data from the entanglement
 measurement output. Each folder stores the results of two homodyne
 measurements, collected while varying different experimental parameters.
 The homodyne measurements are taken in the x and p quadrature bases for a
 specific experimental parameter. All data are saved in h5
 format.
description: # Broadband realtime measurement of optical Einstein–Podolsky–Rosen states
 using optical parametric oscillators
 [https://doi.org/10.5061/dryad.dbrv15fbq](https://doi.org/10.5061/dryad.dbrv15fbq) ## Description of the data and file structure This dataset contains the raw data from the entanglement measurement output. Each folder stores the results of two homodyne measurements, collected while varying different experimental parameters. The homodyne measurements are taken in the x and p quadrature bases for a specific experimental parameter. All data are saved in the HDF5 (.h5) format. ### Files and variables #### File: bEPR\_for\_dryad.zip **Description:** This file contains  1, 20230807_EPR1_pump1 2, 20230807_EPR2_pump2 3, 20230807_EPR3_loss 4, 20230808_bEPR_circuitnoise 1-3 correspond to the results of experiment where pump1, pump2, loss are the variable parameter, respectively.  4 corresponds to the circuit noise data of homodyne 1 and 2. 1-3 contain subfolders named "^^mW^^mW^^dB" .The first ^^ represents pump1 power, the second represents pump2 power, and the last represents additional loss. Each subfolder contains files named "^^_hd^^.h5".\ The first ^^ has four variations: * "x" represents the result of the x basis measurement in homodyne detection, * "p" represents the result of the p basis measurement, * "shot_before" indicates the shot noise level before the measurement, * "shot_after" indicates the shot noise level after the measurement. The second ^^ represents the identifier of one of the two homodyne detectors.
DOI: 10.5061/dryad.sn02v6xf1
title: Data from: Fatty acid binding protein 7 plays an important modulatory sex-dependent role on brain THC metabolism

description: Fatty acid binding protein 7 (FABP7) is present in the brain, but its
 interaction with the endocannabinoid system and phytocannabinoids is still
 not well understood. FABP7 has been proposed as a shuttle protein for
 trafficking endogenous cannabinoids, as well as an intracellular carrier
 of THC. In a mouse model of FABP7 global deletion, we used ultra-high
 performance liquid chromatography- tandem mass spectrometry (UPLC-MS/MS)
 to measure brain levels of Δ9 tetrahydrocannabinol (THC) as well as its
 primary metabolite, 11-hydroxy-THC (11-OH-THC), in male and female mice
 after acute inhalation of THC, compared to wild-type controls. We also
 measured brain levels of endogenous cannabinoids anandamide (AEA) and
 2-arachidonoylglycerol (2-AG) both at baseline and after acute THC
 inhalation. We found that in females, brain concentrations of 11-OH-THC
 were significantly reduced in FABP7-/- mice compared to FABP7+/+.
 Additionally, FABP7-/- females had significantly reduced AEA levels and
 significantly increased 2-AG levels in brain tissue compared to FABP7+/+.
 Vaporized THC administration had trending, but not significant, impacts on
 endocannabinoid concentrations in both males and females. Our findings
 suggest a sex-specific role of FABP7 in the metabolism of THC as well as
 the regulation of endocannabinoid levels in the brain.
description: # Fatty acid binding protein 7 plays an important modulatory sex-dependent
 role on brain THC metabolism
 [https://doi.org/10.5061/dryad.sn02v6xf1](https://doi.org/10.5061/dryad.sn02v6xf1) ## Description of the data and file structure Mice were administered (inhaled) vaporized THC (20 mg) for 10 minutes. 15 minutes post-inhalation, animals were euthanized and brains were harvested, flash frozen, and stored at -80 °C until analysis. Homogenized brain tissue was analyzed using HPLC-MS/MS for 9THC and metabolites 11OHTHC and 11COOHTHC, and normalized to bodyweight as weight significantly varied across genotype and sex. ### Files and variables #### File: PONE-D-24-27112R1\_SuppData.xlsx **Description:** Excel file including the following info for each subject: Sex (0-male, 1-female), genotype, bodyweight, 9THC brain concentration, 11OHTHC brain concentration, 11COOHTHC brain concentration. All concentrations are ng/gram brain tissue/kg bodyweight for each ID. ##### Variables * Sex * Genotype **Abbreviations** * g: gram (unit of body weight) * ng/g/kg: nanogram of analyte/gram brain tissue/kilogram bodyweight (unit of metabolite concentration) * 9THC: delta-9-tetrahydrocannabinol * 11OHTHC: 11-hydroxy-THC * 11COOHTHC: 11-carboxy-THC * BLLOQ: below lower limit of quantification ## Code/software Excel software is needed to view the file.
DOI: 10.5061/dryad.3tx95x6rh
title: Prenatal treatment with the antidepressant fluoxetine on maternal and neonatal behavior in sheep

description: Background: Fluoxetine is commonly prescribed to treat depression during
 pregnancy. We aimed to evaluate the effects of prenatal fluoxetine
 exposure on maternal-offspring behavior in a non-depressed sheep model.
 Methods: On day 119 ± 1 of a 151-day expected gestation, Hampshire ewes
 were randomly assigned to receive intravenous fluoxetine (10 mg/kg for the
 first two days and 5 mg/kg daily thereafter until parturition) or a
 control vehicle. Video was recorded of 8 fluoxetine-treated ewes and 10
 control ewes for 2 hours before and after parturition. Results: Fluoxetine
 did not alter dam behavior during the peripartum period, including time
 spent lying before the first birth, lying bout duration, probability of
 needing birth assistance, duration of birth assistance when provided, and
 time spent touching her lambs. However, in utero exposure impaired
 neonatal vigor as lambs spent less time standing and tended to spend less
 time nursing compared to unexposed lambs. Conclusion: Neonatal behavioral
 impairments are consistent with those associated with fluoxetine exposure
 during human gestation. This effect appears to be independent of maternal
 behavior, which was unaffected by antidepressant use.
description: # Prenatal treatment with the antidepressant fluoxetine on maternal and
 neonatal behavior in sheep
 [https://doi.org/10.5061/dryad.3tx95x6rh](https://doi.org/10.5061/dryad.3tx95x6rh) ## Description of the data and file structure These materials provide the data and R script used in this experiment and are referenced in the corresponding paper by the same name. Domingues_etal_SSRI Behavior Data_241011.xlsx: Excel file containing the behavioral data for ewes and lambs during the peripartum period. The second sheet contains descriptions of each column variable. Domingues_etal_SSRI Behavior Data Analysis_241011.nb.html: R script runs the statistical analyses on the data in the Excel file and generates Figure 1 in the corresponding paper. The nb.html file, which includes annotated code and output, can be opened in any web browser or in RStudio (e.g., using File -&gt; Open File).
DOI: 10.6084/m9.figshare.28873565.v2
title: S1 Cover letter

description: Cover Letter
DOI: 10.5066/p138uuwv
title: Model Archive Summary for Suspended-Sediment Concentration at station 06329500, Yellowstone River near Sidney, Montana, 2017-2021

description: This model archive summary (MAS) and associated model calibration dataset documents the suspended-sediment concentration (SSC) model developed to compute 15-minute, near-real-time SSC at U.S. Geological Survey (USGS) streamgage station 06329500, Yellowstone River near Sidney, Montana (MT) for calendar years 2017-2021. This model is specific to USGS site 06329500, Yellowstone River near Sidney, MT, during this study period and cannot be applied to data collected from other locations on the Yellowstone River or data collected from other water bodies. The methods used follow USGS guidance as referenced in relevant Office of Surface Water (OSW)/Office of Water Quality (OWQ) technical memoranda and USGS techniques and methods, book 3, chapter C4 (Rasmussen and others, 2009).

References:

Rasmussen, P.P., Gray, J.R., Glysson, G.D., and Ziegler, A.C., 2009, Guidelines and procedures for computing time-series suspended-sediment concentrations and loads from in-stream turbidity-sensor and streamflow data: U.S. Geological Survey Techniques and Methods book 3, chap. C4, 53 p., accessed September 2025 at https://pubs.usgs.gov/tm/tm3c4/pdf/TM3C4.pdf
DOI: 10.15468/dl.w8z9m2
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Raneya brasiliensis",
 "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 33 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004161-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17172/nomad/2026.01.28-4
title: NOMAD dataset: EG/Sn(1x1)/SiC heterostructure
DOI: 10.6084/m9.figshare.28873565
title: S1 Cover letter

description: Cover Letter
DOI: 10.6084/m9.figshare.28873565.v4
title: S1 Cover letter

description: Cover Letter
DOI: 10.6084/m9.figshare.28873565.v3
title: S1 Cover letter

description: Cover Letter
DOI: 10.5061/dryad.rjdfn2zn5
title: Demographic rescue falters when pathogens are present

description: As natural populations continue to decline globally, direct forms of
 intervention are increasingly necessary to prevent extinction. One type of
 intervention, known as demographic rescue, occurs when individuals are
 added directly to a population to increase abundance and ultimately
 prevent population extinction. However, the role of infectious disease in
 demographic rescue remains unknown. To examine the effects of pathogens on
 demographic rescue, we used a host-pathogen system with the aquatic
 crustacean Daphnia dentifera as the host and the fungus Metschnikowia
 bicuspidata as the pathogen. We constructed a randomized 3 x 2 factorial
 experiment with three rescue treatments (none, low, high) and two pathogen
 treatments (unexposed, exposed), where the pathogen was introduced via
 infected individuals during rescue events. We found that adding more
 individuals to demographically depressed populations increased abundance
 over the short term; highly supplemented populations initially had 62%
 more individuals than populations that had no introduced individuals.
 However, by the end of the experiment, populations that did not have any
 individuals introduced averaged 640% higher abundance than populations
 where infected individuals had been added. Thus, the introduction of
 infected individuals can result in worse demographic outcomes for
 populations than if no rescue is attempted.
description: # Demographic rescue falters when pathogens are present Each of the below
 is a column heading and its description, grouped by Experimental details
 and Response variables. #### Experimental Details: week = week in which
 sampling occurred (where 1 = 7 days after the beginning of the experiment,
 2 = 14 days after the beginning of the experiment, etc.) beaker.id =
 unique identifier for each replicate beaker (population) block = the block
 (timing) of a beaker (two blocks total) beaker.num = a randomly generated
 value for the order in which beakers were sampled each week treat.id = an
 indicator of the combined pathogen + rescue treatment. A = unexposed, no
 rescue, B = unexposed, low rescue, C = unexposed, high rescue, D =
 pathogen-exposed, no rescue, E = pathogen-exposed, low rescue, F =
 pathogen-exposed, high rescue metsch.treat = pathogen (*Metschnikowia
 bicuspidata*) treatment. UN = unexposed to the pathogen. INF = exposed to
 the pathogen sup.treat = rescue (supplementation) treatment: none, low or
 high #### Response Variables Values are the number of individuals in each
 category found in the 55mL subsample of the population on a given sampling
 day. ad.female = adult female juv.female = juvenile female ad.male = adult
 male juv.male = juvenile male ad.inf.female = infected adult female
 juv.inf.female = infected juvenile female ad.inf.male = infected adult
 male juv.inf. male = infected juvenile male