cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mw6m90627
title: Data for: The buzzOmeter system: In situ audio recordings of pollinators in flight

description: The role of sounds produced by free-flying insects is challenging to
 research due to technical difficulties in obtaining audio recordings
 suitable for playback experiments. Experimental studies using flight
 sounds are needed to understand if buzzes carry information and by whom it
 is perceived. We developed the ‘buzzOmeter system’ for recording
 untethered, flying insects in their habitat, followed by file processing
 that allows precise measurements of acoustic parameters, including those
 dependent on the distance of the sound source from the microphone, i.e.
 signal magnitude measurements. The system consists of commercially
 available elements and open-source software. We provide a practical guide
 for the assembly and use of two alternative setups of the buzzOmeter
 system, followed by a video tutorial on file processing and an R script
 for the assignment of audio recordings to the corresponding species based
 on mixture discriminant analysis. Recordings of nine insect species (bees,
 wasps and lepidopterans) obtained with the use of our system in various
 habitats demonstrate its feasibility for field studies. Diverse species
 interactions are based on sound, and our new tool can aid researchers
 studying acoustical signalling in predator-prey, pollinator-plant and
 mimic-model complexes, among others.
description: The audio recordings were obtained with the use of the buzzOmeter
 system (Volponi P, Dapporto L & Skowron Volponi M, 2023). Audio
 fragments for analysis (units) were selected and filtered in DaVinci
 Resolve and Praat software. Data were analysed in R.
DOI: 10.5061/dryad.wpzgmsbsm
title: Adult presence does not ameliorate juvenile feeding challenges in a leaf-footed bug

description: Herbivores often grapple with structural defenses in their host plants,
 which may pose especially difficult challenges for juveniles due to their
 underdeveloped feeding morphology. The degree to which juvenile herbivore
 survival is limited by structural defenses as well as the strategies used
 to overcome them are not well understood. We hypothesized that juveniles
 benefit from feeding near adults because adults pierce through physical
 barriers while feeding, enabling juveniles to access nutrients that they
 otherwise could not. We tested this feeding facilitation hypothesis in the
 leaf-footed bug Leptoglossus zonatus (Hemiptera: Coreidae). Bugs were
 raised with an adult or a juvenile conspecific and fed a diet of pecans
 with or without shells. As predicted, we found that juveniles suffered
 greater mortality when fed nuts with shells than when fed nuts without
 shells. Contrary to our expectations, the presence of an adult feeding on
 the same nut did not lessen this effect. Therefore, the presence of an
 adult does not ameliorate the feeding difficulties faced by juvenile L.
 zonatus, despite evidence for feeding facilitation in related insect
 species. This study adds to our understanding of how host plant defenses
 can limit the survival of even highly generalist herbivores.
DOI: 10.5061/dryad.z612jm6h6
title: Supporting data for: Development of alternate climate divisions for Colorado based on gridded data

description: The official climate divisions for the contiguous United States are used
 for a wide range of purposes, including ongoing climate monitoring, and
 through NOAA's long-standing nClimDiv dataset. In Colorado, the
 climate divisions are based around the basins of the large rivers that
 flow out of the state. However, considering the complex topography and
 climate of the state, these divisions do not always represent key climate
 variations and changes. This study builds upon an approach first developed
 by Wolter and Allured to establish alternate climate divisions that more
 closely reflect observed climate variability across Colorado. Hierarchical
 cluster analysis is applied to gridded temperature and precipitation data
 (NOAA's nClimGrid) from 1950–2021 to identify areas with similar
 climate variability, then manual inspection is used to establish 11
 divisions. These resulting divisions are being used in an updated
 state-level climate change assessment. The method is flexible and uses
 open-source tools that could be extended to other regions or datasets.
description: Because NOAA's nClimGrid data sometimes changes
 retrospectively (owing to late-arriving observations, etc.), the version
 of the data used for the cluster analysis (obtained in April 2022) is
 provided here.
description: # Supporting data for "Development of alternate climate divisions for
 Colorado based on gridded data"
 NOAA's nClimGrid
 monthly temperature and precipitation dataset, originally obtained from
 [NOAA](https://www.ncei.noaa.gov/thredds/catalog/data-in-development/nclimgrid/catalog.html) in April 2022 and spatially subset to Colorado. ## Description of the data and file structure Two files are provided, the monthly average temperature and the monthly average precipitation, from 1895-2021 over Colorado. File format is netCDF; data are on a latitude/longitude grid with approximately 4-km horizontal grid spacing. ## Sharing/Access information Data was derived from
DOI: 10.6078/d1ch98
title: Replication data for impact evaluation of two large-scale forestry incentive programs in Guatemala

description: This study evaluates the impacts of over 16,000 individual PES projects
 funded through two incentive programs in Guatemala using synthetic
 controls to understand the impacts and trade-offs of large-scale forest
 conservation and tree planting programs. Data for the impact estimation
 was extracted from remotely sensed or modeled datasets, with datasets on
 forest extent, height, and loss extending from 2000 to 2020. Projects
 evaluated in this study were enrolled in incentives on a rolling basis,
 beginning in 2010, with most projects ending by 2018. Program impacts were
 estimated by comparing changes in forest cover, forest height and forest
 loss after treatment between the synthetic control and treated units.
description: Initial data on project
 location was collected from the Guatemalan Forestry Institute GIS portal
 https://sig.inab.gob.gt/portal/home/gallery.html. Project sites were
 accessed as point location data, and we estimate the area of each project
 site using available metadata. To generate a valid control, we randomly
 generated 100,000 untreated 3.1 hectare sites. Relevant data on forest
 cover and covariates such as population, accessibility to towns,
 elevation, and rainfall was accessed and extracted from gridded datasets
 for each treated and untreated site. We accessed these gridded datasets
 via Google Earth Engine where possible, but also downloaded the raw data
 from the source (info on specific dataset access in README file). The
 extracted data were combined into a panel dataset, which was cleaned
 before untreated sites were weighted to create the synthetic control. We
 provide initial raster files in .tif format and treated and untreated
 polygons as .shp files. Extracted tables, before they were combined into a
 panel dataset, is stored in .csv files. Final panel datasets for untreated
 and treated sites are also stored as .csv files. Outputs of the analysis
 are provided as .Rdata files, and we provide the scripts that combine and
 analyze the data.
description: Much of our unprocessed data is stored in .tif and shapefile
 formats. We extracted this data to .csv tables using ArcPro, a proprietary
 software, however the data format is open sources and there are many open
 source options for visualizing and processing this data, including QGIS, R
 (sf & terra packages), and Python (geopandas & fiona
 packages).  Tables in this analysis are all stored in
 .csv format, and we generally use R to clean, combine, and analyze these
 files. We use python via jupyter notbooks in one instance because the
 geopandas and matplotlib packages are useful for producing figures with
 spatial datasets. Our results files (synthetic control results) are stored
 in .Rdata files, which can be read into R using the load()
 function.
DOI: 10.5061/dryad.0p2ngf25s
title: Multispecies coinfections and presence of antibiotics shape resistance and fitness costs in a pathogenic bacterium

description: Increasing antimicrobial resistance (AMR) poses a challenge for treatment
 of bacterial diseases. In real life, bacterial infections are typically
 embedded within complex multispecies communities and influenced by the
 environment, which can shape costs and benefits of AMR. However, knowledge
 of such interactions and their implications for AMR in vivo is limited. To
 address this knowledge gap, we investigated fitness-related traits of a
 pathogenic bacterium (Flavobacterium columnare) in its fish host,
 capturing the effects of bacterial antibiotic resistance, multispecies
 coinfections (metazoan fluke Diplostomum pseudospathaceum), and antibiotic
 exposure. We quantified real-time replication and virulence of sensitive
 and resistant bacteria and demonstrate that both bacteria can benefit from
 coinfection in terms of persistence and replication, depending on the
 coinfecting partner and antibiotic presence. We also show that antibiotics
 can benefit resistant bacteria by increasing bacterial replication under
 coinfection with flukes. These results emphasize the importance of
 diverse, inter-kingdom coinfection interactions and antibiotic exposure in
 shaping costs and benefits of AMR, supporting their role as significant
 contributors to the spread and long-term persistence of resistance.
description: This dataset comprises bacterial growth data and fish survival
 data. Bacterial growth data comprises qPCR data and
 high-resolution melting assays (HRM) data. For qPCR data, Cq values were
 estimated from qPCR runs and exported as tabular files by the machine
 manufacturer's software (BioRad, CFX Manager Version 3.1.1517.0823).
 For HRM data, relative fluorescence values were measured for each plate
 well at different temperatures and exported as tabular files using the
 machine manufacturer's software (same software as for the qPCR
 data). For fish survival data, fish (kept in individual
 tanks) were monitored for disease symptoms and morbidity at one-hour
 intervals. Moribund fish that had lost their natural swimming buoyancy
 and/or did not react to external stimuli were euthanized. The fish
 surviving until the end of the experiment were also euthanized. Time of
 death and survival until the end of the experiment (yes/no event) were
 recorded for each fish.
description: The data is provided as plain text, tab-separated tabular files.
 This format ensures that the data files can be read easily by most
 programs, for example with R.
DOI: 10.5061/dryad.8cz8w9gwn
title: Grow up, be persistent and stay focused: keys for solving foraging problems by free-ranging possums

description: Individuals within a species often vary in both their problem-solving
 approach and ability, affecting their capacity to access novel food
 resources. Testing problem-solving in free-ranging individuals is crucial
 for understanding the fundamental ecological implications of
 problem-solving capacity. To examine the factors affecting problem-solving
 in free-ranging animals we presented three food-extraction tasks of
 increasing difficulty to urban common brushtail possums (Trichosurus
 vulpecula). We quantified two measures of problem-solving performance:
 trial outcome (success/failure) and time to solve, and tested the
 influence of a range of potential drivers including individual traits
 (personality, body weight, sex, and age), mechanistic behaviors that
 quantify problem-solving approach (work time, functional behavior time,
 behavioral diversity, and flexibility), and prior experience with the
 puzzles. We found that mechanistic behaviors were key drivers of
 performance. Individuals displaying greater persistence (higher work and
 functional behavior time) were more likely to solve a food-extraction task
 on their first attempt. Individuals also solved problems faster if they
 were more persistent and had lower behavioral flexibility. Personality
 indirectly affected time to solve one of the three problems, by
 influencing time allocated to functional behaviors. Finally, adults solved
 the most difficult problem faster than juveniles. Overall, our study
 provides rare insight into the drivers underlying problem-solving
 performance of wild animals. Such insight could be used to improve
 management strategies and conservation efforts, such as food or bait
 deployment, tailored to suit the foraging innovative abilities of target
 individuals in new and changing environments.
DOI: 10.34740/kaggle/dsv/14653016
title: BOS Kemdikbud
DOI: 10.5061/dryad.hqbzkh1n2
title: Data for: Evidence for a maintenance cost for birds maintaining highly flexible basal, but not summit, metabolic rates

description: Reversible phenotypic flexibility allows organisms to better match
 phenotypes to prevailing environmental conditions and may produce fitness
 benefits. Costs and constraints of phenotypic flexibility may limit the
 capacity for flexible responses but are not well understood or documented.
 Costs could include expenses associated with maintaining the flexible
 system or with generating the flexible response. One potential cost of
 maintaining a flexible system is an energetic cost reflected in the basal
 metabolic rate (BMR), with elevated BMR in individuals with more flexible
 metabolic responses. We accessed data from thermal acclimation studies of
 birds where BMR and/or Msum (maximum cold-induced metabolic rate)
 were measured before and after acclimation, as a measure of metabolic
 flexibility, to test the hypothesis that flexibility in BMR
 (ΔBMR), Msum (ΔMsum), or metabolic scope (Msum – BMR; ΔScope) is
 positively correlated with BMR. When temperature treatments lasted at
 least three weeks, three of six species showed significant positive
 correlations between ΔBMR and BMR, one species showed a significant
 negative correlation, and two species showed no significant correlation.
 ΔMsum and BMR were not significantly correlated for any species and ΔScope
 and BMR were significantly positively correlated for only one species.
 These data suggest that support costs exist for maintaining high BMR
 flexibility for some bird species, but high flexibility in Msum
 or metabolic scope does not generally incur elevated maintenance
 costs. 
description: Literature search – data collected from co-authors.
DOI: 10.7280/d1gh5q
title: Ancient medicinal plant rosemary contains a highly efficacious and isoform-selective KCNQ potassium channel opener

description: Voltage-gated potassium (Kv) channels in the KCNQ subfamily serve
 essential roles in the nervous system, heart, muscle and epithelia.
 Different heteromeric KCNQ complexes likely serve distinct functions in
 the brain but heteromer subtype-specific small molecules for research or
 therapy are lacking. Rosemary (Salvia rosmarinus) is an evergreen plant
 used medicinally for millennia for nervous system and other disorders.
 Here, we discovered that rosemary extract is a highly efficacious opener
 of heteromeric KCNQ3/5 channels, with weak effects on KCNQ2/3. Using
 functional screening we found that carnosic acid, a phenolic diterpene
 from rosemary, is a potent, highly efficacious, PIP2 depletion-resistant
 KCNQ3 opener with lesser effects on KCNQ5 and none on KCNQ1 or KCNQ2.
  Carnosic acid is also highly selective for KCNQ3/5 over KCNQ2/3
 heteromers. Medicinal chemistry, in silico docking, and mutagenesis
 revealed that carboxylate-guanidinium ionic bonding with an S4-5 linker
 arginine underlies the KCNQ3 opening proficiency of carnosic acid, the
 effects of which on KCNQ3/5 suggest unique therapeutic potential and a
 molecular basis for ancient neurotherapeutic use of rosemary.
DOI: 10.5061/dryad.rjdfn2zhs
title: What happens when the lights are left on? Transcriptomic and phenotypic habituation to light pollution

description: Artificial light at night (ALAN) is one of the most ubiquitous
 human-induced environmental stressors. ALAN can induce immediate
 behavioral and physiological changes in animals, sometimes leading to
 severe health consequences. Nevertheless, many organisms persist in
 light-polluted environments and may have mechanisms of habituating to
 ALAN, reducing responses to repeated exposure over time. The capacity for
 animals to habituate to ALAN has yet to be tested experimentally. We
 conducted a 6-month repeated-measures experiment with zebra finches
 (Taeniopygia guttata) to test whether birds can habituate to repeated ALAN
 exposure. We measured individual changes in behavior, physiology
 (oxidative stress and telomere attrition), and gene expression to test for
 concordance among behavioral, physiological, and transcriptomic responses
 to ALAN. We present evidence of tolerance to chronic ALAN exposure,
 persistent behavioral responses lasting 8 weeks post-exposure, and
 habituation to subsequent re-exposure. We found no changes in telomere
 attrition and a decrease in oxidative stress associated with ALAN
 exposure, indicating potential protective effects of long-term dim ALAN.
 Changes in blood transcriptome within individuals revealed unique
 responses to both previous ALAN exposure and subsequent re-exposure. These
 results represent organismal resilience to chronic stressors and shed
 light on the capacity of individuals to persist in an increasingly
 light-polluted world.
DOI: 10.5061/dryad.j9kd51chr
title: Spatiotemporal variation in pup abundance and preweaning survival of harbour seals (Phoca vitulina) in the St. Lawrence Estuary, Canada (2023)

description: Marine mammal populations worldwide greatly benefitted from conservation
 measures put in place since the 1970s following overexploitation, and many
 pinniped populations have recovered. However, threats due to bycatch,
 interspecific interactions or climate change remain, and detailed
 knowledge on vital rates, population dynamics and their responses to
 environmental changes is essential for efficient management and
 conservation of wild populations. In this study, we quantified pup
 abundance and survival of individually marked harbour seal (Phoca vitulina
 Linnaeus, 1758) pups during the preweaning period at Bic Island and Métis
 sites in the St. Lawrence Estuary from 1998 – 2019. We used mark-recapture
 models to evaluate competing hypotheses regarding variation in daily
 preweaning survival rates and capture probability during the pups’ first
 30 days of life. Pup abundance increased from 76 (95% CI: [59, 101]) to
 323 [95% CI: 233, 338] in the past two decades at Bic Island and from 66
 [95% CI:47, 91] to 285 [95% CI: 204, 218] at Métis. Preweaning survival
 was generally higher at Bic (0.73 [95% CI: 0.58,0.82]) than at Métis (0.68
 [95% CI: 0.52,0.79]). We hypothesize that differences between habitats and
 human disturbance contribute to lower preweaning survival at Métis, but
 behavioural studies are needed to understand the impacts of disturbance on
 mother-pup interactions during the nursing period.
DOI: 10.5061/dryad.866t1g1w0
title: American alligator ultrasound and microCT

description: Unlike the majority of sauropsids, which breathe primarily through costal
 and abdominal muscle contractions, extant crocodilians have evolved the
 hepatic piston pump, a unique ventilatory mechanism powered by the
 diaphragmaticus muscle. This muscle attaches to the pelvis and the liver,
 pulling the liver and viscera caudally during inspiration and lowering
 pressure in the pleuroperitoneal cavity, helping to inflate the lungs. It
 has been hypothesized that the hepatic piston pump is coupled to
 modifications in the axial skeleton that result in a smooth interior
 thoracic ceiling, facilitating craniocaudal translation of the viscera
 during ventilation. We assess this using ultrasound video to visualize the
 hepatic-piston apparatus in breathing sub-adult and adult individuals (n =
 7) of the American alligator (Alligator mississippiensis). The magnitude
 of displacement of the liver was calculated by measuring the distance
 between the most cranial and most caudal positions of the liver during a
 breath cycle. These data demonstrate that pleural tissues are freely
 sliding cranially and caudally along the thoracic ceiling. Based on our
 results, we suggest that features associated with the presence or absence
 of a smooth thoracolumbar ceiling are viable osteological correlates for
 reconstructing the evolution of the hepatic piston pump in extinct
 crocodyliform archosaurs.
description: All research was conducted on living individuals of American
 alligator (<em>Alligator mississippiensis</em>) and was
 approved by the LSUHSC Institutional Animal Care and Use Committee (IACUC
 #6341). Data was collected with an ultrasound machine at  Louisiana State
 University Health Sciences Center (LSUHSC) in New Orleans and at the
 Rockefeller Wildlife Refuge in Grand Chenier, Louisiana. Two individuals
 were part of the collection of Dr. Raul Diaz (while he was faculty at
 Southeastern Louisiana University) and five individuals were collected by
 Dr. Ruth Elsey and staff (Rockefeller Wildlife Refuge). Individuals were
 relaxed and not sedated and videos were taken during both 1) relaxed
 breathing in normal atmospheric conditions and 2) breathing a
 CO<sub>2,</sub> balance N<sub>2</sub> gas to
 induce deep breaths.
description: The file format is mp4 and can be opened on either a Mac or PC
 platform. Any video software should be compatible. Files are confirmed to
 work with both QuickTime and Microscoft video players and on a Mac and
 PC.
DOI: 10.5061/dryad.bcc2fqzj2
title: Estimates of ecosystem metabolism for 59 rivers in North America, 2008-2021

description: This dataset is companion with the github repository
 https://github.com/nmarzolf91/usgs_metabolism_project that accesses USGS
 water quality and hydrologic data to estimate ecosystem metabolism in 59
 rivers across the US from 2007-2021. Contained in this data citation are
 information about sites, raw time-series data at sub-daily intervals,
 prepared time series for modeling metabolism, metabolism outputs in raw
 form, processed and QAQC'd metabolism estimates, and supplementary
 information for the associated manuscript(s).
description: See USGS for how discharge and water quality sensor data are
 collected and processed. We access no data that has not passed USGS
 internal checks or that are considered provisional data.
 We convert data from USGS to multivariate time series that
 contain DO, DO_sat, temperature, light, discharge, and depth for sub-daily
 intervals and this serves as the input to metabolism model framework. The
 model framework returns a wide range of outputs that are processed for a
 variety of checks, ultimately returning 'real-world' estimates
 of gross primary productivity, ecosystem respiration, and gas exchange for
 each day in the 59 rivers contained.
description: All data access, manipulation, modeling, evaluation, and
 exploration was in R, using packages detailed in the github repository:
 https://github.com/nmarzolf91/usgs_metabolism_project