cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.x95x69pp8
title: Data for: Small reductions in cargo vessel speed dramatically reduce noise impacts to marine mammals

description: Global reductions in the underwater radiated noise levels from cargo
 vessels are needed to reduce increasing cumulative impacts to marine
 wildlife. We use a vessel exposure simulation model to examine how
 reducing vessel source levels through slowdowns and technological
 modifications can lessen impacts on marine mammals. We show that the area
 exposed to ship noise reduces dramatically with moderate source level
 reductions that can be readily achieved with small reductions in speed.
 Moreover, slowdowns reduce all impacts to marine mammals despite the
 longer time that a slower vessel takes to pass an animal. We conclude that
 cumulative noise impacts from the global fleet can be reduced immediately
 by slowdowns. This solution requires no modification to ships and is
 scalable – from local speed reductions in sensitive areas to ocean basins.
 Speed reductions can be supplemented by routing vessels away from critical
 habitats and by technological modifications to reduce vessel noise.
description: For detailed information on the methods please see Findlay et al.
 2023. Small reductions in cargo vessel speed dramatically reduce noise
 impacts to marine wildlife. Science Advances.
description: Software: All code and custom-written
 functions were written in MATLAB 2021a (MathWorks, Natick, MA,
 USA). Code/Functions:
 Findlay_etal_ScienceAdvances.m This file
 contains the code which will allow the user to reproduce components of
 Findlay et al. 2023. Small reductions in cargo vessel speed dramatically
 reduce noise impacts to marine wildlife. Science Advances. The associated
 custom-written functions are detailed below.
 VesselSLSpectrumModel.m This file is a
 MATLAB Version of the JOMOPANS-ECHO Vessel Reference Spectrum Model
 proposed by Alexander MacGillivray and Christ de Jong (2021).
 <br><strong>REFERENCE: </strong>Macgillivray, A., de
 Jong, C., 2021. A reference spectrum model for estimating source levels of
 marine shipping based on automated identification system data.
 <em>Journal of Marine Science and Engineering</em>. 9, 1–15.
 https://doi.org/10.3390/jmse9040369. areaExposed.m This function will calculate the area exposed to underwater noise from fixed-pitch propeller vessels for a range of source level reductions as the percentage of max (100%). Area exposed includes the vessel noise swathe, instantaneous acoustic footprint, and the normalised acoustic footprint. mmimpacts.m This function will calculate the received levels (dB re 1 μPa RMS) and change in received levels (dB/min) from a vessel passage experienced by a marine mammal at a given closest point of approach distance.
DOI: 10.5061/dryad.5tb2rbp7z
title: Sequences of bacterial and fungal communities by Next-Generation Sequencing (NGS) associated to wall patinas

description: These data are the DNA sequences obtained from samples of house plaster
 with chromatic alteration facies. Three areas (VA1, VA3 and VNA6) of the
 wall were sampled. the DNA was extracted using the Spin Kit For Soil
 MPBio.  The DNA extracts were sequenced by NGS using Illumina
 MiSeq Two regions were selected V3V5 16S for Bacteria and ITS1
 ITS for Fungi.
DOI: 10.5061/dryad.3r2280gm4
title: Solidago hybrid-sequence capture probe set

description: Premise of the study: The phylogenetic relationships among the ca. 138
 species of goldenrods (Solidago; Asteraceae) have been difficult to infer
 due to species richness, and shallow interspecific genetic
 divergences.  This study aims to overcome these obstacles by
 combining extensive sampling of goldenrod herbarium specimens with the use
 of a custom Solidago hybrid-sequence capture probe set. Methods: A set of
 tissues from herbarium samples comprising ca. 90% of Solidago species was
 assembled, and DNA was extracted. A custom hybrid-sequence capture probe
 set was designed, and data from 854 nuclear regions were obtained and
 analyzed from 209 specimens. Maximum likelihood and coalescent approaches
 were used to estimate the genus phylogeny for 157 diploid samples. Key
 results: Although DNAs from older specimens were both more fragmented and
 produced fewer sequencing reads, there was no relationship between
 specimen age and our ability to obtain sufficient data at the target loci.
 The Solidago phylogeny was generally well supported, with 88/155 (57%)
 nodes receiving ≥95% bootstrap support. Solidago was supported as
 monophyletic, with Chrysoma pauciflosculosa identified as sister. A clade
 comprising Solidago ericameriodes, Solidago odora, and Solidago chapmanii
 was identified as the earliest diverging Solidago lineage. The previously
 segregated genera Brintonia and Oligoneuron were identified as placed well
 within Solidago. These and other phylogenetic results were used to
 establish four subgenera and fifteen sections within the genus.
 Conclusions: The combination of expansive herbarium sampling and
 hybrid-sequence capture data allowed us to quickly and rigorously
 establish the evolutionary relationships within this difficult,
 species-rich group.
DOI: 10.5061/dryad.z612jm6gd
title: Aphid male wing polymorphisms are transient and have evolved repeatedly

description: Polymorphic phenotypes have long been used to examine the maintenance of
 genetic variation within and between species. Most studies have focused on
 persistent polymorphisms, which are retained across species boundaries,
 and their positive effects on speciation rates. Far less is known about
 the macroevolutionary impacts of more transient polymorphisms, which are
 also common. Here we investigated male wing polymorphisms in aphids. We
 estimated the phylogenetic history of wing states across species, along
 with several other traits that could affect wing evolution. We found that
 male wing polymorphisms are transient: they are found in only ~4% of
 extant species but have likely evolved repeatedly across the phylogeny. We
 reason that the repeated evolution of transient polymorphisms might be
 facilitated by the existence of the asexual female wing plasticity, which
 is common across aphids, and would maintain the wing development program
 even in species with wingless males. We also discovered that male winged
 morphs and wing polymorphisms are associated with higher speciation rates,
 and male wingedness correlates positively with host plant alternation and
 host plant breadth, and that winged morphs and wing polymorphisms may be
 associated with higher speciation rates. Our results provide new
 evolutionary insights into this well-studied group and suggest that even
 transient polymorphisms may impact species diversification rates.
description: This dataset uses a previously published aphid phylogeny and maps
 male wing states. These states were compiled from various aphid
 monographs, publications, private and public datasets and collections (all
 sourced and cited in the Supplementary References of the manuscript). They
 were then analyzed using phylogenetic simulations including ancestral
 state reconstructions, stochastic character mapping, and
 speciation/extinction diversification models.
description: All the analyses were done in R using public and published
 phylogenetics packages.
DOI: 10.15468/dl.8rsnx2
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Trimeresurus salazar"
 ]
}

 The dataset includes 38 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003454-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/nmf4nzh47j
title: Codificacao Desenvolvimento Endogeno

description: Casos selecionados e lista de códigos aplicados a cada caso.
DOI: 10.17632/nmf4nzh47j.1
title: Codificacao Desenvolvimento Endogeno

description: Casos selecionados e lista de códigos aplicados a cada caso.
DOI: 10.5061/dryad.08kprr564
title: Habitat heterogeneity, environmental feedbacks, and species coexistence across timescales (code and figures)

description: Classic ecological theory explains species coexistence in variable
 environments. While spatial variation is often treated as an intrinsic
 feature of a landscape, it may be shaped and even generated by the
 resident community. All species modify their local environment to some
 extent, driving changes that can feed back to affect the composition and
 coexistence of the community, potentially over timescales very different
 from population dynamics. We introduce a simple, nested modeling framework
 for community dynamics in heterogeneous environments, including the
 possible evolution of heterogeneity over time due to community-environment
 feedbacks. We use this model to derive analytical conditions for species
 coexistence in environments where heterogeneity is either fixed or shaped
 by feedbacks. Among other results, our approach reveals how dispersal and
 environmental specialization interact to shape realized patterns of
 habitat association and demonstrates that environmental feedbacks can tune
 landscape conditions to allow the stable coexistence of any number of
 species. Our flexible modeling framework helps explain feedback dynamics
 that arise in a wide range of ecosystems and offers a generic platform for
 exploring the interplay between species and landscape diversity.
description: Code for numerical simulations.
description: All code in R.
DOI: 10.17632/swbjmks934
title: BEHAVIORAL AND ENDOCRINE ADAPTATIONS TO TIME-RESTRICTED FEEDING COMBINED WITH SUCROSE ACCESS IN MICE

description: This dataset contains raw data on body weight, food intake, adipose tissue weight, glucose and insulin tolerance tests, insulin and glucagon secretion, and pancreatic islet morphometry from an experimental mouse model.
DOI: 10.5061/dryad.jsxksn0f2
title: Data from: Retrogressive moulting in khapra beetle, Trogoderma granarium (Coleoptera: Dermestidae)

description: Insect larvae typically moult to grow, but here we investigate insect
 larvae that moult to shrink; that is, retrogressive moulting or
 retrogressive development. We demonstrate this phenomenon in the khapra
 beetle, Trogoderma granarium Everts (Dermestidae), among the world's
 most invasive pests of stored grains and cereal products, and a quarantine
 pest of interest for many countries. Larvae survived a 3‐month period of
 starvation, moulting up to six times and reducing their body mass by about
 half, on average. When reprovisioned with food, most larvae resumed the
 normal trajectory of development and pupated within a month. Thus,
 retrogressive development is a mechanism that may favour species whose
 resources exhibit feast‐or‐famine dynamics. By enabling survival during
 periods of privation, retrogressive development contributes to the
 invasiveness of the khapra beetle by allowing them to persist for long
 periods in empty storage facilities or empty containers used for
 international grain shipments.
DOI: 10.17632/swbjmks934.1
title: BEHAVIORAL AND ENDOCRINE ADAPTATIONS TO TIME-RESTRICTED FEEDING COMBINED WITH SUCROSE ACCESS IN MICE

description: This dataset contains raw data on body weight, food intake, adipose tissue weight, glucose and insulin tolerance tests, insulin and glucagon secretion, and pancreatic islet morphometry from an experimental mouse model.
DOI: 10.17632/227nxwx653
title: Viral Priming SA-AKI Characterization

description: Supplemental Files for "A Novel Two-Hit Murine Model of Viral Primed Sepsis-Associated Acute Kidney Injury"
DOI: 10.17632/227nxwx653.2
title: Viral Priming SA-AKI Characterization

description: Supplemental Files for "A Novel Two-Hit Murine Model of Viral Primed Sepsis-Associated Acute Kidney Injury"
DOI: 10.5061/dryad.nk98sf7x4
title: Data from: Drivers of geomorphic heterogeneity in unconfined non‐perennial river corridors

description: River corridors along non-perennial stream networks are known to provide
 diverse physical and ecological functions that are thought to be related
 to geomorphic heterogeneity. Geomorphic heterogeneity refers to the
 spatial and temporal variability of geomorphic units, which are geomorphic
 patches within the river corridor formed by a given set of processes.
 While studies on the magnitude and drivers of geomorphic heterogeneity are
 emerging in perennial streams, similar studies in ephemeral streams are
 lacking. Given the ubiquity of non-perennial streams globally, we aim to
 answer questions regarding the magnitude and drivers of geomorphic
 heterogeneity in non-perennial river corridors as well as how geomorphic
 units and heterogeneity reflect processes related to flood disturbance.
 Geomorphic units were mapped in 30 unconfined river corridors within six
 non-perennial watersheds in Utah and Arizona, USA. Landscape heterogeneity
 metrics – Shannon’s Diversity Index, Shannon’s Evenness Index, and patch
 density – were used to quantify geomorphic heterogeneity within each
 reach. Additionally, variables that may potentially constrain or drive
 heterogeneity were quantified, including floodplain shape, grain size,
 large wood abundance, and proxies for flood disturbance. While
 heterogeneity positively correlated with metrics for morphology and
 disturbance, statistical models suggest that morphologic context,
 particularly floodplain width, was a more important predictor for
 estimating geomorphic heterogeneity. Still, geomorphic units reflected
 aggradation processes indicative of a range of flood energies, suggesting
 a strong tie between heterogeneity and disturbance. Results suggest that
 geomorphic heterogeneity may be resilient to changes in flood disturbance
 frequency or magnitude, but future studies investigating long-term
 temporal heterogeneity are needed.
DOI: 10.15468/dl.8kr3he
title: Occurrence Download

description: A dataset containing 82 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Guibourtia hymenaeifolia",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 82 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003455-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6071/m3mx1b
title: Data for: Biochar co-compost improves nitrogen retention and reduces carbon emissions in a winter wheat cropping system

description: Organic amendments, such as compost and biochar, mitigate the
 environmental burdens associated with wasting organic resources and close
 nutrient loops by capturing, transforming, and resupplying nutrients to
 soils. While compost or biochar application to soil can enhance an
 agroecosystem’s capacity to store carbon and produce food, there have been
 few field studies investigating the agroecological impacts of amending
 soil with biochar co-compost, produced through the composting of
 nitrogen-rich organic material, such as manure, with carbon-rich biochar.
 Here, we examine the impact of biochar co-compost on soil properties and
 processes by conducting a field study in which we compare the
 environmental and agronomic impacts associated with the amendment of
 either dairy manure co-composted with biochar, dairy manure compost, or
 biochar to soils in a winter wheat cropping system. Organic amendments
 were applied at equivalent C rates (8 Mg C ha-1). We found that all three
 treatments significantly increased soil water holding capacity and total
 plant biomass relative to the no-amendment control. Soils amended with
 biochar or biochar co-compost resulted in significantly less greenhouse
 gas emissions than the compost or control soils. Biochar co-compost also
 resulted in a significant reduction in nutrient leaching relative to the
 application of biochar alone or compost alone. Our results suggest that
 biochar co-composting could optimize organic resource recycling for
 climate change mitigation and agricultural productivity while minimizing
 nutrient losses from agroecosystems.
description: This data file includes five datasets: 
 The first dataset describes soil available nitrogen content
 (average and 1x standard error, n = 4) across different soil depths in
 different treatment plots at the mid- and end-growing seasons.
 The second dataset describes the concentration of available
 nitrogen and phosphorus (average and 1x standard error, n = 4) in leachate
 samples collected monthly at the treatment plots. The
 third dataset describes the cumulative soil greenhouse gas emissions
 (average, 1x standard error, n = 4, and 95% confidence interval) at
 different sampling days throughout the field experiment.
 The fourth dataset describes the soil greenhouse gas fluxes and
 soil volumetric water content measured at each sampling day in all
 treatment plots throughout the field experiment. The
 fifth dataset describes the soil greenhouse gas emissions, plant total
 biomass, and soil greenhouse gas emissions per unit of plant total biomass
 at all field treatment plots at the end of the growing season.
DOI: 10.5061/dryad.j0zpc86jm
title: Data from: Transforming medical education in Liberia through an international community of inquiry (2017 dataset)

description: A critical component of building capacity in Liberia’s physician workforce
 involves strengthening the country’s only medical school, A.M. Dogliotti
 College of Medicine. Beginning in 2015, senior health sector stakeholders
 in Liberia invited faculty and staff from U.S. academic institutions and
 non-governmental organizations to join a partnership focused on improving
 undergraduate medical education in Liberia. Over the subsequent six years,
 the members of this partnership came together through an iterative,
 mutual-learning process and created what William Torbert et al describe as
 a “community of inquiry,” in which practitioners and researchers pair
 action and inquiry toward evidence-informed practice and organizational
 transformation. This community of inquiry developed around a few key
 institutional and interpersonal relationships but expanded over time.
 Incorporating faculty, practitioners, and students from Liberia and the
 U.S., the community of inquiry consistently focused on following the
 vision, goals, and priorities of leadership in Liberia, irrespective of
 funding source or institutional affiliation. The work of the community of
 inquiry has incorporated multiple mixed methods assessments, stakeholder
 discussions, strategic planning, and collaborative self-reflection,
 resulting in transformation of M.D. education in Liberia. We suggest that
 the community of inquiry approach reported here can serve as a model for
 others seeking to form sustainable, international global health
 partnerships focused on organizational transformation.
description: To develop a more comprehensive
 understanding of financial needs and challenges for students at AMD as
 well as factors to consider for long-term financial sustainability for
 AMD, the research team developed a 20-question survey exploring basic
 personal financial information. The research team included faculty and
 students from both the University of Liberia and Yale University. Surveys
 were distributed in paper format by a fifth-year medical student who was a
 member of the research team, and respondents’ answers were entered into
 Microsoft Excel and compiled as summary statistics.     The Yale University Institutional Review
 Board (IRB) Human Subjects Committee deemed the 2017 study exempt from IRB
 review (IRB #2000021882) in October 2017. Despite the exemption
 determinations, all members of the research teams completed Human Subjects
 Research Protection training prior to the start of data collection. Verbal
 or check-box informed consent was obtained prior to each survey.
DOI: 10.17632/454pf5jc2j
title: Mg/Ca and stable isotope data on G.ruber-Reorganization of the Arabian Sea Oxygen Minimum Zone in Response to Monsoon Fluctuations During Dansgaard–Oeschger Events 12–11
DOI: 10.17632/454pf5jc2j.1
title: Mg/Ca and stable isotope data on G.ruber-Reorganization of the Arabian Sea Oxygen Minimum Zone in Response to Monsoon Fluctuations During Dansgaard–Oeschger Events 12–11
DOI: 10.25349/d9762j
title: Data for: Pre-vegetation, single-thread rivers sustained by cohesive, fine-grained bank sediments: Mesoproterozoic Stoer Group, NW Scotland

description: The Silurian-age shift in fluvial stratigraphic architecture is associated
 with the predominance of shallow pancontinental braidplains in the
 vegetation-free, pre-Silurian period. Recognition of deep, single-threaded
 channels in pre-Silurian strata challenge this paradigm; however, it is
 unclear how these rivers sustained stable banks. Here, we combine
 measurements of fluvial cross-strata from the 1.2 Ga Stoer Group with
 quantitative paleohydraulic tools to reconstruct river geometry and
 planform. We show that the deposits are consistent with deep (4-7 m),
 low-sloping rivers (5.6x10-4 to 4.5x10-5), similar in morphometry to
 modern single-threaded rivers. We show that mud in floodplain sediments
 provides sufficient resistance to erosion to withstand the reconstructed
 bank shear stress, indicating that sediment cohesion from mud alone can
 foster deep pre-Silurian rivers. We suggest that the apparent
 stratigraphic shift coeval with the greening of continents marks a
 kinematic change in channel migration rates rather than a geometric shift
 in river planform.
description: Primary data (data sets 1 and 2) was collected by authors at
 Stoer Group outcrops across NW Scotland. Additional data (data set 3) used
 in comparative analysis is from Galeazzi et al. (2021). Hydraulic
 reconstructions were conducted using general purpose calculating functions
 in Microsoft Excel and MATLAB. All formulas are defined and all
 calculations are described in the main text and supporting information,
 therefore no unique/novel code or scripts are required to reproduce these
 results.
description: All data is held in Microsoft Excel files, and can be opened in
 any spreadsheet software.