cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j0zpc86hd
title: A unique mitochondrial gene bock inversion in Antarctic Trematomin fishes: A cautionary tale

description: Many Antarctic notothenioid fishes have major rearrangements in their
 mitochondrial (mt) genomes. Here we report the complete mt genomes of
 three trematomin notothenioids: the bald notothen (Trematomus (Pagothenia)
 borchgrevinki); the spotted notothen (T. nicolai); and the emerald
 notothen (T. bernacchii). The three mt genomes were sequenced using
 next-generation Illumina technology, and the assemblies verified by Sanger
 sequencing. When compared with the canonical mt gene order of the
 Antarctic silverfish (Pleuragramma antarctica), we found a large gene
 inversion in the three trematomin mt genomes that included tRNAIle, ND1,
 tRNALeu2, 16S, tRNAVal, 12S, tRNAPhe and the control region. The
 trematomin mt genomes contained three intergenic spacers, which are
 thought to be the remnants of previous gene and control region
 duplications. All control regions included the characteristic conserved
 regulatory sequence motifs. Although next-generation DNA sequencing
 technology has allowed the rapid and cost-effective sequencing of a large
 number of complete mt genomes, it is essential in all cases to verify the
 assembly in order to prevent the publication and use of erroneous data.
description: See manuscript for details.
description: Data includes fourteen fastq files and one md5 file detailed in
 the accompanying README.
DOI: 10.22008/promice/data/ice_discharge/d/v02/liujkk
title: README.txt

description: README. Git hash: 7d4b133
DOI: 10.22008/promice/data/ice_discharge/d/v02/xpl0i9
title: region_coverage.csv

description: Regional coverage. Git hash: 7d4b133
DOI: 10.22008/promice/data/ice_discharge/d/v02/io1dhi
title: region_D.csv

description: Regional discharge. Git hash: 7d4b133
DOI: 10.22008/promice/data/ice_discharge/d/v02/lkdtfn
title: region.nc

description: Regional discharge, coverage, and error. Git hash: 7d4b133
DOI: 10.22008/promice/data/ice_discharge/d/v02/mollzo
title: region_err.csv

description: Regional error. Git hash: 7d4b133
DOI: 10.5061/dryad.5x69p8d5z
title: Data from: Ontogeny can provide insight into the roles of natural and sexual selection in cricket cuticular hydrocarbon evolution

description: The often complex cocktails of hydrocarbon compounds found on the cuticles
 of insects can serve both naturally and sexually selected functions,
 contributing to an individual’s ability to withstand water loss and
 attract mating partners. However, whether natural and sexual selection act
 synergistically or antagonistically on a species’  cuticular
 hydrocarbon (CHC) profile remains unclear. Here we examined the ontogeny
 of the CHC profile in a species of cricket Teleogryllus oceanicus while
 manipulating humidity during development. We predicted that juvenile
 crickets should produce only those compounds that contribute to
 desiccation resistance, while those compounds contributing specifically to
 male attractiveness should be produced only at sexual maturity. Further,
 if attractive CHCs come at a cost to desiccation resistance as predicted
 by some models of sexual selection, then males reared under low humidity
 should be constrained to invest less in attractive CHCs. Crickets reared
 under low humidity produced more long chained methyl branched alkanes,
 alkenes and alkadienes than did crickets reared under high humidity. The
 abundance of n-alkanes was unaffected by humidity treatment. Sexual
 dimorphism in the CHC profile was not apparent until adult emergence and
 became exaggerated 10 days after emergence when crickets were sexually
 mature. Males produced more of the same compounds that were increased in
 both sexes under low humidity, but the humidity treatment did not interact
 with sex in determining CHC abundance. The data suggest that CHC profiles
 which protect crickets from desiccation might have synergistic effects on
 male attractiveness, as there was no evidence to suggest males trade-off a
 CHC profile produced in response to low humidity for one associated with
 sexual signalling.
DOI: 10.22008/promice/data/ice_discharge/d/v02/1nbdw1
title: sector_coverage.csv

description: Sector coverage. Git hash: 7d4b133
DOI: 10.22008/promice/data/ice_discharge/d/v02/pp7ytx
title: sector_D.csv

description: Sector discharge. Git hash: 7d4b133
DOI: 10.22008/promice/data/ice_discharge/d/v02/qv3yb0
title: sector_err.csv

description: Sector error. Git hash: 7d4b133
DOI: 10.22008/promice/data/ice_discharge/d/v02/nubaks
title: sector.nc

description: Sector discharge, coverage, and error. Git hash: 7d4b133
DOI: 10.22008/promice/data/ice_discharge/d/v02/ultk2e
title: gate_coverage.csv

description: Gate coverage. Git hash: 4f25b39
DOI: 10.5061/dryad.37pvmcvnn
title: Data for: Estimating density dependence, environmental variance and long-term selection on a stage-structured life history

description: We model growth of a density-dependent stage-structured population
 undergoing small or moderate fluctuations around a deterministically
 stable equilibrium in a stochastic environment, assuming that a weighted
 sum of stage abundances, N, exerts density dependence on the
 stage-specific vital rates of survival and reproduction. We approximate
 the dynamics of N as a onedimensional stochastic process with three key
 parameters: the density-independent growth rate and the net density
 dependence and environmental variance in the life history. Comparisons of
 populations and species with different life histories are facilitated
 using the key parameters, which we show how to estimate from long-term
 demographic data on fluctuations in the vital rates. We also show that
 life history evolution is a stochastic maximization of a simple function
 of the key parameters. Elements in the long-term selection gradient acting
 on the life history can be expressed as sensitivities of this function
 with respect to density-independent, density-dependent, and stochastic
 components of the vital rates. Using years of demographic data on a great
 tit population, we estimate the key demographic parameters, which
 accurately predict the observed mean, coefficient of variation, and
 fluctuation rate of N, and also evaluate the long-term selection gradient
 on the population.
description: Data are in plain tab separated text format.
DOI: 10.22008/promice/data/ice_discharge/d/v02/c1obkn
title: gate_D.csv

description: Gate discharge. Git hash: 4f25b39
DOI: 10.22008/promice/data/ice_discharge/d/v02/yeqfu3
title: gate_err.csv

description: Gate errors. Git hash: 4f25b39
DOI: 10.22008/promice/data/ice_discharge/d/v02/torh4o
title: gate.nc

description: Gate discharge, coverage, error, and metadata. Git hash: 4f25b39
DOI: 10.5061/dryad.rjdfn2zdk
title: Temporal dynamics of soil fungi in a pyrodiverse dry-sclerophyll forest

description: Fire is a major evolutionary and ecological driver that shapes
 biodiversity in forests. While above-ground community responses to fire
 have been well-documented, those below-ground are much less understood.
 However, below-ground communities, including fungi, play key roles in
 forests and facilitate the recovery of other organisms after fire. Here,
 we used internal transcribed spacer (ITS) meta-barcoding data from forests
 with three different times since fire [short (3 years), medium
 (13–19 years) and long (&gt;26 years)] to characterize the temporal
 responses of soil fungal communities across functional groups,
 ectomycorrhizal exploration strategies and inter-guild associations. Our
 findings indicate that fire effects on fungal communities are strongest in
 the short to medium term, with clear distinctions between communities in
 forests with a short time (3 years) since fire, a medium time
 (13–19 years) and a long time (&gt;26 years) since fire.
 Ectomycorrhizal fungi were disproportionately impacted by fire relative to
 saprotrophs, but the direction of the response varied depending on
 morphological structures and exploration strategies. For instance,
 short-distance ectomycorrhizal fungi increased with recent fire, while
 medium-distance (fringe) ectomycorrhizal fungi decreased. Further, we
 detected strong, negative inter-guild associations between ectomycorrhizal
 and saprotrophic fungi but only at medium and long times since fire. Given
 the functional significance of fungi, the temporal changes in fungal
 composition, inter-guild associations and functional groups after fire
 demonstrated in our study may have functional implications that require
 adaptive management to curtail.
description: Please see the README document ("README_dryad.csv") and
 the accompanying published article: <strong>Bowd, E. J.,
 </strong>Egidi, E., Lindenmayer,
 D. B., Wardle, D. A., Kardol, P., & Foster, C. (2023). Temporal
 dynamics of soil fungi in a pyrodiverse dry-sclerophyll forest. Molecular
 Ecology, 32(15), 4181–4198. https://doi.org/10.1111/mec.17036
description: Excel
DOI: 10.22008/promice/data/ice_discharge/d/v02/cmuimx
title: GIS_coverage.csv

description: Greenland coverage. Git hash: 4f25b39
DOI: 10.22008/promice/data/ice_discharge/d/v02/g9fxy7
title: GIS_D.csv

description: Greenland discharge. Git hash: 4f25b39
DOI: 10.22008/promice/data/ice_discharge/d/v02/5jox6g
title: GIS_err.csv

description: Greenland error. Git hash: 4f25b39
DOI: 10.22008/promice/data/ice_discharge/d/v02/fkury8
title: README.txt

description: README. Git hash: 4f25b39
DOI: 10.22008/promice/data/ice_discharge/d/v02/o3abvx
title: GIS.nc

description: Greenland discharge, coverage, and error. Git hash: 4f25b39
DOI: 10.5061/dryad.h18931zpd
title: Population genomics and sexual signals identify reproductive interference in Uperoleia

description: When closely related species come into contact via range expansion, both
 may experience reduced fitness as a result of the interaction. Selection
 is expected to favor traits that minimize costly interspecies reproductive
 interactions (such as mismating) via a phenomenon called reproductive
 character displacement (RCD). Research on RCD frequently assumes secondary
 contact between species, but the geographic history of species
 interactions is often unknown. Landscape genomic data allows tests of
 geographic hypotheses about species origins and secondary contact through
 range expansion. We used landscape genomic data from single nucleotide
 polymorphisms (SNPs), mitochondrial sequence data, advertisement call
 data, and morphological data to investigate a species complex of toadlets
 (Uperoleia borealis, U. crassa, U. inundata) from northern Australia.
 Although the three species of frogs were morphologically indistinguishable
 in our analysis, we determined that U. crassa and U. inundata form a
 single species (synonymized here) based on an absence of genomic
 divergence. SNP data identified the phylogeographic origin of U. crassa as
 the Top End, with subsequent westward invasion into the range of U.
 borealis in the Kimberley. We identified six F1 hybrids, all of which had
 the U. borealis mitochondrial haplotype, suggesting unidirectional
 hybridization. Consistent with the RCD hypothesis, U. borealis and U.
 crassa sexual signals differ more in sympatry than in allopatry. Hybrid
 males have intermediate calls, which likely reduces attractiveness to
 females. Integrating landscape genomic data, mitochondrial sequencing,
 morphology, and behavioral approaches supplies us an unusually detailed
 collection of evidence for reproductive character displacement following
 range expansion and secondary contact.
description: Please see associated manuscript: Population genomics and sexual signals support
 reproductive character displacement in <em>Uperoleia
 </em>(Anura: Myobatrachidae) in a contact zone
description: Acoustic and morphological datasets are xlsx files and opened in
 Microsoft excel or alternatives. SNP datasets are .csv
 and can be opened in R with the package dartR. R
 scripts can be opened in R.
DOI: 10.22008/promice/data/ice_discharge/d/v02/j0vexm
title: region_D.csv

description: Regional discharge. Git hash: 4f25b39
DOI: 10.22008/promice/data/ice_discharge/d/v02/x70ubo
title: region_coverage.csv

description: Regional coverage. Git hash: 4f25b39
DOI: 10.22008/promice/data/ice_discharge/d/v02/y5lgby
title: region_err.csv

description: Regional error. Git hash: 4f25b39
DOI: 10.22008/promice/data/ice_discharge/d/v02/h7qusf
title: sector_coverage.csv

description: Sector coverage. Git hash: 4f25b39
DOI: 10.22008/promice/data/ice_discharge/d/v02/zqkjwr
title: region.nc

description: Regional discharge, coverage, and error. Git hash: 4f25b39
DOI: 10.5061/dryad.73n5tb30d
title: Genomes and associated scripts for paper: Potential millennial-scale avian declines by humans in southern China

description: Mounting observational records demonstrate human-caused faunal decline in
 recent decades, while accumulating archaeological
 evidence suggests an early biodiversity impact of human
 activities during the Holocene. A fundamental question arises concerning
 whether modern wildlife population declines began during early human
 disturbance. Here, we performed population genomic analysis of six common
 forest birds in East Asia to address this question. For five of them,
 demographic history inference based on 25-33 genomes of each species
 revealed dramatic population declines by 4-48-fold over millennia
 (two to five thousand years ago). Nevertheless, ecological niche
 models predicted extensive range persistence during the Holocene and imply
 limited demographic impact of historical climate change. Summary
 statistics further suggest high negative correlations between these
 population declines and human disturbance intensities and indicate a
 potential driver of human activities. These findings provide deep-time and
 large-scale insight into the recently recognized avifaunal decline and
 support an early origin hypothesis of human effects on
 biodiversity. Overall, our study sheds light on the current biodiversity
 crisis in the context of long-term human-environment interactions and
 offers a multievidential framework for quantitatively
 assessing the ecological consequences of human
 disturbance.
DOI: 10.22008/promice/data/ice_discharge/d/v02/sptcaj
title: sector_err.csv

description: Sector error. Git hash: 4f25b39
DOI: 10.22008/promice/data/ice_discharge/d/v02/wyafje
title: sector_D.csv

description: Sector discharge. Git hash: 4f25b39
DOI: 10.22008/promice/data/ice_discharge/d/v02/9fih73
title: sector.nc

description: Sector discharge, coverage, and error. Git hash: 4f25b39
DOI: 10.22008/promice/data/ice_discharge/d/v02/hva9us
title: gate_D.csv

description: Gate discharge. Git hash: 0362770
DOI: 10.22008/promice/data/ice_discharge/d/v02/se1tdw
title: gate_coverage.csv

description: Gate coverage. Git hash: 0362770
DOI: 10.5061/dryad.t4b8gtj4p
title: Adaptation to starvation requires a flexible circadian clockwork in Neurospora crassa (RNAseq)

description: The circadian clock governs rhythmic cellular functions by driving
 expression of a substantial fraction of the genome and thereby
 significantly contributes to the adaptation to changing environmental
 conditions. Using the circadian model organism Neurospora crassa, we show
 that molecular timekeeping is robust even under severe limitation of
 carbon sources, however, stoichiometry, phosphorylation and subcellular
 distribution of the key clock components display drastic alterations.
 Protein kinase A, protein phosphatase 2A and glycogen synthase kinase are
 involved in the molecular reorganization of the clock. RNA-seq analysis
 reveals that the transcriptomic response of metabolism to starvation is
 highly dependent on the positive clock component WC-1. Moreover, our
 molecular and phenotypic data indicate that a functional clock facilitates
 recovery from starvation.  We suggest that the molecular clock is
 a flexible network that allows the organism to maintain a rhythmic
 physiology and preserve fitness even under long-term nutritional stress.
description: Liquid cultures were grown
 under standard and glucose starving conditions in 12-12 hours light-dark
 cycles for 48 hours and samples were harvested at ZT12 (n=4 for each
 group). RNA was purified using the TriReagent® (Sigma Aldrich #93289)
 isolation reagent. Following DNase treatment RNA quality was controlled by
 the Nanodrop<sup>TM</sup> OneC spectrophotometer, the
 Qubit<sup>TM</sup> 4.0 Fluorometer (Invitrogen) and the
 Agilent TapeStation 4150 System. Library preparation and sequencing were
 performed by BGI Genomics, China, using PE-100 library. Sequencing quality
 check was performed with FastQC (Andrews, 2010). Mapping was performed with STAR
 (Dobin et al.,
 2013) to the N.c. genome
 from Ensembl (Neurospora_crassa.NC12.48) (Yates et al., 2020), and the indexing and duplicate filtering with
 samtools (Li et al.,
 2009). Read counting was
 done using HTSeq-count (Anders et al., 2015). Differential expression analysis was done with
 DESeq2 (Love et al.,
 2014) package in R
 (R Core Team,
 2020).
DOI: 10.22008/promice/data/ice_discharge/d/v02/kb6ofq
title: gate_err.csv

description: Gate errors. Git hash: 0362770
DOI: 10.22008/promice/data/ice_discharge/d/v02/s1uiex
title: gate.nc

description: Gate discharge, coverage, error, and metadata. Git hash: 0362770
DOI: 10.22008/promice/data/ice_discharge/d/v02/v1e1wb
title: GIS_coverage.csv

description: Greenland coverage. Git hash: 0362770
DOI: 10.22008/promice/data/ice_discharge/d/v02/tcfdxl
title: GIS_err.csv

description: Greenland error. Git hash: 0362770
DOI: 10.22008/promice/data/ice_discharge/d/v02/xf02cm
title: GIS_D.csv

description: Greenland discharge. Git hash: 0362770
DOI: 10.5061/dryad.gf1vhhmsh
title: Assessment of Apple Watch Series 6 pulse oximetry and electrocardiograms in a pediatric population

description: Background: Recent technologic advances have resulted in increased
 development and utilization of direct-to-consumer cardiac wearable devices
 with various functionality. This study aimed to assess Apple Watch Series
 6 (AW6) pulse oximetry and electrocardiography (ECG) in a cohort of
 pediatric patients. Results: A total of 84 patients were enrolled over a
 5-week period. 68 patients (81%) were placed into the SpO2 and ECG arm,
 with 16 patients (19%) placed into the SpO2 only arm. Pulse oximetry data
 was successfully collected in 71/84 (85%) patients and ECG data in 61/68
 (90%). ΔSpO2 between modalities was 2.0±2.6% (r=0.76). ΔRR was 43±44msec
 (r=0.96), ΔPR 19±23msec (r=0.79), ΔQRS 12±13msec (r=0.78), and ΔQT
 20±19msec (r=0.9). The AW6 automated rhythm analysis yielded a 75%
 specificity and found:  1) 40/61 (65.6%) “accurate”, 2) 6/61
 (9.8%) “accurate with missed findings”, 3) 14/61 (23%) “inconclusive”, and
 4) 1/61 (1.6%) incorrect. Conclusion: The AW6 can accurately measure
 oxygen saturation when compared to hospital pulse oximeters in pediatric
 patients and provide good quality single lead ECGs that allow for accurate
 measurement of RR, PR, QRS, and QT intervals with manual interpretation.
 The AW6-automated rhythm interpretation algorithm has limitations for
 smaller pediatric patients and patients with abnormal ECGs.
description: This single-center, prospective study enrolled pediatric patients
 ³ 3kg and having an ECG and/or pulse oximetry (SpO2) as part of their
 planned evaluation. Exclusion criteria: 1) non-English speaking patients
 and 2) patients in state custody. Simultaneous tracings were obtained for
 SpO2 and ECG with concurrent standard pulse oximeter and 12-lead ECG. AW6
 automated rhythm interpretations were compared to physician over-read and
 categorized as accurate, accurate with missed findings, inconclusive
 (automated interpretation: “inconclusive”), or inaccurate.
DOI: 10.5281/zenodo.17609029
title: Quadrupolar gyration of a Brownian particle in a confining ring

description: We develop a minimal theoretical model that reveals a structured steady-state flux field with  four alternating local circulation, a phenomenon we refer to as quadrupolar gyration. A passive Brownian particle is confined to move in a ring-shaped trap and driven far from equilibrium solely by anisotropic thermal fluctuations from two orthogonal heat baths held at different temperatures. By breaking detailed balance, this fundamental temperature anisotropy induces a robust nonequilibrium steady state characterized by probability currents of the particle's motion. Remarkably, these currents self-organize into a distinctive quadrupolar vortex pattern, providing a clear signature of emergent symmetry breaking, irreversible entropy production, and coherent motion in minimal passive systems.    Our theoretical predictions, based on the narrow-ring approximation and the assumption of small thermal anisotropy, are validated by numerical simulations.
DOI: 10.5281/zenodo.17609030
title: Quadrupolar gyration of a Brownian particle in a confining ring

description: We develop a minimal theoretical model that reveals a structured steady-state flux field with  four alternating local circulation, a phenomenon we refer to as quadrupolar gyration. A passive Brownian particle is confined to move in a ring-shaped trap and driven far from equilibrium solely by anisotropic thermal fluctuations from two orthogonal heat baths held at different temperatures. By breaking detailed balance, this fundamental temperature anisotropy induces a robust nonequilibrium steady state characterized by probability currents of the particle's motion. Remarkably, these currents self-organize into a distinctive quadrupolar vortex pattern, providing a clear signature of emergent symmetry breaking, irreversible entropy production, and coherent motion in minimal passive systems.    Our theoretical predictions, based on the narrow-ring approximation and the assumption of small thermal anisotropy, are validated by numerical simulations.
DOI: 10.22008/promice/data/ice_discharge/d/v02/1tl25g
title: README.txt

description: README. Git hash: 0362770
DOI: 10.22008/promice/data/ice_discharge/d/v02/3xmxag
title: GIS.nc

description: Greenland discharge, coverage, and error. Git hash: 0362770
DOI: 10.22008/promice/data/ice_discharge/d/v02/kxxvuc
title: region_coverage.csv

description: Regional coverage. Git hash: 0362770
DOI: 10.22008/promice/data/ice_discharge/d/v02/dxxa1u
title: region_err.csv

description: Regional error. Git hash: 0362770
DOI: 10.22008/promice/data/ice_discharge/d/v02/ndl2hy
title: region_D.csv

description: Regional discharge. Git hash: 0362770
DOI: 10.22008/promice/data/ice_discharge/d/v02/abajvs
title: sector_coverage.csv

description: Sector coverage. Git hash: 0362770
DOI: 10.22008/promice/data/ice_discharge/d/v02/tu6ywa
title: region.nc

description: Regional discharge, coverage, and error. Git hash: 0362770
DOI: 10.22008/promice/data/ice_discharge/d/v02/e9zxnd
title: sector_D.csv

description: Sector discharge. Git hash: 0362770