cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.x69p8czhq
title: Supporting data for identifying microclimate tree seedling refugia in post-wildfire landscapes

description: High-severity wildfire in arid regions has caused ecological state change,
 transforming previously forested areas into shrublands. This dramatically
 alters the climatic envelope for tree seedlings, rendering the likelihood
 of returning post-wildlife landscapes to their previous state relatively
 low. We used a combination of sUAS imagery, satellite data and in-situ
 microclimate data recordings, together with a machine learning approach,
 to model monthly near-ground minimum, mean and max temperature as well as
 relative humidity and vapor pressure deficit in a previously forested
 area, which is now dominated by shrubs species. Spatially explicit models
 predicted recorded microclimate well (r = 0.73 to 0.97), and projections
 of models highlighted the solar buffering capacity of existing vegetation
 to alter the maximum temperature in the hottest month by ~12oC, increase
 relative humidity by ~20% and reduced vapor pressure deficit by 0.3mbar in
 locations 2m apart. By harnessing these microclimate refugia, the success
 rate of reforestation efforts in post-wildfire landscapes could be
 substantially increased and mitigate seedlings from climate warming at
 local scales.
description: These data were collected using iButton temperature and relative
 humidity data loggers, Watchdog meteorological stations, and small
 unmanned aircraft systems.  The code to process the data are included as
 part of this dataset.
DOI: 10.5281/zenodo.18396893
title: SYMBOLIC REPRESENTATION OF PSYCHOLOGICAL ALIENATION IN NAZAR ESHONQUL'S SHORT STORIES

description: This article explores the symbolic representation of psychological alienation in the short stories of contemporary Uzbek writer Nazar Eshonqul. The study focuses on how inner conflict, loneliness, and existential anxiety are conveyed through narrative structure, symbolism, and metaphor. By analyzing selected stories, the article reveals the author’s distinctive narrative strategy, which combines modernist aesthetics with national literary traditions. The research highlights Eshonqul’s contribution to modern Uzbek prose through his deep psychological insight and innovative artistic techniques.
DOI: 10.5061/dryad.kprr4xh4g
title: Data from: Coronary blood flow influences tolerance to environmental extremes in fish

description: Approximately half of all fishes have, in addition to the luminal venous
 O2 supply, a coronary circulation supplying the heart with fully
 oxygenated blood. Yet, it is not fully understood how coronary O2 delivery
 affects tolerance to environmental extremes such as warming and hypoxia.
 Hypoxia reduces arterial oxygenation, while warming increases overall
 tissue O2 demand. Thus, as both stressors are associated with reduced
 venous O2 supply to the heart, we hypothesised that coronary flow benefits
 hypoxia and warming tolerance. To test this hypothesis, we blocked
 coronary blood flow (via surgical coronary ligation) in rainbow trout
 (Oncorhynchus mykiss) and assessed how in vivo cardiorespiratory
 performance and wholeanimal tolerance to acute hypoxia and warming was
 affected. While coronary ligation reduced routine stroke volume relative
 to trout with intact coronaries, cardiac output was maintained by an
 increase in heart rate. However, in hypoxia, coronary ligated trout were
 unable to increase stroke volume to maintain cardiac output when
 bradycardia developed, which was associated with a slightly reduced
 hypoxia tolerance. Moreover, during acute warming, coronary ligation
 caused cardiac function to collapse at lower temperatures and reduced
 overall AQ2 heat tolerance relative to trout with intact coronary
 arteries. We also found a positive relationship between individual hypoxia
 and heat tolerance across treatment groups, and tolerance to both
 environmental stressors was positively correlated with cardiac
 performance. Collectively, our findings show that coronary perfusion
 improves cardiac O2 supply and therefore cardiovascular function at
 environmental extremes, which benefits tolerance to natural and
 anthropogenically induced environmental perturbations.
DOI: 10.5281/zenodo.18396892
title: SYMBOLIC REPRESENTATION OF PSYCHOLOGICAL ALIENATION IN NAZAR ESHONQUL'S SHORT STORIES

description: This article explores the symbolic representation of psychological alienation in the short stories of contemporary Uzbek writer Nazar Eshonqul. The study focuses on how inner conflict, loneliness, and existential anxiety are conveyed through narrative structure, symbolism, and metaphor. By analyzing selected stories, the article reveals the author’s distinctive narrative strategy, which combines modernist aesthetics with national literary traditions. The research highlights Eshonqul’s contribution to modern Uzbek prose through his deep psychological insight and innovative artistic techniques.
DOI: 10.5061/dryad.6wwpzgmz4
title: Summarized voucher information on vertebrate genomes

description: A voucher is a permanently preserved specimen that is maintained in an
 accessible collection. In genomics, vouchers serve as the physical
 evidence for the taxonomic identification of genome assemblies.
 Unfortunately, the vast majority of vertebrate genomes stored in NCBI do
 not refer to voucher specimens. Here, we urge researchers generating new
 genome assemblies to deposit voucher specimens in accessible, permanent
 research collections, and to link these vouchers to publications, public
 databases, and repositories. We also encourage scientists to deposit
 voucher specimens in order to recognize the work of local field biologists
 and promote a diverse and inclusive knowledge base, and we recommend best
 practices to in voucher deposition to prevent taxonomic errors and ensure
 reproducibility and legality in genetic studies.
description: We surveyed the NCBI list of vertebrate genomes with
 an assembly publication date up to January 1, 2020
 (https://www.ncbi.nlm.nih.gov/genome/browse#!/eukaryotes/vertebrates)
 and coverage of 30X or greater. (Although we
 focused on reviewing vertebrate genomes, the lack
 of vouchers is a problem among genetic sequences
 submitted from many different types of
 organisms). When available, we also cross-checked the original
 publications reporting the genome sequences for references to a deposited
 voucher specimen. There were times we found no papers associated with the
 genome and no contact information could be found on NCBI. Summarized
 information on the genomes included in this assessment can be found in the
 supplemental information.
DOI: 10.5061/dryad.5mkkwh75n
title: How to render species comparable taxonomic units through deep time: A case study on intraspecific osteological variability in extant and extinct lacertid lizards

description: Generally, the species is considered to be the only naturally occurring
 taxon. However, species recognized and defined using different species
 delimitation criteria cannot readily be compared, impacting studies of
 biodiversity through Deep Time. This comparability issue is particularly
 marked when comparing extant with extinct species because the only
 available data for species delimitation in fossils are derived from their
 preserved morphology, which is generally restricted to osteology in
 vertebrates. Here, we quantify intraspecific, intrageneric, and
 intergeneric osteological variability in extant species of lacertid
 lizards using pairwise dissimilarity scores based on a data set of 253
 discrete osteological characters for 99 specimens referred to 24 species.
 Variability is always significantly lower intraspecifically than between
 individuals belonging to distinct species of a single genus, which is in
 turn significantly lower than intergeneric variability. Average values of
 intraspecific variability and associated standard deviations are
 consistent (with few exceptions), with an overall average within a species
 of 0.208 changes per character scored. Application of the same methods to
 six extinct lacertid species (represented by 40 fossil specimens) revealed
 that intraspecific osteological variability is inconsistent, which can at
 least in part be attributed to different researchers having unequal
 expectations of the skeletal dissimilarity within species units. Such a
 divergent interpretation of intraspecific and interspecific variability
 among extant and extinct species reinforces the incomparability of the
 species unit. Lacertidae is an example where extant species recognized and
 defined based on a number of delimitation criteria show comparable and
 consistent intraspecific osteological variability. Here, as well as in
 equivalent cases, application of those skeletal dissimilarity values to
 paleontological species delimitation potentially provides a way to
 ameliorate inconsistencies created by the use of morphology to define
 species.
description: Personal visits to scientific collections by Emanuel Tschopp and
 Lukardis Wencker. Some specimens were scored based on
 figures in published literature. Python and R scripts
 were developed by Lukardis Wencker and James Napoli,
 respectively.
description: The complete character matrix is also available on MorphoBank
 (http://morphobank.org/permalink/?P4084), where sources for characters and character scores are marked within the matrix as comments.
DOI: 10.5061/dryad.02v6wwq2v
title: Grylloblattidan insects from Sperbersbach and Cabarz (Germany), two new early Permian and insect-rich localities

description: New fossil insect specimens from two new localities in Germany, namely
 Sperbersbach and Cabarz (Goldlauter Formation; early Permian), belonging
 to the Grylloblattida, are described. Abundant material is assigned to
 Pictoborella clara n. gen. n. sp., regarded as closely related to
 Pictoborella germanica (Prokop et al., 2012) n. comb., from the Saar-Nahe
 Basin (Germany; early Permian). Liomopterum fuscatum n. sp., represented
 by fewer specimens, is delimited based on previously published and new
 data on various Liomopterum spp. Two other Liomopteridae, Uralioma
 thuringiensis n. sp. and Liomopterites sperbersbachensis n. sp., each
 known from a single forewing, are also described. Finally, Cabarzopterum
 magnificus n. gen. n. sp., with unclear familial affinities, is described
 based on three forewings. The assemblages of grylloblattidan insects at
 Sperbersbach and Cabarz are generally similar, with differences probably
 related to different depositional environments and local paleoclimatic
 conditions.
description: Each RTI file was computed from 42 original photographs taken
 using a ca. 30-cm diameter automated light dome driving a digital camera
 Canon EOS 5D Mark III coupled to a Canon MP-E 65 mm macro lens. Original
 photographs were optimized using Adobe Photoshop CS6 prior to
 RTI-processing, itself achieved using the RTIbuilder software (Cultural
 Heritage Imaging).
description: The software RTIviewer is needed to open the contained
 files.
DOI: 10.5061/dryad.q2bvq83jb
title: COMSOL models of fluid flow in the sarcomere

description: A highly organized and densely packed lattice of molecular machinery
 within the sarcomeres of muscle cells powers contraction. Although many of
 the proteins that drive contraction have been studied extensively, the
 mechanical impact of fluid shearing within the lattice of molecular
 machinery has received minimal attention. It was recently proposed that
 fluid flow augments substrate transport in the sarcomere, however, this
 analysis used analytical models of fluid flow in the molecular machinery
 that could not capture its full complexity. By building a finite element
 model of the sarcomere, we estimate the explicit flow field, and contrast
 it with analytical models. Our results demonstrate that viscous drag
 forces on sliding filaments are surprisingly small in contrast to the
 forces generated by single myosin molecular motors. This model also
 indicates that the energetic cost of fluid flow through viscous shearing
 with lattice proteins is likely minimal. The model also highlights a steep
 velocity gradient between sliding filaments and demonstrates that the
 maximal radial fluid velocity occurs near the tips of the filaments. To
 our knowledge, this is the first computational analysis of fluid flow
 within the highly structured sarcomere.
description: This dataset was created using COMSOL models of a 1/8th wedge of
 the sarcomere. The results of these models provide an estimate of the
 fluid flow field occurring within the sarcomere during muscle contraction
 and the resulting viscous drag forces that resist filament sliding. We
 created multiple models to capture how the flow field and the incumbent
 drag forces depend on sarcomere geometry (e.g. filament packing ratio,
 sarcomere length, filament diameters and interfilament spacing).
DOI: 10.5061/dryad.9s4mw6mg8
title: Data from: An Early Oligocene age for the oldest known monkeys and rodents of South America

description: The Santa Rosa fossil locality in eastern Perú produced the first
 Paleogene vertebrate fauna from the Amazon Basin, including the oldest
 known monkeys from South America. This diverse paleofauna was originally
 assigned an Eocene age, based largely on the stage of evolution of the
 site’s caviomorph rodents and marsupials. Here we present new detrital
 zircon dates that indicate that the maximum composite age of Santa Rosa is
 29.6±0.8 Ma (Lower Oligocene), although several zircons from Santa Rosa
 date to the Upper Oligocene. The first appearance datum for Caviomorpha in
 South America is purported to be the CTA-27 site in the Contamana region
 of Perú, which is hypothesized to be ~41 Ma (Middle Eocene) in age.
 However, the presence of the same caviomorph species and/or genera at both
 CTA-27 and at Santa Rosa is now difficult to reconcile with a &gt;11
 Myr age difference. To further test the Middle Eocene age estimate for
 CTA-27, we ran multiple Bayesian tip-dating analyses of Caviomorpha,
 treating the ages of all Paleogene species from Perú as unknown. These
 analyses produced mean age estimates for Santa Rosa that overlap with the
 maximum 29.6±0.8 Ma composite date provided by detrital zircons, but
 predict that CTA-27 is much younger than currently thought (~31-30 Ma). We
 conclude that the ~41 Ma age proposed for CTA-27 is incorrect and that
 there are currently no compelling Eocene records of either rodents or
 primates in the known fossil record of South America.
DOI: 10.5061/dryad.wstqjq2ks
title: Biodiversity across the Greater Cape Floristic Region

description: Aim: With plant biodiversity under global threat, there is an
 urgent need to monitor the spatial distribution of multiple axes of
 biodiversity. Remote sensing is a critical tool in this endeavor. One
 remote sensing approach in detecting biodiversity is based on the
 hypothesis that the spectral diversity of plant communities is a surrogate
 of multiple dimensions of biodiversity. We investigated the generality of
 this “surrogacy” for spectral, species, functional, and phylogenetic
 diversity across 1,267 plots in the Greater Cape Floristic Region (GCFR),
 a hyper-diverse region comprising several biomes and two adjacent global
 biodiversity hotspots. Location: The GCFR centered in
 southwestern and western South Africa. Time Period: All data were
 collected between 1978–2014. Major taxa studied: Vascular plants
 within the GCFR. Methods: Spectral diversity was calculated using
 leaf reflectance spectra (450–950 nm) and was related to other dimensions
 of biodiversity via linear models. The accuracy of
 different spectral diversity metrics was compared using ten-fold
 cross-validation. Results: We found that a distance-based
 spectral diversity metric was a robust predictor of species, functional,
 and phylogenetic biodiversity. This result serves as a
 proof-of-concept that spectral diversity is a potential surrogate of
 biodiversity across a hyper-diverse biogeographic region. While our
 results support the generality of spectral diversity as a biodiversity
 surrogate, we also find that relationships vary between different
 geographic subregions and biomes, suggesting that differences in
 broad-scale community composition can affect these relationships. Main
 Conclusions: Spectral diversity was shown to be a robust
 surrogate of multiple dimensions of biodiversity across biomes and a
 widely varying biogeographic region. We also extend these
 surrogacy relationships to ecological redundancy to demonstrate the
 potential for additional insights into community structure based on
 spectral reflectance.
DOI: 10.5061/dryad.v15dv41vz
title: Attention and distraction in the modular visual system of a jumping spider

description: Animals must selectively attend to relevant stimuli and avoid being
 distracted by unimportant stimuli. Jumping spiders (Salticidae) do this by
 coordinating eyes with different capabilities. Objects are examined by a
 pair of high-acuity principal eyes, whose narrow field of view is
 compensated for by retinal movements. The principal eyes overlap in field
 of view with motion-sensitive anterior-lateral eyes (ALEs), which direct
 their gaze to new stimuli. Using a salticid-specific eyetracker, we
 monitored the gaze direction of the principal eyes as they examined a
 primary stimulus.We then presented a distractor stimulus visible only to
 the ALEs and observed whether the principal eyes reflexively shifted their
 gaze to it or whether this response was flexible. Whether spiders
 redirected their gaze to the distractor depended on properties of both the
 primary and distractor stimuli. This flexibility suggests that
 higher-order processing occurs
DOI: 10.5061/dryad.s4mw6m967
title: Data for: Many-body thermodynamics on quantum computers via partition function zeros

description: Partition functions are ubiquitous in physics: they are important in
 determining the thermodynamic properties of many-body systems, and in
 understanding their phase transitions. As shown by Lee and Yang,
 analytically continuing the partition function to the complex plane allows
 us to obtain its zeros and thus the entire function. Moreover, the scaling
 and nature of these zeros can elucidate phase transitions. Here we show
 how to find partition function zeros on noisy intermediate-scale trapped
 ion quantum computers in a scalable manner, using the XXZ spin chain model
 as a prototype, and observe their transition from XY-like behavior to
 Ising-like behavior as a function of the anisotropy. While quantum
 computers cannot yet scale to the thermodynamic limit, our work provides a
 pathway to do so as hardware improves, allowing the future calculation of
 critical phenomena for systems beyond classical computing limits.
description: The experimental raw-data is obtained from trapped ion quantum
 computer. Data after post-selection to this raw-data is also used. Other
 data is from computer simulations.
DOI: 10.5061/dryad.crjdfn33p
title: Data from: Compensatory growth is accompanied by changes in insulin-like growth factor-1 but not markers of cellular aging in a long-lived seabird

description: Developing organisms often plastically modify growth in response to
 environmental circumstances, which may be adaptive, but is expected to
 entail long-term costs. However, the mechanisms that mediate these growth
 adjustments and any associated costs are less well understood. In
 vertebrates, one mechanism that may be important in this context is the
 highly conserved signaling factor insulin-like growth factor-1 (IGF-1),
 which is often positively related to post-natal growth and negatively
 related to longevity. To test this idea, we exposed captive Franklin’s
 gulls (Leucophaeus pipixcan) to a physiologically relevant nutritional
 stressor by restricting food availability during post-natal development
 and examined the effects on growth, IGF-1, and two potential biomarkers of
 cellular and organismal aging (oxidative stress, and telomeres). During
 food restriction, experimental chicks gained body mass more slowly and had
 lower IGF-1 levels than controls. Following the food restriction,
 experimental chicks underwent compensatory growth, which was accompanied
 by an increase in IGF-1 levels. Interestingly however, there were no
 significant effects of the experimental treatment or of variation in IGF-1
 levels on oxidative stress or telomeres. These findings suggest that IGF-1
 is responsive to changes in resource availability but is not associated
 with increased markers of cellular aging during development in this
 relatively long-lived species.
description: This dataset contains multiple CSV files and the accompanying R
 script. The "primarydataset.csv" file includes feeding period,
 sampling period, absolute growth rates (g/day), IGF-1 concentrations
 (ng/mL), T/S ratios (note: this is a comparative metric- these values can
 only be compared to other T/S ratios that were run on the same plates),
 regression to the mean values (note: this value was calculated using a
 separate formula described in Verhulst 2013), principle component values
 (values calculated from wing chord (mm), head to bill length (mm), and
 culmen length (mm)), and daily body mass (in grams). This file also
 contains two measures associated with measuring oxidative stress including
 antioxidant capacity and protein carbonyl content.  Median absolute growth
 rates were calculated from the daily body mass values. Several
 supplementary datasets have also been included in this folder, including
 the "hatch.csv" dataset which contains chick hatch date, whether
 or not chicks hatched, time hatched, Chick ID, treatment, collection date
 (Early or Late), and hatch mass (g). The eggs for the early collection
 date were collected on May 7th, and the eggs for the late collection date
 were collected on May 25th. The "PCAdataset.csv" includes the
 structural growth data including wing chord (mm), head-to-bill length
 (mm), and culmen length (mm), values used for the PCA analysis.
description: R is needed to open the R script, all excel files have been
 uploaded as .csv.
DOI: 10.5061/dryad.2v6wwpzmw
title: Data from: Native forest cover safeguards stream water quality under a changing climate

description: This dataset contains water quality data from 286 water monitoring
 stations in the state of São Paulo, Brazil, used in the paper: “Piffer,
 P.R., Tambosi, L.R., Ferraz, S.F., Metzger, J.P. & Uriarte,
 M. (2021) Native forest cover safeguards stream water quality
 under a changing climate. Ecological Applications”. The data was
 obtained from the São Paulo State Environmental Agency and is publicly
 available at https://sistemainfoaguas.cetesb.sp.gov.br for
 download. More information on the dataset, analysis
 and results can be found in the associated manuscript
 referenced above.
description: The readme file contains an explanation of each of the variables
 in the dataset and its measurement units. More information can be found in
 the associated manuscript referenced above.