cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b8gtht7g1
title: Machine learning on syngeneic mouse tumor profiles to model clinical immunotherapy response

description: Most cancer patients are refractory to immune checkpoint blockade (ICB)
 therapy, and proper patient stratification remains an open question.
 Primary patient data suffer from high heterogeneity, low accessibility,
 and lack of proper controls. In contrast, syngeneic mouse tumor models
 enable controlled experiments with ICB treatments. Using transcriptomic
 and experimental variables from &gt;700 ICB-treated/control syngeneic
 mouse tumors, we developed a novel machine learning framework to model
 tumor immunity and identify factors influencing ICB response. Projected on
 human immunotherapy trial data, we found that the model can predict
 clinical ICB response. We further applied the model to predicting
 ICB-responsive/resistant cancer types in TCGA, which agreed well with
 existing clinical reports. Finally, feature analysis implicated factors
 associated with ICB response. In summary, our novel computational
 framework based on mouse tumor data reliably stratified patients regarding
 ICB response, informed resistance mechanisms, and has the potential for
 wide applications in disease treatment studies.
DOI: 10.5061/dryad.zpc866tbv
title: Evolutionary processes in an undescribed eucalypt: implications for the translocation of a critically endangered species

description: Background and Aims Knowledge of the evolutionary processes responsible
 for the distribution of threatened and highly localised species is
 important for their conservation. Population genomics can provide insights
 into evolutionary processes to inform management practices, including the
 translocation of threatened plant species. In this study, we focus on a
 critically endangered eucalypt, Eucalyptus sp. Cattai, which is restricted
 to a 40 km 2 area of Sydney, Australia and is threatened by increased
 urbanisation. Eucalyptus sp. Cattai is yet to be formally described in
 part due to its suspected hybrid origin. Here, we examined evolutionary
 processes and species boundaries in E. sp. Cattai to determine whether
 translocation was warranted. Methods We used genome-wide scans to
 investigate the evolutionary relationships of E. sp. Cattai with related
 species, and to assess levels of genetic health and admixture.
 Morphological trait and genomic data were obtained from seedlings of E.
 sp. Cattai propagated in a common garden to assess their genetic
 provenance and hybrid status. Key Results All analyses revealed that E.
 sp. Cattai was strongly supported as a distinct species. Genetic diversity
 varied across populations, and clonality was unexpectedly high.
 Interspecific hybridisation was detected, and was more prevalent in
 seedlings compared to in situ adult plants, indicating that post-zygotic
 barriers may restrict the establishment of hybrids. Conclusions Multiple
 evolutionary processes (e.g., hybridisation and clonality) can operate
 within the one rare and restricted species. Insights regarding
 evolutionary processes from our study were used to assist with the
 translocation of genetically ‘pure’ and healthy ex situ seedlings to
 nearby suitable habitat. Our findings demonstrate that it is vital to
 provide an understanding of evolutionary relationships and processes with
 an examination of population genomics in the design and implementation of
 an effective translocation strategy.
DOI: 10.5061/dryad.m37pvmd54
title: Pink salmon distribution in Sweden: the calm before the storm?

description: Pink salmon distribution has recently expanded substantially across
 northern Europe. On the Swedish west coast, relatively few pink salmon
 have been observed to date, nonetheless a notable rise in 2021 (70
 observations). However, with no national monitoring together with a ceased
 Atlantic salmon commercial fishery, there is little opportunity to
 understand the extent of the spread in this region. Here we present the
 current data and address the need for future monitoring and research in
 order to understand the potential impacts of this invasive species in
 Sweden’s aquatic ecosystems.
DOI: 10.5061/dryad.v41ns1s06
title: Data from: Out of the tropics: Macroevolutionary size trends in an old insect order are shaped by temperature and predators

description: Global body size distributions are shaped by selection pressures arising
 from biotic and abiotic factors such as temperature, predation and
 parasitism. Here, we investigated the ecological and evolutionary drivers
 of global latitudinal size gradients in an old insect order (Odonata;
 dragonflies and damselflies). Phylogenetic comparative analyses revealed
 that global size variation of extant taxa is negatively influenced by both
 regional avian diversity and temperature. Interestingly, fossil data show
 that the relationship between wing size and latitude has shifted:
 latitudinal size trends had initially negative slopes but became shallower
 or positive following the emergence of birds 150 MYA. These changing
 size-latitude trends over geological time were likely driven by bird
 predation and high dispersal ability of large dragonflies. Our results
 therefore suggest that latitudinal size gradients were shaped by
 temperature but also by predators driving the dispersal of large-sized
 clades out of the tropics and in to the temperate zone.
description: The phylogenetic tree that we
 use in this study was constructed from odonate DNA-sequences downloaded
 from GenBank, using a traditional morphological taxonomy as our backbone
 (Waller and Svensson
 2017). Our phylogeny
 comprised 1322 taxa, about a fifth of all known extant odonate species
 (about 6400 in total) (Schorr and Paulson 2015; Waller et al.
 2019). Further and more
 detailed information about phenotypic data collection and phylogeny
 reconstruction is provided elsewhere (Waller and Svensson 2017; Waller et al.
 2019) and  from our open online resource “The Odonate
 Phenotypic Database”: http://www.odonatephenotypicdatabase.org/shiny/odonates/. Size data (wing lengths) from extinct odonate fossil taxa were obtained from Clapham and Karr (2012). Although we use our previously published Odonata phylogeny in the present study (Waller and Svensson 2017) and we have published data on interspecific body size variation from the Odonate Phenotypic Database (Waller et al. 2019), all of the analyses in the present paper are new and have not been published elsewhere. Thus, there is no overlap between the results in the present study and our previous work.
description: All our statistical analysis have been carried out in the R
 statistical environment. We enclose a README-file in text-format,
 CSV-files with data and two R-files with code and functions to replicate
 all the analyses in the current paper.
DOI: 10.5061/dryad.djh9w0w31
title: Data From: Geographically persistent clusters of La Crosse virus disease in the Appalachian region of the United States from 2003 to 2021

description: La Crosse virus (LACV) is a mosquito-borne pathogen that causes more
 pediatric neuroinvasive disease than any other arbovirus in the United
 States. The geographic focus of reported LACV neuroinvasive disease
 (LACV-ND) expanded from the Midwest into Appalachia in the 1990s, and most
 cases have been reported from a few high-risk foci since then. Here, we
 provide the county-level LACV-ND dataset that we used to investigate
 changes in the distribution of geographic LACV-ND clusters between 2003
 and 2021 and to investigate socioeconomic and demographic predictors of
 county-level disease risk in states with persistent clusters. We used
 spatial scan statistics to identify high-risk clusters from 2003–2021 and
 a generalized linear mixed model to identify socioeconomic and demographic
 predictors of disease risk.
description: We received the annual number of reported La Crosse virus
 neuroinvasive disease cases for each county in the United States from 2003
 to 2021 from the Centers for Disease Control and Prevention Division of
 Vector-Borne Diseases. This data is publicly viewable in the United States
 national arbovirus surveillance system, ArboNET, but a request must be
 submitted to receive the data in tabular form. Here, we aggregated the
 data into four time periods: 2003–2007, 2008–2012, 2013–2017, and
 2018–2021 by summing the number of cases for each county in each time
 period. We also provide a period-specific estimate of the total population
 in the county from United States census data.
DOI: 10.6084/m9.figshare.28000433
title: Cognitive advantages of large brains persist during an experimental heatwave

description: Heatwaves negatively impact behaviour with associated cognitive impairment in humans. A growing body of literature reports negative effects of heatwaves on cognition also in animals. A larger brain is known to generate enhanced cognitive abilities that may buffer against environmental changes and thereby potentially increase fitness in large-brained individuals. Yet, how a larger brain buffer against adverse effects on cognitive abilities induced by thermal stress, such as that experienced during heatwaves, remains unknown. We examined detour problem solving and working memory during an experimental heatwave in guppies artificially selected on brain size with matching differences in neuron number. Overall, detour problem solving was impaired among guppies during the heatwave, while working memory was unaffected. Large-brained guppies outperformed small-brained guppies in detour problem solving and working memory in both the heatwave and control temperature treatments. During the heatwave, large-brained guppies exhibited cognitive performance levels comparable to those of small-brained guppies under normal temperature conditions in the detour task. Our study thus suggests that small-brained individuals might have lower fitness also during heatwaves if increased temperature impair cognitive abilities required for survival and reproduction. Furthermore, our results open up the possibility that cognition-driven brain size evolution may have been influenced by abiotic factors.
DOI: 10.6084/m9.figshare.28000433.v1
title: Cognitive advantages of large brains persist during an experimental heatwave

description: Heatwaves negatively impact behaviour with associated cognitive impairment in humans. A growing body of literature reports negative effects of heatwaves on cognition also in animals. A larger brain is known to generate enhanced cognitive abilities that may buffer against environmental changes and thereby potentially increase fitness in large-brained individuals. Yet, how a larger brain buffer against adverse effects on cognitive abilities induced by thermal stress, such as that experienced during heatwaves, remains unknown. We examined detour problem solving and working memory during an experimental heatwave in guppies artificially selected on brain size with matching differences in neuron number. Overall, detour problem solving was impaired among guppies during the heatwave, while working memory was unaffected. Large-brained guppies outperformed small-brained guppies in detour problem solving and working memory in both the heatwave and control temperature treatments. During the heatwave, large-brained guppies exhibited cognitive performance levels comparable to those of small-brained guppies under normal temperature conditions in the detour task. Our study thus suggests that small-brained individuals might have lower fitness also during heatwaves if increased temperature impair cognitive abilities required for survival and reproduction. Furthermore, our results open up the possibility that cognition-driven brain size evolution may have been influenced by abiotic factors.
DOI: 10.5061/dryad.k98sf7m8k
title: Data from: Mosaic adaptive peak shifts underlie body shape diversification in Pelagiaria fishes (Acanthomorpha: Percomorpha)

description: Extreme body elongation in fishes is a major evolutionary transformation
 that extends the boundaries of morphological diversity and alters aspects
 of function, behavior, and ecology. Prior studies have identified features
 of the cranial and axial skeleton that characterize elongate fishes, but a
 lack of detailed reconstructions of anatomical evolution has limited
 inferences about factors that underlie major shifts in body shape. In this
 study, we fit multi-peak adaptive (Ornstein-Uhlenbeck) evolutionary models
 to species body shape and anatomical dimensions in Pelagiaria, a radiation
 of open-ocean fishes whose species span a continuum from deep-bodied to
 highly elongate. We inferred an ancestral fusiform adaptive peak that is
 retained by several major pelagiarian lineages (e.g., Scombridae) and
 found robust support for multiple transitions to deep-bodied (in the
 families Stromateidae, Bramidae, and Caristiidae) and elongate-bodied
 optima (within Trichiuroidei), including two instances of sequential
 shifts toward increasingly elongate optima that followed distinct paths of
 anatomical evolution. Within Trichiuridae, initial increases in head
 length and vertebral number were followed by changes in head and vertebral
 shape. Within an elongate-bodied subclade of taxa traditionally identified
 as ‘gempylids’, shifts in head and vertebral shape as well as number of
 precaudal vertebrae preceded an increase in number of caudal vertebrae.
 Altogether, this mosaic of anatomical peak shifts suggests that body shape
 transformations were associated with differing selective demands and
 developmental changes.
description: Note: Absalomichthys_velifer measurements are from an image in
 David LR. 1943. Miocene fishes of southern California. Geological Society
 of America Special Papers 43: 1-186.
DOI: 10.5061/dryad.dncjsxm31
title: Local temperature increases reduce soil microbial residues and carbon stocks

description: Warming is known to reduce soil carbon (C) stocks by promoting microbial
 respiration, which is associated with the decomposition of microbial
 residue C (MRC). However, the relative contribution of MRC to soil organic
 C (SOC) across temperature gradients is poorly understood. Here,
 we investigated the contribution of MRC to SOC along two independent
 elevation gradients of our model system (i.e., the Tibetan
 Plateau and Shennongjia Mountain in China). Our results showed that local
 temperature increases were negatively correlated with MRC and SOC. Further
 analyses revealed that rising temperature reduced SOC via decreasing
 MRC, which helps to explain future reductions in SOC under
 climate warming. Our findings demonstrate that climate warming
 has the potential to reduce C sequestration by
 increasing the decomposition of MRC, exacerbating the
 positive feedback between rising temperature and CO2 efflux. Our
 study also considered the influence of multiple environmental factors such
 as soil pH and moisture, which were more important in controlling SOC than
 microbial traits such as microbial life-style strategies and metabolic
 efficiency. Together, our work suggests an important mechanism underlying
 long-term soil C sequestration, which has important implications for the
 microbial-mediated C process in the face of global climate change.
DOI: 10.25824/redu/cyblwy
title: Characterization zein and chitosan-based films with added oregano and thyme essential oils

description: This dataset comprises raw data obtained from experimental analyses conducted to characterize films incorporated with essential oils. The files include measurements of thickness, density, water vapor permeability, moisture content, solubility, and mechanical properties. Additionally, the dataset provides results from scanning electron microscopy (SEM) and microbiological analyses, aimed at evaluating the films’ potential application as antifungal agents against Aspergillus niger, Aspergillus flavus, and Penicillium roqueforti.
DOI: 10.5061/dryad.rfj6q57df
title: Genetic monitoring of steelhead in the Klickitat River to estimate productivity, straying, and migration timing

description: Salmonids with complex life history variation present challenges for
 conservation management, but genetic approaches alongside fisheries
 monitoring can address questions regarding viability of natural
 populations. We genotyped adult (n=3,108) and juvenile (n=2,624) samples
 of anadromous Oncorhynchus mykiss that were collected in the Klickitat
 River, WA, USA at traps in the lower drainage to examine tributary level
 productivity, straying from outside sources and variation in adult
 migration timing. Genetic assignment of steelhead from this system
 indicated that the majority were produced within or near tributaries of
 the middle Klickitat River (juvenile mean = 72.8%; adult mean = 87.3%).
 Analyses with parentage-based tagging identified that most hatchery-origin
 adults were assigned to the Skamania Hatchery (80.8%) as expected since
 this has been the release stock for decades within the Klickitat River
 drainage. Hatchery-origin adults were also identified from programs
 operating outside the Klickitat River, which were primarily strays from
 Snake River hatcheries. Most natural-origin steelhead were assigned to the
 Klickitat River, but there were also natural-origin fish identified as
 strays from other regions of the Columbia River (22.3% of natural
 returns). We also examined genes known to be associated with migration
 timing in adult steelhead observed at the trap and observed a strong
 relationship between migration date and alleles for early and late
 migration, but individual outliers were detected across seasons. Our
 results indicate that genetic variation of steelhead in the Klickitat
 River has been influenced by hatchery programs as well as natural-origin
 straying from other sub-basins, but genetic diversity remains high
 throughout the sub-basin, and both early and late migration alleles are
 maintained. The genetic diversity present in Klickitat River steelhead may
 enable this Endangered Species Act listed (threatened) species to better
 adapt to stochastic environmental conditions compared to less diverse
 populations.
DOI: 10.34740/kaggle/dsv/14650395
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.7d7wm37z5
title: Data for: Industrial energy development decouples ungulate migration from the green wave

description: The ability to freely move across the landscape to track the emergence of
 nutritious spring green-up (termed “green-wave surfing”), is key to the
 foraging strategy of migratory ungulates. Across the vast landscapes
 traversed by many migratory herds, habitats are being altered by
 development with unknown consequences for surfing. Using a unique
 long-term tracking dataset, we found that when energy development occurs
 within mule deer (Odocoileus hemionus) migration corridors, migrating
 animals become decoupled from the green wave. During the early phases of a
 coalbed natural gas development, deer synchronized their movements with
 peak green-up. But faced with increasing disturbance as development
 expanded, deer altered their movements by holding up at the edge of the
 gas field and letting the green wave pass them by. Development often
 modified only a small portion of the migration corridor but had
 far-reaching effects on behavior before and after migrating deer
 encountered it, thus reducing surfing along the entire route by 38.65%
 over the 14-year study period. Our study suggests that industrial
 development within migratory corridors can change the behavior of
 migrating ungulates and diminish the benefits of migration. Such
 disruptions to migratory behavior present a common mechanism whereby
 corridors become unprofitable and could ultimately be lost on highly
 developed landscapes.
DOI: 10.5061/dryad.qnk98sfkk
title: RNAScope analysis of human fetal tooth germ

description: This data was collected to verify the spatial localization of human fetal
 tooth germ cell types identified via sn-RNA-seq. Using this and other
 data, we have proposed a more precise developmental timeline and
 trajectory for human tooth development.
description: Description of methods used for collection/generation of data: We
 used a RNAscope™ HiPlex12 Reagent Kit (488, 550, 650, 750) v2 Standard
 Assay (Advanced Cell Diagnostics, Inc.) and probes against 13 transcripts
 VWDE, SALL1, FGF4, IGFBP5, FGF10, PRRX1, FBN2, ENAM, PCDH7, SOX5, KRT5,
 and either DSPP or LGR6. 
 Probe/Channel Key: Round 1
 DAPI R1C1
 VWDE R1C2
 SALL1 R1C3
 FGF4 R1C4
 IGFBP5 R1C5
 Round 2 
 DAPI R2C1
 DSPP R2C2
 LGR6 R2C2
 FGF10 R2C3
 PRRX1 R2C4
 FBN2 R2C5
 Round 3 
 DAPI R3C1
 PCDH7 R3C3
 SOX5 R3C4
 KRT5 R3C5
 Fresh frozen human fetal
 tooth germ tissue sections were stained according to the ACD protocol:
 https://acdbio.com/sites/default/files/UM%20324409%20RNAscope%20HiPlex%20v2%20User%20Manual%20%28488%2C%20550%2C%20650%2C750%29.pdf and imaged using a Nikon Ti2 with an Aura light engine and BrightLine Sedat filter set optimized for DAPI, FITC, TRITC, Cy5 & Cy7 (LED-DA/FI/TR/Cy5/Cy7-5X5M-A-000) for samples 1-4 or using a Yokogawa CSU-X1 spinning disk confocal microscope with a Celesta light engine and ORCA-Fusion scientific CMOS camera for sample 5. Methods for processing the data: DAPI channel images for imaging rounds two and three were aligned to the DAPI image for imaging round one using the BigDataViewer &gt; BigWarp plugin in Fiji. The resultant landmark tables were used in a custom .groovy script to align the DAPI, FITC, Cy3, Cy5, and Cy7 images from the three rounds of imaging in Fiji. Aligned images were background corrected and converted to a hyperstack in Fiji. Describe any quality-assurance procedures performed on the data: Thresholding determined using positive and negative control sections
description: Instrument- or software-specific information needed to interpret
 the data: Fiji (ImageJ2 v2.3.0).
DOI: 10.15468/dl.wb6df2
title: Occurrence Download

description: A dataset containing 129 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Liparis campylostalix"
 ]
}

 The dataset includes 129 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003181-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57967/hf/7662
title: nfr_bt_nmt_english-ukrainian