cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.575md
title: Data from: The adaptive genomic landscape of beak morphology in Darwin’s finches

description: Beak shape in Darwin's ground finches (Geospiza) is emblematic of
 natural selection and adaptive radiation, yet our understanding of the
 genetic basis of beak shape variation, and thus the genetic target of
 natural selection, is still evolving. Here we reveal the genomic
 architecture of beak shape variation using genomewide comparisons of four
 closely related and hybridizing species across 13 islands subject to
 parallel natural selection. Pairwise contrasts among species were used to
 identify a large number of genomic loci that are consistently related to
 species differences across a complex landscape. These loci are associated
 with hundreds of genes that have enriched GO categories significantly
 associated with development. One genomic region of particular interest is
 a section of Chromosome 1A with many candidate genes and increased
 linkage. The distinct, pointed beak shape of the cactus finch is linked to
 an excess of intermediate frequency alleles and increased heterozygosity
 in significant SNPs, but not across the rest of the genome. Alleles
 associated with pointier beaks among species were associated with
 pointier-beaked populations within each species, thus establishing a
 common basis for natural selection, species divergence and adaptive
 radiation. The adaptive genomic landscape for Darwin's finches
 mirrors theoretical expectations based on morphological variation. The
 implication that a large number of genes are actively maintained to
 facilitate beak variation across parallel populations with documented
 interspecies admixture challenges our understanding of evolutionary
 processes in the wild.
description: MLM_GLM_FortScanResults from G. fortis/G.scandens GLM and MLM contrasts, including ensembl and GO analysisMLM_GLM_FuligMagResults from G. fuliginosa/G. magnirostris GLM and MLM contrasts, including ensembl and GO analysisMLM_GLM_FortMagResults from G. fortis/G. magnirostris GLM and MLM contrasts, including ensembl and GO analysisMLM_GLM_FortFuligResults from G. fortis/G. fuliginosa GLM and MLM contrasts, including ensembl and GO analysis83Hapmap_simple2_filteredHapmap file of all SNPs for the four focal Geospiza species. Produced through Tassel pipeline
DOI: 10.5061/dryad.8f0v4
title: Data from: Calling louder and longer: how bats use biosonar under severe acoustic interference from other bats

description: Active-sensing systems such as echolocation provide animals with distinct
 advantages in dark environments. For social animals, however, like many
 bat species, active sensing can present problems as well: when many
 individuals emit bio-sonar calls simultaneously, detecting and recognizing
 the faint echoes generated by one's own calls amid the general
 cacophony of the group becomes challenging. This problem is often termed
 ‘jamming’ and bats have been hypothesized to solve it by shifting the
 spectral content of their calls to decrease the overlap with the jamming
 signals. We tested bats’ response in situations of extreme interference,
 mimicking a high density of bats. We played-back bat echolocation calls
 from multiple speakers, to jam flying Pipistrellus kuhlii bats, simulating
 a naturally occurring situation of many bats flying in proximity. We
 examined behavioural and echolocation parameters during search phase and
 target approach. Under severe interference, bats emitted calls of higher
 intensity and longer duration, and called more often. Slight spectral
 shifts were observed but they did not decrease the spectral overlap with
 jamming signals. We also found that pre-existing inter-individual spectral
 differences could allow self-call recognition. Results suggest that the
 bats’ response aimed to increase the signal-to-noise ratio and not to
 avoid spectral overlap.
description: DryadRaw data of research -
 acoustic parameters derived from echolocation calls.
DOI: 10.34740/kaggle/dsv/14637953
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.4ff53
title: Data from: An integrated occupancy and space-use model to predict abundance of imperfectly detected, territorial vertebrates

description: It is often highly desirable to know not only where species are likely to
 occur (i.e., occupancy) but also how many individuals are supported by a
 given habitat (i.e., density). For many animals, occupancy and density may
 be determined by distinct ecological processes. Here we develop a novel
 abundance model as the product of landscape-scale occupancy probability
 and habitat-scale density given occupancy. One can conceptualize our model
 as fully packing a landscape with home ranges or territories based on
 habitat quality, and then subtracting territories based on a probabilistic
 process that accounts for the fact that species rarely exhibit full
 occupancy across heterogeneous landscapes. The model is designed to
 predict abundance at fine spatial scales, using resolutions equal to or
 smaller than a single home range or territory. We demonstrate this model
 on the Black-backed Woodpecker (Picoides arcticus), a species of
 management concern linked to post-fire forests. Occupancy is derived from
 a regional monitoring effort, while density given occupancy comes from a
 telemetry study of variation in territory size. A Bayesian framework is
 used to combine independent occupancy and home-range size models and
 predict abundance of Black-backed Woodpeckers at 4 fires that burned in
 2012 or 2013. Predictions are evaluated with independently collected
 survey data, showing that the model is successful at predicting both
 absolute abundance at fires as well as relative abundance within and among
 fires. The conceptual model presents a promising new framework for
 fine-scale modeling of density and abundance for other territorial yet
 elusive species. Telemetry and occupancy data are widely collected for
 many species, but rarely utilized in combination, and the ecological
 exploration of the factors that determine occurrence versus home-range
 size may provide useful biological insight. As applied to the Black-backed
 Woodpecker, the model provides a tool for resource managers to explore
 trade-offs in retaining burned forest habitat versus managing for other
 post-fire goals, such as salvage logging or reforestation efforts that
 require snag removal.
description: Code and data
 filesPlease peruse readme.rtf
 file for full description and instructions.BBWO_abundance.zip
DOI: 10.5061/dryad.33b9s
title: Data from: Small-mammal isotope ecology tracks climate and vegetation gradients across western North America

description: Stable carbon, nitrogen, hydrogen and oxygen isotopes have been used to
 infer aspects of species ecology and environment in both modern ecosystems
 and the fossil record. Compared to large mammals, stable isotopic studies
 of small-mammal ecology are limited; however, high species and ecological
 diversity within small mammals presents several advantages for quantifying
 resource use and organism–environment interactions using stable isotopes
 over various spatial and temporal scales. We analyzed the isotopic
 composition of hair from two heteromyid rodent species, Dipodomys ordii
 and Perognathus parvus, from localities across western North America in
 order to characterize dietary variation in relation to vegetation and
 climatic gradients. Significant correlations between the carbon isotopic
 composition (δ13C) of these species and several climatic variables imply
 that seasonal temperature and precipitation control the composition and
 distribution of dietary resources (grass seeds). Our results also suggest
 a moisture influence on the nitrogen isotopic composition (δ15N) of
 heteromyid diets. Population- and species-level variation in δ13C and δ15N
 values record fine-scale habitat heterogeneity and significant differences
 in resource use between species. Using classification and regression-tree
 techniques, we modeled the geographic variation in heteromyid δ13Cdiet
 values based on 10 climatic variables and generated an isotope landscape
 model (‘isoscape’). The isoscape predictions for δ13Cdiet differ from
 expectations based on observed C4 distributions and instead indicate that
 D. ordii and P. parvus record seasonally abundant grass resources, with
 additional model deviations potentially attributed to geographic variation
 in dietary selection. The oxygen and hydrogen isotopic composition of D.
 ordii is enriched relative to local meteoric water and suggests that
 individuals rely on highly evaporated water sources, such as seed
 moisture. Based on the climatic influences on vegetation and diet
 documented in this study, the isotopic composition of small mammals has
 high potential for recording ecological responses to environmental changes
 over short and long time scales.
description: Small-mammal isotopes,
 SM Appendices 1 and 2Supplemental Material,
 including locality, specimen and isotopic data as well as results from
 conditional forest analysis described in the paper.TSmiley_Oikos_Appendices.pdf
DOI: 10.5061/dryad.k18nk
title: Data from: Biological introduction threats from shipping in a warming Arctic

description: Several decades of research on invasive marine species have yielded a
 broad understanding of the nature of species invasion mechanisms and
 associated threats globally. However, this is not true of the Arctic, a
 region where ongoing climatic changes may promote species invasion. Here,
 we evaluated risks associated with non-indigenous propagule loads
 discharged with ships' ballast water to the high-Arctic archipelago,
 Svalbard, as a case study for the wider Arctic. We sampled and identified
 transferred propagules using traditional and DNA barcoding techniques. We
 then assessed the suitability of the Svalbard coast for non-indigenous
 species under contemporary and future climate scenarios using
 ecophysiological models based on critical temperature and salinity
 reproductive thresholds. Ships discharging ballast water in Svalbard
 carried high densities of zooplankton (mean 1522 ± 335 SE individuals
 m−3), predominately comprised of indigenous species. Ballast water
 exchange did not prevent non-indigenous species introduction.
 Non-indigenous coastal species were present in all except one of 16
 ballast water samples (mean 144 ± 67 SE individuals m−3), despite five of
 the eight ships exchanging ballast water en route. Of a total of 73 taxa,
 36 species including 23 non-indigenous species were identified. Of those
 23, sufficient data permitted evaluation of the current and future
 colonization potential for eight widely known invaders. With the exception
 of one of these species, modelled suitability indicated that the coast of
 Svalbard is unsuitable presently; under the 2100 Representative
 Concentration Pathway (RCP) 8·5 climate scenario, however, modelled
 suitability will favour colonization for six species. Synthesis and
 applications. We show that current ballast water management practices do
 not prevent non-indigenous species from being transferred to the Arctic.
 Consequences of these shortcomings will be shipping-route dependent, but
 will likely magnify over time: our models indicate future conditions will
 favour the colonization of non-indigenous species Arctic-wide. Invasion
 threats will be greatest where shipping transfers organisms across
 biogeographic realms, and for these shipping routes ballast water
 treatment technologies may be required to prevent impacts. Our results
 also highlight critical gaps in our understanding of ballast water
 management efficacy and prioritization. Thereby, our study provides an
 agenda for research and policy development.
description: Ware et al
 ClimateSurfacesThe zip file contains
 six netCDF files. These are global ocean climatologies for three time
 points (2011, 2050, and 2100) for the variables sea surface temperature
 (SST) and sea surface salinity (SSS).
DOI: 10.13140/rg.2.2.33439.62880
title: Dataset for predicting thermal stresses in hardening massive monolithic foundation slabs based on temperature monitoring data
DOI: 10.5061/dryad.9pn24
title: Data from: Parental influence on begging call structure in zebra finches (Taeniopygia guttata): evidence of early vocal plasticity

description: Begging calls are signals of need used by young birds to elicit care from
 adults. Different theoretical frameworks have been proposed to understand
 this parent–offspring communication. But relationships between parental
 response and begging intensity, or between begging characteristics and
 proxies of a young’s need remain puzzling. Few studies have considered the
 adjustment of nestling begging features to previous experience as a
 possible explanation of these discrepancies. In this study, we tested the
 effect of a heterospecific rearing environment on individual developmental
 trajectories of the acoustic structure of nestling begging calls.
 Fifty-two zebra finch chicks were fostered either to Bengalese finch or to
 zebra finch parents, and begging calls were recorded at several stages of
 nestling development. Acoustic analyses revealed that the development of
 the spectral features of the begging calls differed between experimental
 conditions: chicks reared by Bengalese finches produced higher pitched and
 less broadband begging calls than chicks reared by conspecific parents.
 Differences were stronger in males than females and were not explained by
 differences in growth rate. We conclude that nestling begging calls can be
 plastic in response to social interactions with parents.
description: villain_dataset_RSOS_villain_beggingcalls_ZF_dryad
DOI: 10.5061/dryad.1tf47
title: Data from: Morphometric analysis of graphoglyptid trace fossils in two dimensions: implications for behavioral evolution in the deep sea

description: Graphoglyptids are deep-marine trace fossils, often found preserved as
 casts in positive relief on the base of turbidites. Previous analyses of
 the behavioral evolution of graphoglyptids suggested they were slowly
 diversifying, becoming optimized, and getting smaller over time until the
 Late Cretaceous, when a sudden increase in diversification occurred. This
 current study quantifies the morphology of approximately 400 different
 graphoglyptid specimens, ranging in age from the Cambrian to the present,
 in order to evaluate the behavioral evolutionary interpretations made
 previously. Results from this study indicate that although some general
 evolutionary patterns can be discerned, they are not as straightforward as
 previously reported. Different topological categories of trace fossils
 represent organisms’ responses to evolutionary pressures in unique ways.
 While burrow widths of meandering traces were becoming smaller over time,
 as predicted by previous workers, the burrow widths of the network traces
 were becoming smaller only until the Late Cretaceous, when they started to
 get larger again. The times of significant evolutionary changes in
 behavior were not consistent among various topological categories, with
 some morphological features being affected in the Late Cretaceous and
 others during the beginning of the Eocene. It is likely that the
 behavioral evolution of graphoglyptids was influenced by deep-marine
 global influences linked to climate change, glaciation, and deep-ocean
 warming. These influences affected each topological group uniquely,
 suggesting that different species or genera of trace makers were creating
 each of the topological categories. This is contrary to the hypothesis
 that all graphoglyptids were created by closely related species.
description: Supplemental File 1 -
 List of turbidite LocalitiesComprehensive list of
 turbidite localities worldwide.Supplemental File 2 -
 Sample ImagesA comprehensive list of
 all samples used in the analyses, including photographs, if available,
 line tracings, and deposit information.Supplemental File 3 -
 Sample Locality MapsPaleogeographic maps
 showing sample localities during their appropriate time
 periods.Supplemental File 4 -
 Data tables of analyses resultsData results from all
 analyses run for the article.Supplemental File 5 -
 Analytical Procedural AdjustmentsAn update on the
 analytical procedures run on the trace fossils.Supplemental File 6 -
 Network Tortuosity ScriptUpdated Matlab network
 tortuoisty script.Supplemental File 7 -
 Analysis Consistency TestA test to determine
 analysis consistency of the trace fossil analyses.
DOI: 10.25919/5dsa-qp66
title: NBDL-HK3RC4D5GA39BD
DOI: 10.25919/r8se-2055
title: NBDL-HK3R7JRSH12SZE
DOI: 10.6084/m9.figshare.25843372
title: Single-nucleus and spatial transcriptomic profiling of human temporal cortex and white matter reveals key associations with AD pathology

description: This extended data is associated with the single-nucleus transcriptome analysis of both gray and white matter of 40 individuals. The file contains various sheets containing samples/nuclei information of TC region as well as spatial transcriptomics details. Since we also compared TC region with other brain regions, the extended supplemental table contains these details as well.
DOI: 10.6084/m9.figshare.25843372.v1
title: Single-nucleus and spatial transcriptomic profiling of human temporal cortex and white matter reveals key associations with AD pathology

description: This extended data is associated with the single-nucleus transcriptome analysis of both gray and white matter of 40 individuals. The file contains various sheets containing samples/nuclei information of TC region as well as spatial transcriptomics details. Since we also compared TC region with other brain regions, the extended supplemental table contains these details as well.
DOI: 10.25919/5sc8-6p37
title: NBDL-HK3RC4ERQA6ETW
DOI: 10.25919/fddv-fb47
title: NBDL-HK3RZTNQM4QF90
DOI: 10.6084/m9.figshare.29151998
title: Comparative transcriptome atlas as an assistive modality for complex classification of rare kidney cancers

description: This dataset includes the code and raw or processed data used in our study of 219 renal tumors.
Multi-omics analyses such as RNA-seq and whole genome sequencing (WGS) were performed.
DOI: 10.6084/m9.figshare.29151998.v1
title: Comparative transcriptome atlas as an assistive modality for complex classification of rare kidney cancers

description: This dataset includes the code and raw or processed data used in our study of 219 renal tumors.
Multi-omics analyses such as RNA-seq and whole genome sequencing (WGS) were performed.
DOI: 10.25919/yync-q309
title: NBDL-HK3RZTNRP4Q754
DOI: 10.25919/g09e-4938
title: NBDL-HK3RC4ENHA7ZCG
DOI: 10.25919/wjek-sr95
title: NBDL-HK3RDJR1M2S772
DOI: 10.25919/t52d-kj71
title: NBDL-HK3RDJS8J36FRY
DOI: 10.25919/tk37-3m47
title: NBDL-HK3RDJT0H326GV
DOI: 10.25919/1b51-sx49
title: NBDL-HK3RDJQSK2EMFH
DOI: 10.25919/s4q6-6161
title: NBDL-HK3RC4CWJAE0NH
DOI: 10.25919/7n5c-tg06
title: NBDL-HK3RC4CEPA1ATS
DOI: 10.25919/kqm2-s967
title: NBDL-HK3RC4E0QA4MXW
DOI: 10.25919/jfb7-b959
title: NBDL-HK3RDJQNK211B1
DOI: 10.25919/kdbt-mt85
title: NBDL-HK3RDJS4J37NJE
DOI: 10.17605/osf.io/zejm7
title: Data

description: data for the project
DOI: 10.25919/f1ze-vq19
title: NBDL-HK3RX9EDKZBZ4Y
DOI: 10.25919/gdq8-s998
title: NBDL-HK3RDJSYP375VP
DOI: 10.25919/b2pr-0e05
title: NBDL-HK3R7JQPP1NPK1
DOI: 10.6084/m9.figshare.29939348
title: Dimensionality-Tailored Pure Organic Semiconductor with High Hole Mobility for Low-dose X-ray Imaging

description: The Source Data underlying all figures and results are provided within this document.
DOI: 10.6084/m9.figshare.29939348.v1
title: Dimensionality-Tailored Pure Organic Semiconductor with High Hole Mobility for Low-dose X-ray Imaging

description: The Source Data underlying all figures and results are provided within this document.
DOI: 10.25919/7g5n-zk89
title: NBDL-HK3R7JQ0J1JSZS
DOI: 10.25919/n58s-qh77
title: NBDL-HK3RC4D4JA38YH
DOI: 10.25919/71j1-g851
title: NBDL-HK3R7JSCK14JT2
DOI: 10.6084/m9.figshare.30206509
title: Strongly cohesive Chang’e-6 lunar soil

description: Source data of Figs. 1-4, source data of Extended Data Figs. 1, 3-6, 8, sources data of Supplement Figs. 1g, 2f, 3
DOI: 10.6084/m9.figshare.30206509.v1
title: Strongly cohesive Chang’e-6 lunar soil

description: Source data of Figs. 1-4, source data of Extended Data Figs. 1, 3-6, 8, sources data of Supplement Figs. 1g, 2f, 3
DOI: 10.25919/j5xx-ef57
title: NBDL-HK3R7JR7N12N06
DOI: 10.6084/m9.figshare.29910884
title: In-Situ Dynamic Regulation of Strain at the Buried Interface for Stable Perovskite Solar Cells

description: J-V, MPPT, EQE, and so on.
DOI: 10.6084/m9.figshare.29910884.v1
title: In-Situ Dynamic Regulation of Strain at the Buried Interface for Stable Perovskite Solar Cells

description: J-V, MPPT, EQE, and so on.
DOI: 10.25919/hvk3-6z70
title: NBDL-HK3RDJSFG36AKT
DOI: 10.5281/zenodo.17708260
title: Mass cytometry analysis of CaCo2 cell lines expressing various oncogenes

description: This dataset contains the measurements of a CyTOF experiment of CaCo2 cell lines that where transduced with different oncogenes
DOI: 10.25919/h5x9-9712
title: NBDL-HK3R7JQQM1NRXX
DOI: 10.5281/zenodo.17708259
title: Mass cytometry analysis of CaCo2 cell lines expressing various oncogenes

description: This dataset contains the measurements of a CyTOF experiment of CaCo2 cell lines that where transduced with different oncogenes
DOI: 10.25919/btps-9b11
title: NBDL-HK3RC4EAKA74NM
DOI: 10.25919/e4hp-zh63
title: NBDL-HK3R5BR3GX45E9
DOI: 10.25919/f6m9-d685
title: NBDL-HK3RC4E8QA77GW
DOI: 10.25919/80dt-3616
title: NBDL-HK3RC4D7MA3C7N
DOI: 10.25919/a4f3-jd98
title: NBDL-HK3RX9D6GZPCXQ
DOI: 10.25919/erm3-vv96
title: NBDL-HK3R7JQJP1NWAH
DOI: 10.25919/e6xn-hz05
title: NBDL-HK3RX9DAGZP5A7
DOI: 10.15468/dl.89gpn4
title: Occurrence Download

description: A dataset containing 1000134 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is NIEK_NES"
 ]
}

 The dataset includes 1000134 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007171-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/9cnn8jmhh9.1
title: The role of behavioural traits in successful fishway passage during seasonal brown trout (Salmo trutta) migrations

description: Here, we provide data.
DOI: 10.5281/zenodo.17451657
title: Quantum enhanced metrology based on flipping trajectory of cold Rydberg gases

description: These folders contain data used to reproduce figures in main text.

 

Folder Figure3 contains the raw data for Figure 3a (Folder 3a), and phase boundary data (Figure3a(phase_boundaries_data).csv). Additionally, the files Figure3b.csv, Figure3c.csv, and Figure3d.csv represent the raw data for Figures 3b, 3c, and 3d, respectively. The raw data for Figure 3e in the Folder 3a.

 

Folder Figure4 contains the raw data for Figure 4a (Folder Figure4a1(original data), Figure4a2(original data), Figure4a3(original data), Figure4a4(original data), Figure4a5(original data), andFigure4a6(original data)), and phase boundary data (Figure4a(phase_boundaries_data).csv). Additionally, the files Figure4b.csv, Figure4c.csv, and Figure4d.csv represent the raw data for Figures 4b, 4c, and 4d, respectively.

 

Folder Figure5 contains the raw data for Figure 5a, 5b, and 5c (Folder Figure5a(original data), Figure5b(original data), and Figure5c(original data)), and corresponding phase boundary data (Figure5a(phase_boundaries_data).csv, Figure5b(phase_boundaries_data).csv, and Figure5c(phase_boundaries_data).csv). Additionally, the files Figure5d.csv, Figure5e.csv, Figure5f.csv, Figure5g.csv, and Figure5hcsv represent the raw data for Figures 5d, 5e, 5f, 5g, and 5h respectively.



Folder Figure6 contains the raw data for Figure 6a, 6b, 6c, and 5d (Folder Figure6a(original data), Figure6b(original data), Figure6c(original data), and Figure6d(original data)), and corresponding phase boundary data (Figure6a(phase_boundaries_data).csv, Figure6b(phase_boundaries_data).csv, Figure6c(phase_boundaries_data).csv, and Figure6d(phase_boundaries_data).csv).