cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4qrfj6q72
title: Influence of past climate change on phylogeography and demographic history of narwhals, Monodon monoceros

description: The Arctic is warming at an unprecedented rate, with unknown consequences
 for endemic fauna. However, Earth has experienced severe climatic
 oscillations in the past, and understanding how species responded to them
 might provide insight into their resilience to near-future climatic
 predictions. Little is known about the responses of Arctic marine mammals
 to past climatic shifts, but narwhals (Monodon monoceros) are considered
 one of the endemic Arctic species most vulnerable to environmental change.
 Here, we analyze 121 complete mitochondrial genomes from narwhals sampled
 across their range, and use them in combination with species distribution
 models to elucidate the influence of past and ongoing climatic shifts on
 their population structure and demographic history. We find low levels of
 genetic diversity and limited geographic structuring of genetic clades. We
 show that narwhals experienced a long-term low effective population size,
 which increased after the Last Glacial Maximum (LGM), when the amount of
 suitable habitat expanded. Similar post-glacial habitat release has been a
 key driver of population size expansion of other Polar marine predators.
 Our analyses indicate that habitat availability has been critical to the
 success of narwhals, raising concerns for their fate in an increasingly
 warming Arctic.
description: Details about DNA extraction, library preparation, bioinformatics
 can be found in the methods of our manuscript. The data file is the fasta
 alignment of the 121 mitochondrial genomes of narwhals, which was used for
 the analyses.
DOI: 10.5061/dryad.bzkh1895s
title: Investigation of damping effects on low-frequency steady-state acoustical behaviour of coupled spaces

description: In the low-frequency range, the acoustical behaviour of enclosed spaces is
 strongly influenced by excited acoustic modes resulting in a spatial
 irregularity of a steady-state sound field. In the paper, this problem has
 been examined theoretically and numerically for a system of coupled spaces
 with complex-valued conditions on boundary surfaces. Using a modal
 expansion method, an analytic formula for the Green's function was
 derived allowing to predict the interior sound field for a pure-tone
 excitation. To quantify the spatial irregularity of steady-state sound
 field, the parameter referred to as the mean spatial deviation was
 introduced. A numerical simulation was carried out for the system
 consisting of two coupled rectangular subspaces. Eigenfunctions and
 eigenfrequencies for this system were determined using the high-accuracy
 eigenvalue solver. As was evidenced by computational data, for small sound
 damping on absorptive walls the mean spatial deviation peaks at
 frequencies corresponding to eigenfrequencies of strongly localized modes.
 However, if the sound damping is much higher, the main cause of spatial
 irregularity of the interior sound field is the appearance of sharp
 valleys in a spatial distribution of a sound pressure level.
DOI: 10.5061/dryad.qz612jmbb
title: Lorentzian filter correction of turbulence measurements on oscillating floating platforms: impact on wind spectra and eddy covariance fluxes

description: Turbulence and eddy covariance measurements on a floating platform over
 water surfaces can be contaminated by platform oscillations, which may
 affect the calculated air–water exchange. The conventional method for
 decontamination of the platform oscillations from the wind velocity
 measurements requires the installation of an additional sensitive, and
 often costly, motion sensor. This paper examines a new mathematical
 decontamination method, termed Lorentzian filter, which avoids the need
 for such an instrument. The method, based on the Lorentzian function,
 capitalizes on the pseudo-harmonic behavior of the platform oscillations
 and reduces the amplitude of turbulent wind velocity data detected as
 artifacts at the specific natural frequencies of the platform. The
 Lorentzian filter was applied to wind velocity data measured by sonic
 anemometer and eddy covariance system over the Dead Sea, Israel, for 30
 days. We examined three approaches of dealing with motion contamination:
 Lorentzian filter decontamination, motion sensor decontamination, and
 non-filtered raw wind velocity. Using the 3D wind velocity series, we
 examined the wind spectra, the co-spectra of water vapor concentration and
 horizontal wind speed with vertical wind speed and H2O and momentum
 fluxes. The Lorentzian filter performed very well in decontaminating the
 wind spectrum, meaning that it efficiently identified the contamination in
 the natural oscillation frequency and returned a decontaminated wind
 velocity time series. The co-spectra and fluxes were less prone to the
 contamination of platform oscillations, presumably due to low correlations
 between the spurious wind velocity components and other measured scalars,
 such as water vapor.
description: The Loretzian filter is a
 MATLAB code.  Raw
 data was acquired from Eddy Covariance stations and processed through
 MATLAB using the Lorentzian filter or the code of Ikawa and Oechel et al.
 (2015) mentioned in the paper to achieve filtered data. Then, the data was
 processed through the EddyPro software (Licor) to achieve wind spectra,
 co-spectra and the different fluxes.  
description: ReadMe and an instruction
 file for the Lorentzian filter are attached.
DOI: 10.15468/dl.vjnbex
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anarthrophyllum patagonicum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 15 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002296-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.66t1g1jzq
title: Data from: Quantifying spatiotemporal occupancy dynamics and multi-year core-use areas at a species range boundary

description: Aim Many species face large-scale range contractions and predicted
 distributional shifts in response to climate change, shifting forest
 characteristics, and anthropogenic disturbances. Canada lynx (Lynx
 canadensis) are listed as threatened under the U.S. Endangered Species Act
 and were recently recommended for delisting. Predicted climate-driven
 losses in habitat quality and quantity may negatively affect the
 northeastern Minnesota lynx population, one of six remaining resident
 populations in the contiguous United States. We develop a large-scale
 monitoring protocol and dynamic occupancy modeling framework to identify
 multi-year core use areas and track spatiotemporal occurrence at the
 southern periphery of the species range.   Location Northeastern
 Minnesota lynx geographic unit, Superior National Forest, and designated
 critical habitat, Minnesota, USA.   Methods Spatially and
 temporally replicated snow track surveys were used to collect lynx
 detection/non-detection data across five winters (2014–15 to 2018–19)
 covering &gt;17,000 km within the 22,100 km2 study area. We used a
 dynamic occupancy model to evaluate lynx occupancy, persistence,
 colonization, and habitat covariates affecting these processes.  
 Results Lynx occupancy probabilities displayed high spatial and temporal
 variability, with grid cell-specific probabilities ranging from 0.0 in
 periphery regions to consistently near 1.0 in multi-year core use areas,
 indicating low turnover rates in those areas. Lynx colonization and
 persistence increased in areas with more evergreen forest and greater
 average snowfall, while forest characteristics (3–5 m and 10–30 m
 vegetation density) had mixed relationships with occupancy dynamics. We
 identified 55 grid cells classified as multi-year core use areas across
 relatively contiguous regions of high average snowfall and percent conifer
 forest.   Main conclusions Our study demonstrates a
 landscape-scale multi-year monitoring program assessing the effects of
 habitat characteristics and anthropogenic factors on species
 distributional changes and landscape-level occupancy dynamics. Our
 framework incorporating landscape-scale resource selection, core use area
 concepts, and dynamic occupancy models provides a flexible approach to
 identify population-level mechanisms driving species persistence and key
 areas for conservation protection.
description: This dataset and R script provides the final formatted data to
 run the dynamic occupancy model presented in: Hostetter NJ, D Ryan, D
 Grosshuesch, T Catton, S Malick-Wahls, TA Smith, and B
 Gardner. Quantifying spatiotemporal occupancy dynamics and multi-year core
 use areas at a species range boundary. Diversity and
 Disributions. 
description: Please contact D. Ryan or NJ Hostetter for additional data or
 usage requests.
DOI: 10.5061/dryad.rv15dv457
title: Data from: Remission of type 2 diabetes following a short-term intervention with insulin Glargine, Metformin and Dapagliflozin.

description: This dataset contains Supplemental Tables for the manuscript.
DOI: 10.6071/m3238r
title: Data from: Single-cell transcriptomic analysis of tumor-derived fibroblasts and normal tissue-resident fibroblasts reveals fibroblast heterogeneity in breast cancer

description: Cancer-associated fibroblasts (CAFs) are a prominent stromal cell type in
 solid tumors and molecules secreted by CAFs play an important role in
 tumor progression and metastasis. CAFs coexist as heterogeneous
 populations with potentially different biological functions. Although CAFs
 are a major component of the breast cancer stroma, molecular and
 phenotypic heterogeneity of CAFs in breast cancer is poorly understood. In
 this study, we investigated CAF heterogeneity in triple-negative breast
 cancer (TNBC) using a syngeneic mouse model, BALB/c-derived 4T1 mammary
 tumors. Using single-cell RNA sequencing (scRNA-seq), we identified six
 CAF subpopulations in 4T1 tumors including: 1) myofibroblastic CAFs,
 enriched for α-smooth muscle actin and several other contractile proteins;
 2) ‘inflammatory’ CAFs with elevated expression of inflammatory cytokines;
 and 3) a CAF subpopulation expressing major histocompatibility complex
 (MHC) class II proteins that are generally expressed in antigen-presenting
 cells. Comparison of 4T1-derived CAFs to CAFs from pancreatic cancer
 revealed that these three CAF subpopulations exist in both tumor types.
 Interestingly, cells with inflammatory and MHC class II-expressing CAF
 profiles were also detected in normal breast/pancreas tissue, suggesting
 that these phenotypes are not tumor microenvironment-induced. This work
 enhances our understanding of CAF heterogeneity, and specifically
 targeting these CAF subpopulations could be an effective therapeutic
 approach for treating highly aggressive TNBCs.
description: We performed
 scRNA-seq of all viable cells from 4T1 tumors, immune-depleted stromal
 cells from 4T1-Thy1.1 tumor, immune-depleted cells from mT3 subcutaneous
 tumors and fibroblasts isolated from normal mammary fat pads. Tissues were
 processed to obtain single cell suspensions of cell populations of
 interest as described before (Hum et al, Cancers 2020;
 doi.org/10.3390/cancers12030690) and prepared for single cell sequencing
 using Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X
 Genomics, Pleasanton, CA, USA; Catalog no. 1000075) on a 10X Genomics
 Chromium Controller following manufacturers protocol. scRNA-Seq libraries
 were sequenced using Illumina NextSeq 500. The Cell Ranger Single-Cell
 Software Suite (10X Genomics, Pleasanton, CA, USA) was used to perform
 sample demultiplexing, barcode processing, and single-cell 3′gene
 counting. Samples were aligned to the mouse genome (mm10) using
 “cellranger mkfastq” with default parameters. Unique molecular identifier
 (UMI) counts were generated using “cellranger count”. Further analysis was
 performed in R using the Seurat package.
description: Raw gene
 expression counts are provided for: all viable
 cells from 4T1 tumors (4T1_vaibale_raw_counts.txt), CAFs from
 4T1-Thy1.1 tumor (4T1_Thy1.1_CAF_raw.txt), CAFs from mT3
 tumor (MT3_CAF_raw.txt) and normal mammary
 fibroblasts (Normal_mammary_fibroblasts_raw.txt).
DOI: 10.5281/zenodo.18312113
title: Pneumonia and antibiotic use in a northern Pakistani village

description: Data describing the use of antibiotics to treat cases of pneumonia in children in Oshikhandass, a village in northern Pakistan. Additional files describe maternal understanding of antibiotic use and case/control data.
DOI: 10.15468/dl.4bveq3
title: Occurrence Download

description: A dataset containing 5422 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Moroteuthopsis ingens",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 5422 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002295-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.fj6q573r3
title: Data from: Plants’ ability to sense and respond to airborne sound is likely to be adaptive: reply to comment by Pyke et al.

description: (Veits et al. 2019) demonstrated, for the first time, a rapid response of
 a plant to the airborne sounds of pollinators. Pyke et al. argue that this
 response is unlikely to be adaptive. Here we clarify some
 misunderstandings, and demonstrate the potential adaptive value using
 theoretical modelling and field observations.
DOI: 10.5061/dryad.p8cz8w9mc
title: Activation of astrocytes in hippocampus decreases fear memory through adenosine A1 receptors

description: Astrocytes respond to and regulate neuronal activity, yet their role in
 mammalian behavior remains incompletely understood. Especially unclear is
 whether, and if so how, astrocyte activity regulates contextual fear
 memory, the dysregulation of which leads to pathological fear-related
 disorders. We generated GFAP-ChR2-EYFP rats to allow the specific
 activation of astrocytes in vivo by optogenetics. We found that after
 memory acquisition within a temporal window, astrocyte activation
 disrupted memory consolidation and persistently decreased contextual but
 not cued fear memory accompanied by reduced fear-related anxiety behavior.
 In vivo microdialysis experiments showed astrocyte photoactivation
 increased extracellular ATP and adenosine concentrations. Intracerebral
 blockade of adenosine A1 receptors (A1Rs) reversed the attenuation of fear
 memory. Furthermore, intracerebral or intraperitoneal injection of A1R
 agonist mimicked the effects of astrocyte activation. Therefore, our
 findings provide a deeper understanding of the astrocyte-mediated
 regulation of fear memory, and suggest a new and important therapeutic
 strategy against pathological fear-related disorders.
DOI: 10.5061/dryad.zkh189373
title: Detecting phylogenetic signal and adaptation in papionin cranial shape by decomposing variation at different spatial scales

description: Phylogenetic reconstruction based on morphometric data is hampered by
 homoplasies. For example, many similarities in cranial form between
 primate taxa more strongly reflect ecological similarities rather than
 phylogenetic relatedness. However, the way in which the different cranial
 bones constitute cranial form is, if at all, of less functional relevance
 and thus largely hidden from selection. We propose that these
 “constructional details” are better indicators of phylogenetic history
 than any large-scale shape feature or raw form variable. Within a
 geometric morphometric context, we show how to analyze the relative extent
 of bones independently of differences in overall shape. We also show how
 to decompose total shape variation into small-scale and large-scale shape
 variation. We apply both methods to the midsagittal cranial morphology of
 papionin monkeys, which are well known for the discrepancy between
 morphological similarities and phylogenetic relationships. We study
 phylogenetic signal and functional adaptation using a molecular phylogeny
 and contextual data on feeding ecology and locomotor behavior. As
 expected, total cranial shape, bone outline shape, and large-scale shape
 features were only weakly associated with phylogenetic distance. But the
 relative bone contributions and small-scale shape features were both
 highly correlated with phylogenetic distances. By contrast, the
 association with ecological and behavioral variables was strongest for the
 outline shape and large-scale shape features. Studies of morphological
 adaptation and phylogenetic history thus profit from a decomposition of
 shape variation into different spatial scales.
description: - Supplementary tables and figures for the main manuscript
 (Grunstra et al., Systematic Biology) - 2D coordinates
 of 70 midsagittal landmarks, collected for 61 specimens from 16 different
 papionin species as well as 6 specimens from two non-papionin Old World
 monkey taxa, <i>Cercopithecus mitis </i>and <i>Colobus
 guereza.</i> Each line in the text file contains the coordinates of
 one specimen, ordered as (x1, y1, x2, y2, x3, y3, ...). These data were
 collected by N. Grunstra and S. Bartsch. - Species
 labels for the 67 specimens - R package
 "prWarps" (written by Anne Le Maítre) with functions to
 decompose total shape variation into outline and resudial variation and
 into small-scale and large-scale variation (see main
 manuscript). - Worked example using the R package and
 the landmark data (written by Anne Le Maítre) .
DOI: 10.5061/dryad.rfj6q5776
title: Multituberculate mammals from the Middle Jurassic of Western Siberia, Russia, and the origin of Multituberculata

description: Tashtykia primaeva gen. et sp. nov. and Tagaria antiqua gen. et sp. nov.
 (Multituberculata incertae sedis) are described based on isolated teeth
 from the Middle Jurassic (Bathonian) Itat Formation from the Berezovsk
 coal mine in Krasnoyarsk Territory, Western Siberia, Russia. Tashtykia
 primaeva gen. et sp. nov. is characterized by a P5 with three rows of
 cusps (cusp formula 2B:4M:6L) and a high sectorial p4 with two triangular
 lobes, five serrations associated with labial and lingual ridges, and a
 unique distal cusp. Tagaria antiqua gen. et sp. nov. differs from all
 other multituberculates by a very long P5 with flat crown and many cusps
 arranged in three rows (4B:6M:7L). Morphologically the teeth of
 Kermackodon and Megaconus are transitional between Euharamiyida and Middle
 Jurassic Multituberculata. Kermackodon shares several characteristics with
 Euharamiyida, such as pointed cusps on the molars connected by
 longitudinal ridges, a distolabial cusp on the M2 that is higher than the
 other cusps, and a single large sectorial premolar (p4) with a distal
 basin. The euharamiyidan characters of Megaconus are an ultimate upper
 premolar with a shorter lingual side, a p4 with a distal basin, and one
 cusp on the molars being larger than the other cusps. In addition,
 Megaconus shares an ultimate upper premolar with three rows of cusps,
 horizontal wear on the molars, and pyramidal cusps on the molars separated
 by transverse grooves with multituberculates. The multituberculate
 characters of Kermackodon include horizontal rather than basined wear on
 the surface of the molars and serrations on the p4.
description: Specimen PIN 5087/108 was
 scanned with a resolution of 3.94 μm using the 180 kV x-ray tube of the
 v|tome|x s μCT device (GE Sensing & Inspection Technologies GmbH
 phoenix|x-ray) housed in the Institut für Geowissenschaften, Universität
 Bonn, Germany. Scan settings were 90 kV and 90 μA with a shutter speed of
 400 ms per capture. The instrument produced isotropic voxels, and the
 single image size is 1024 × 1024 pixels. Specimens LMCCE 010/2 and LMCCE
 010/4 were both scanned at a resolution of 2.82 µm using the 180 kV x-ray
 tube and scan settings were 80 kV and 110 µA with a capture timing of 1000
 ms (the machine has since been improved now producing an image size of
 2048 x 2048). Avizo 8 (Thermo Fisher Scientific) was used for segmentation
 and creating surface models. Polyworks 2014 (innovmetric) was used to
 smooth the surface in case of LMCCE 010/4 using the Gouraud filter
 function (at correction levels 0.1 and 0.3), and for the reduction of data
 sizes.
DOI: 10.5061/dryad.p2ngf1vn1
title: Data from: Flowering plant composition shapes pathogen infection intensity and reproduction in bumble bee colonies

description: Pathogens pose significant threats to pollinator health and food
 security.  Pollinators can transmit diseases during foraging, but
 the consequences of plant species composition for infection is unknown. In
 agroecosystems, flowering strips or hedgerows are often used to augment
 pollinator habitat. We used canola as a focal crop in tents, and
 manipulated flowering strip composition using plant species we had
 previously shown to result in higher or lower bee infection in short-term
 trials. We also manipulated initial colony infection to assess impacts on
 foraging behavior. Flowering strips using high-infection plant species
 nearly doubled bumble bee colony infection intensity compared to
 low-infection plant species, with intermediate infection in canola-only
 tents. Both infection treatment and flowering strips reduced visits to
 canola, but we saw no evidence that infection treatment shifted foraging
 preferences. Although high-infection flowering strips increased colony
 infection intensity, colony reproduction was improved with any flowering
 strips compared to canola alone.  Effects of flowering strips on
 colony reproduction were explained by nectar availability, but effects of
 flowering strips on infection intensity were not. Thus, flowering strips
 benefited colony reproduction by adding floral resources, but certain
 plant species also come with a risk of increased pathogen infection
 intensity.
DOI: 10.5061/dryad.f4qrfj6st
title: Widespread homogenization of plant communities in the Anthropocene

description: Native biodiversity decline and non-native species spread are major
 features of the Anthropocene. Both processes can drive biotic
 homogenization by reducing trait and phylogenetic differences in species
 assemblages between regions, thus diminishing the regional distinctiveness
 of biotas and likely have negative impacts on key ecosystem functions.
 However, a global assessment of this phenomenon is lacking. Here, using a
 dataset of &gt;200,000 plant species, we demonstrate widespread and
 temporal decreases in species and phylogenetic turnover across grain sizes
 and spatial extents. The extent of homogenization within major biomes is
 pronounced and is overwhelmingly explained by non-native species
 naturalizations. Asia and North America are major sources of non-native
 species; however, the species they export tend to be phylogenetically
 close to recipient floras. Australia, the Pacific and Europe, in contrast,
 contribute fewer species to the global pool of non-natives, but represent
 a disproportionate amount of phylogenetic diversity. The timeline of most
 naturalisations coincides with widespread human migration within the last
 ~500 years, and demonstrates the profound influence humans exert on
 regional biotas beyond changes in species richness.