cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7272/q67h1gvs
title: Impairment of endothelial function by cigarette smoke and e-cigarette aerosol requires RAGE

description: Introduction: Although e-cigarette is known to cause detrimental
 physiological alterations in the cardiovascular system, the molecular
 mechanism of e-cigarette-induced vascular impairment is relatively
 unexplored. We investigated whether the inhibition of RAGE prevents
 impairment of vasomotor function from acute and chronic e-cigarette
 exposure.  Hypothesis: RAGE is required to cause
 e-cigarette-induced impairment of endothelial vasodilation. Methods: In
 both exposure settings, anaesthetized rats (n=8/group) were exposed to
 aerosols from flavorless tank-style e-cigarettes with and without freebase
 nicotine (12 mg/mL) or air. For acute exposure, exposure was done in a
 singles session of 10 cycles of pulsatile 5s exposure over 5 minutes using
 a Gram REsearch analytical vaping machine drawing 55ml. All rats received
 RAGEi or DMSO i.p. 1h pre-exposure. FMD was measured pre-exposure and 10
 minutes after the end of the exposure. For sub-acute exposure, the
 exposure consisted of a single session of 120 cycles of pulsatile 5s
 exposure over 1h/day for 2 weeks. All the rats received RAGEi or DMSO i.p.
 1h pre-exposure daily during acclimation and exposure (total of 3 weeks).
 Echocardiography was conducted one day before the end of the experiment.
 FMD was measured before and after the exposure on the last day of the
 experiment.  Results: Exposure to e-cigarette aerosol with and
 without nicotine impaired FMD in vehicle groups in both acute and subacute
 exposures with no change in air control. As expected, the positive control
 of cigarette exposure impaired FMD in the vehicle group in acute settings.
 However, FPS-ZM1 prevented the FMD impairment in e-cigarette aerosol
 exposures and cigarette exposures in both acute and subacute exposures
 with no changes in air control. Conclusions: RAGE plays a role in
 mediating e-cigarette-induced acute and sub-acute impairment of
 endothelial vasodilatory function.
description: For femoral artery diameter data, raw ultrasound data were
 collected by a Vevo 3100LT micro-ultrasound system (VisualSonics Inc.,
 Toronto, Canada). Ultrasound images were processed and femoral artery
 diameter was measured by an automated system (Brachial Analyzer, Medical
 Imaging Applications, Coralville, IA).  For cardiac
 function data, raw echocardiograms was collected by a Vevo 3100LT
 micro-ultrasound system (VisualSonics Inc., Toronto, Canada) and
 echocardiographic parameters were measured by a VevoLab software
 (VisualSonics Inc., Toronto, Canada). 
description: Brachial Analyzer (Medical Imaging Applications, Coralville, IA)
 and VevoLab software are required to open the data files. See Methods
 above for details.
DOI: 10.5061/dryad.612jm6489
title: Dataset for density estimation for an island population of raccoon dogs in Japan

description: Estimation of the population size is essential for understanding
 population dynamics. Estimating animal density using multiple methods
 and/or multiple attempts is required for accurate estimations. Raccoon dog
 (Nyctereutes procyonoides) is native to East Asia, including Japan, and
 has become an invasive species in Europe. Information on raccoon dog
 density in their native range is important to understand their invasion;
 however, relatively few studies have been conducted on raccoon dog density
 in their native range. In this study, we extracted DNA from fecal samples
 of raccoon dogs inhabiting a small island in Japan and conducted density
 estimation over two periods using DNA capture-recapture methods: CAPWIRE
 and SECR. We also investigated sex ratio using genetic sex identification.
 Density estimates using SECR were approximately threefold different
 between the two study periods: 17.2 individuals per km2 in 2018 and 49.0
 individuals per km2 in 2020. In contrast, estimates using CAPWIRE
 were relatively stable: 21.7 individuals per km2 in 2018 and 24.3
 individuals per km2 in 2020. A drastic increase or decrease is
 not expected during the study period, and thus, density estimates using
 CAPWIRE are more reasonable than those using SECR. The small number of
 samples per individual might result in low accuracy of density estimates
 by SECR. The density estimated by CAPWIRE was similar to that in the main
 island in Japan and higher than that in Europe. Feeding competition with
 other omnivorous carnivores and/or predation risk by wolves might maintain
 the low density in Europe. The sex ratio of raccoon dogs was 1:1, which
 was similar to the values in invasive raccoon dogs and other canids.
 Further genetic census, including sex identification in various landscapes
 in their native and invasive range, will enable us to understand not only
 the ecology of raccoon dogs but also their adaptations to their invading
 areas.
DOI: 10.5061/dryad.5x69p8d8w
title: Vegetation and trait data of the Houtman Abrolhos Islands, Australia

description: Dispersal and environmental filtering processes determine plant species
 colonization success on islands and can be identified by functional
 traits. However, the lack of synthesis about the varying methodological
 approaches in functional ecology hampers generalisation of filtering
 processes across island systems. Here, we provide island-plant data for 70
 islands of the Houtman Abrolhos archipelago, Western Australia as well
 list species from their source pool. This data can be used to test the
 predictions made in the accompanying publication as well as for any other
 study requiring island-level species richness, species pool and trait
 (leaf area, seed mass, plant height) data.
description: Please refer to detailed methods stated in main
 publication.
DOI: 10.5061/dryad.9p8cz8wnf
title: Data from: Remotely sensed environmental measurements detect decoupled processes driving population dynamics at contrasting scales

description: The increasing availability of satellite imagery has supported a rapid
 expansion in forward-looking studies seeking to track and predict how
 climate change will influence wild population dynamics. However, these
 data can also be used in retrospect to provide additional context for
 historical data in the absence of contemporaneous environmental
 measurements. We used 167 Landsat-5 Thematic Mapper (TM) images spanning
 13 years to identify environmental drivers of fitness and population size
 in a well-characterized population of banner-tailed kangaroo rats
 (Dipodomys spectabilis) in the southwestern United States. We found
 evidence of two decoupled processes that may be driving population
 dynamics in opposing directions over distinct time frames. Specifically,
 increasing mean surface temperature corresponded to increased individual
 fitness, where fitness is defined as the number of offspring produced by a
 single individual. This result contrasts with our findings for population
 size, where increasing surface temperature led to decreased numbers of
 active mounds. These relationships between surface temperature and (i)
 individual fitness and (ii) population size would not have been identified
 in the absence of remotely sensed data, indicating that such information
 can be used to test existing hypotheses and generate new ecological
 predictions regarding fitness at multiple spatial scales and degrees of
 sampling effort. To our knowledge, this study is the first to directly
 link remotely sensed environmental data to individual fitness in a nearly
 exhaustively sampled population, opening a new avenue for incorporating
 remote sensing data into eco-evolutionary studies.
description: Each file contains the predictor and response variable values
 used in regressions. For the 'type' column, 1 = annual means, 2
 = rainy season means. For the season column where type = 2, 1 = summer
 rainy season means, 2 = winter rainy season means.
DOI: 10.15468/dl.cwd4bh
title: Occurrence Download

description: A dataset containing 7281449 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "TaxonKey is Strigiformes"
 ]
}

 The dataset includes 7281449 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003514-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.vx0k6djxs
title: Data for: Photoperiod effects in a freshwater community: amphibian larvae develop faster and zooplankton abundance increases under an early-season photoperiod

description: Organisms that shift their phenologies in response to global warming will
 experience novel photic environments, as photoperiod (daylength) continues
 to follow the same annual cycle. How different organisms respond to novel
 photoperiods could result in phenological mismatches and altered
 interspecific interactions. We conducted an outdoor mesocosm experiment
 exposing green frog (Rana clamitans) larvae, gray treefrog (Hyla
 versicolor) larvae, phytoplankton, periphyton, and zooplankton to a
 three-month shift in photoperiod: an early-season photoperiod (simulating
 April) and a late-season photoperiod (simulating July). We manipulated
 photoperiod by covering and uncovering tanks with clear or light-blocking
 lids to mimic realistic changes in daylength. We assessed amphibian life
 history traits and measured phytoplankton, periphyton, and zooplankton
 abundances. Green frog larvae and gray treefrog metamorphs were more
 developed under the early-season photoperiod. Gray treefrog total length
 was also reduced, but photoperiod did not affect green frog total length.
 Although phytoplankton and periphyton abundances were not affected by
 photoperiod, copepod nauplii were in greater abundance under the
 early-season photoperiod. Overall, this simplified aquatic community did
 not exhibit significant changes to structure when exposed to a three-month
 shift in photoperiod. Temperate amphibians that breed earlier in the year
 may develop faster, which may have long-term costs to post-metamorphic
 growth and performance. Asynchronous shifts in zooplankton abundances in
 response to altered photoperiods could subsequently affect freshwater
 community structure. While photoperiod has been shown to individually
 affect freshwater organisms, our study using replicated outdoor wetland
 communities shows that the comprehensive effects of photoperiod may be
 less important than other cues such as temperature and precipitation.
DOI: 10.5061/dryad.8931zcrwp
title: Data for: The role of temperature in the start of seasonal infectious disease epidemics

description: Many infectious diseases display strong seasonal dynamics. When
 both hosts and parasites are influenced by seasonal variables, it is
 unclear if the start of an epidemic is limited by host or parasite factors
 or both. The Daphnia-Pasteuria host-parasite system exhibits seasonal
 epidemics. We aimed to ascertain how temperature contributes to the timing
 of P. ramosa epidemics in early spring. To this aim, we experimentally
 disentangled this effect from the effects of temperature on host
 development and phenology and from that of host traits on parasite time to
 visible infection. We hypothesized that the parasite is additionally
 directly limited by low temperatures beyond its need for
 available hosts. We found that parasite time to visible infection
 decreased with increasing temperature at a faster rate than host time to
 hatching and maturity did, consistent with this hypothesis. We also found
 that hosts hatched from sexual resting stages are less likely to become
 infected than those produced clonally and that hosts resistant to many
 known parasite strains are slower to show signs of visible infection
 compared to those susceptible to many. Together, these results imply that
 climate change could lead to earlier seasonal epidemics for this
 host-parasite system, which may also impact longer-term population
 dynamics.
description: Data were collected from experimental epidemics of the bacterial
 endoparasite <em>Pasteuria ramosa</em> in the
 waterflea <em>Daphnia</em> <em>magna </em>at
 different temperatures. Briefly, five different temperature treatments
 were applied to jars of <em>Daphnia</em> juveniles (of either
 a largely resistant phenotype or a largely susceptible phenotype) and jars
 of <em>Daphnia</em> <em>ephippia</em>. Each
 sampling day the number of juveniles, adults and infected individuals were
 counted. To calculate the main outcome variables (time to hatch for
 ephippia, time to maturation, time to infection), the number of newly
 hatched juveniles, number of new adults (with eggs) and number of new
 infections were calculated on each sampling day and multiplied by the day
 of the experiment. These were then divided by the total number hatched,
 matured or infected, respectively, to obtain an average time to hatch,
 maturation or infection for each experimental jar. For prevalence, the
 total number ever infected over the course of the experiment was divided
 by the maxiumum number of individuals ever present in the jar.
description: Raw data file in CSV format can be opened in Excel, R, Google
 Sheets, etc. Code can be opened in R.
 README file can be opened in Notepad.
DOI: 10.25349/d9rp7x
title: Devereux Slough Solinst Levelogger data (2018–2023)

description: The Devereux Slough is a temporary open-closed estuary (TOCE). There are
 pressure transducers placed throughout the watershed wich measure water
 depth fluctuations. Some pressure transducers that are closer to the mouth
 can detect breach events by recording tidal influence and salinity
 changes. Others are placed in freshwater inlets that typically only pick
 up water depth changes during large storms.
description: This data has been collected with Solinst devices listed on the
 Hydrology_equipment_data.csv sheet. Known elevation reference points are
 used to calculate the elevation of water surface. The data is not
 processed therefore any malfunctions in the devices are reflected in the
 data. Any gaps in data are due to removal and maintenance.
description: All data is in CSV format.
DOI: 10.5061/dryad.bzkh189ft
title: Experimental evidence associates burrowing behavior of Castalia ambigua (Bivalvia: Hyriidae) with shell shape and density

description: Information on freshwater mussel behavior in the sediment is scarce
 worldwide, especially in the Amazon. Laboratory experiments were used to
 measure the responses of the single mussel species Castalia ambigua in
 relation to combinations of two co-occurring different morphotypes
 (Morphotype I with an elongated shell and Morphotype II with a
 rounded shell), and three different densities (4, 8 and 16 mussels).
 Horizontal movements (cm) were calculated by summing changes in the
 position of each specimen and the shell exposure at the sediment-water
 interface was obtained by measuring (mm) the exposed part of the shell.
 Castalia ambigua presented different patterns of shell exposure and
 horizontal movements linked with shell shape and density. Castalia ambigua
 Morphotype I remained less exposed with 4 mussels. In contrast, this
 morphotype was more exposed and tended to aggregate in treatments with 8
 and 16 mussels, similar to observations of Morphotype II at all densities.
 Morphotype II is mainly found in low hydrodynamic energy habitats,
 suggesting that patches with high densities may stabilize the substrate
 around the shells of Morphotype I, which is associated with high
 hydrodynamic energy habitats. We suggest that these patterns may be
 associated with intrinsic factors of the species, such as reproduction,
 sexual dimorphism and feeding. Moreover, additional studies using other
 mussel species belonging to the families Hyriidae and Mycetopodidae are
 important, since the behavior of these mussels in the sediment may provide
 useful information on their functional roles in river ecosystems.
description: This dataset was collected by direct observations of freshwater
 mussel movements in aquaria. The data were processed as described in the
 README file.
description: Non-proprietary format: LibreOffice; Microsoft Excel; other
 spreadsheet applications.
DOI: 10.5061/dryad.41ns1rnkm
title: Female lizards (Eremias argus) reverse Bergmann’s rule across altitude

description: The evolution of body size within and among species is predicted to be
 influenced by multifarious environmental factors. However, the specific
 drivers of body size variation have remained difficult to understand
 because of the wide range of proximate factors that covary with ectotherm
 body sizes across populations with varying local environmental conditions.
 Here, we used female Eremias argus lizards collected
 from different populations across their wide range in China and
 constructed linear mixed models to assess how climatic conditions and/or
 available resources at different altitudes shape the geographical patterns
 of lizard body size across altitude. Lizard populations showed significant
 differences in body size across altitudes. Furthermore, we found that
 climatic and seasonal changes along the altitudinal gradient also
 explained variations in body size among populations. Specifically, body
 size decreased with colder and drier environmental conditions at high
 altitudes, reversing Bergmann’s rule. Limited resources at high altitudes,
 measured by the low vegetative index, may also constrain body
 size. Therefore, our study demonstrates that multifarious
 environmental factors could strongly influence the intraspecific variation
 in organisms’ body size.
description: We collected 432 female
 <em>E.
 argus</em> lizards
 between 2011 through
 2021 from field locations
 across China varying in altitude and environmental conditions. We also
 used the <em>Raster</em> package in R to extract environmental
 variables for each population of lizards in our
 study.
DOI: 10.7937/tcia.2019.deg7zg1u
title: High Resolution Prostate Segmentations for the ProstateX-Challenge

description: We created 66 high resolution segmentations for randomly chosen T2-weighted volumes of the ProstateX challenge. The high resolution segmentations were obtained by considering the three scan directions: for each scan direction (axial, sagittal, coronal), the gland was manually delineated by a medical student, followed by a review and corrections of an expert urologist. These three anisotropic segmentations were fused to one isotropic segmentation by means of shape-based interpolation in the following manner: (1) The signed distance transformation of the three segmentations is computed. (2) The anisotropic distance volumes are transformed into an isotropic high-resolution representation with linear interpolation. (3) By averaging the distances, smoothing and thresholding them at zero, we obtained the fused segmentation. The resulting segmentations were manually verified and corrected further by the expert urologist if necessary. Serving as ground truth for training CNNs, these segmentations have the potential to improve the segmentation accuracy of automated algorithms. By considering not only the axial scans but also sagittal and coronal scan directions, we aimed to have higher fidelity of the segmentations especially at the apex and base regions of the prostate.
DOI: 10.7937/tcia.2019.wgllssg1
title: DICOM SR of clinical data and measurement for breast cancer collections to TCIA

description: Abstract: The Data Integration & Imaging Informatics (DI-Cubed) project explored the issue of lack of standardized data capture at the point of data creation, as reflected in the non-image data accompanying various TCIA breast cancer collections. The work addressed the desire for semantic interoperability between various NCI initiatives by aligning on common clinical metadata elements and supporting use cases that connect clinical, imaging, and genomics data. Accordingly, clinical and measurement data was imported into I2B2 and cross-mapped to industry standard concepts for names and values including those derived from BRIDG, CDISC SDTM, DICOM Structured Reporting models and using NCI Thesaurus, SNOMED CT and LOINC controlled terminology.A subset of the standardized data was then exported from I2B2 to CSV and thence converted to DICOM SR according to the the DICOM Breast Imaging Report template [1], which supports description of patient characteristics, histopathology, receptor status and clinical findings including measurements. The purpose was not to advocate DICOM SR as an appropriate format for interchange or storage of such information for query purposes, but rather to demonstrate that use of standard concepts harmonized across multiple collections could be transformed into an existing standard report representation. The DICOM SR can be stored and used together with the images in repositories such as TCIA and in image viewers that support rendering of DICOM SR content.During the project, various deficiencies in the DICOM Breast Imaging Report template were identified with respect to describing breast MR studies, laterality of findings versus procedures, more recently developed receptor types, and patient characteristics and status. These were addressed via DICOM CP 1838, finalized in Jan 2019, and this subset reflects those changes.1. DICOM Breast Imaging Report Templates. Available from: http://dicom.nema.org/medical/dicom/current/output/chtml/part16/sect_BreastImagingReportTemplates.html
DOI: 10.7937/tcia.2020.bry9-4n29
title: Imaging characterization of a metastatic patient derived model of adenocarcinoma colon: PDMR-997537-175-T

description: Pre-clinical animal models of spontaneous metastatic cancer are infrequent; the few that exist are resource intensive because determination of the presence of metastatic disease, metastatic burden, and response to therapy normally require multiple timed cohorts with animal sacrifice and extensive pathological examination. We identified and characterized a patient derived xenograft model with metastatic potential, adenocarcinoma colon xenograft 997537-175-T. In this study we performed a detailed imaging characterization (workflow below) of this model, which develops spontaneous lung metastases, details are provided in the attached standard operating procedures. Tumors in half of the mice were resected in the range 200-300 cm3 size; tumors in the other half were allowed to grow until it was necessary to euthanize them because of tumor size.
DOI: 10.7937/tcia.2020.jit9grk8
title: RIDER Lung CT Segmentation Labels from: Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach

description: This collection contains images from 32 non-small cell lung cancer (NSCLC) patients based on the public open image collection RIDER Lung CT on TCIA. For these subjects a radiation oncologist was blinded to the all delineations of the 3D volume of the gross tumor volume. They were then asked to manually delineate the gross tumour volume in both the test image and the re-test image. The process was repeated using an in-house autosegmentation method. There is no clinical outcome data associated with this dataset. This dataset refers to the RIDER dataset of the study published in Nature Communications (http://doi.org/10.1038/ncomms5006). In short, this publication used the dataset to select for repeatable radiomics features in a test-retest context.