cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30634295
title: Supplementary Material for: Bone Health in Young Individuals with Primary Ciliary Dyskinesia: Insights from a Comparison with Cystic Fibrosis and Healthy Controls

description: Introduction: Bone health screening is established in Cystic Fibrosis (CF). Given the unknown status of bone quality in Primary Ciliary Dyskinesia (PCD), these recommendations have not been adopted. We aimed to evaluate the bone phenotype in PCD compared to healthy controls and CF.
Methods: In this exploratory cross-sectional study, we assessed bone mineral density (BMD) at the whole body and lumbar spine using dual-energy X-ray absorptiometry (DXA), and tibial bone microarchitecture using high-resolution peripheral quantitative computed tomography (HR-pQCT) in 15 individuals with PCD and 45 with CF, aged 12-20 years. Measures were compared to healthy controls matched one-to-one by pubertal stage and sex. Disease-to-healthy differences were compared between PCD and CF, and associations with body mass index (BMI), lean mass, and lung function were analysed.
Results: DXA-measured areal BMD and HR-pQCT-derived total volumetric BMD showed no differences between PCD and controls. HR-pQCT revealed reduced cortical thickness, area, and BMD at the ultradistal tibia in PCD compared to controls. While PCD and CF did not differ, the PCD bone phenotype more closely resembled pancreatic-insufficient than pancreatic-sufficient CF. Dimensional cortical deficits were largely explained by BMI or lean mass, especially in CF, but remained reduced in PCD after adjustment, indicating potentially intrinsic disease-related alterations. Lung function did not clearly correlate with bone outcomes in PCD.
Conclusion: Skeletal health appears compromised in young people with PCD. Despite mostly normal densitometry, tibial bone microarchitecture was altered. This study positions bone health as a research priority in PCD and supports the need for larger confirmatory studies.
DOI: 10.6084/m9.figshare.30634295.v1
title: Supplementary Material for: Bone Health in Young Individuals with Primary Ciliary Dyskinesia: Insights from a Comparison with Cystic Fibrosis and Healthy Controls

description: Introduction: Bone health screening is established in Cystic Fibrosis (CF). Given the unknown status of bone quality in Primary Ciliary Dyskinesia (PCD), these recommendations have not been adopted. We aimed to evaluate the bone phenotype in PCD compared to healthy controls and CF.
Methods: In this exploratory cross-sectional study, we assessed bone mineral density (BMD) at the whole body and lumbar spine using dual-energy X-ray absorptiometry (DXA), and tibial bone microarchitecture using high-resolution peripheral quantitative computed tomography (HR-pQCT) in 15 individuals with PCD and 45 with CF, aged 12-20 years. Measures were compared to healthy controls matched one-to-one by pubertal stage and sex. Disease-to-healthy differences were compared between PCD and CF, and associations with body mass index (BMI), lean mass, and lung function were analysed.
Results: DXA-measured areal BMD and HR-pQCT-derived total volumetric BMD showed no differences between PCD and controls. HR-pQCT revealed reduced cortical thickness, area, and BMD at the ultradistal tibia in PCD compared to controls. While PCD and CF did not differ, the PCD bone phenotype more closely resembled pancreatic-insufficient than pancreatic-sufficient CF. Dimensional cortical deficits were largely explained by BMI or lean mass, especially in CF, but remained reduced in PCD after adjustment, indicating potentially intrinsic disease-related alterations. Lung function did not clearly correlate with bone outcomes in PCD.
Conclusion: Skeletal health appears compromised in young people with PCD. Despite mostly normal densitometry, tibial bone microarchitecture was altered. This study positions bone health as a research priority in PCD and supports the need for larger confirmatory studies.
DOI: 10.15468/dl.ese7f9
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((111.17163 6.80905,138.36593 6.80905,138.36593 17.68212,111.17163 17.68212,111.17163 6.80905))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Trachemys scripta"
 ]
}

 The dataset includes 15 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038540-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eyn9ap
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cypripedium amesianum"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038542-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.30633074
title: LLMAbstractor: LLM-Assisted RTL Abstraction for Hardware Property Checking Acceleration

description: This dataset accompanies the manuscript “LLMAbstractor: LLM‑Assisted RTL Abstraction for Hardware Property Checking Acceleration.” Identities and contacts are withheld for double‑blind review. The Excel includes the detailed experimental results in Figure 7 and Table 3.
DOI: 10.6084/m9.figshare.30633074.v1
title: LLMAbstractor: LLM-Assisted RTL Abstraction for Hardware Property Checking Acceleration

description: This dataset accompanies the manuscript “LLMAbstractor: LLM‑Assisted RTL Abstraction for Hardware Property Checking Acceleration.” Identities and contacts are withheld for double‑blind review. The Excel includes the detailed experimental results in Figure 7 and Table 3.
DOI: 10.15468/dl.excc28
title: Occurrence Download

description: A dataset containing 1807458 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Firmiana major, Luffa acutangula, Lysimachia maritima, Mangifera indica, Pistacia vera, Populus lasiocarpa, Rhododendron vialii, Dryas octopetala, Abrus pulchellus, Actinidia eriantha, Actinidia latifolia, Actinidia rufa, Capparis spinosa, Eucalyptus leucophloia, Eucalyptus pumila, Menispermum dauricum, Ribes nigrum, Hypericum androsaemum, Calotropis procera, Actinidia polygama, Arachis stenosperma, Citrus garrawayi, Dovyalis caffra, Filago pyramidata, Hippophae tibetana, Ipomoea batatas, Periploca sepium, Quercus cerris, Rubus spectabilis, Acer negundo, Eucalyptus decipiens, Rosa hugonis, Salvia divinorum, Stellera chamaejasme, Umbilicus rupestris, Arctium minus, Avena barbata, Cinnamomum camphora, Dianthus caryophyllus, Eucalyptus coolabah, Lagerstroemia indica, Phoebe chekiangensis, Quercus sichourensis, Trifolium striatum, Veronica serpyllifolia, Nasturtium officinale, Prunus mume, Barthea barthei)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1807458 records from 4398 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038523-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/3d2-sk3-gbr
title: Soritidae Ehrenberg, 1839

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/v72-47m-tga
title: Apodemus sylvaticus (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4cc-sxb-w63
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/526-kkw-jye
title: Ammodiscus incertus (d'Orbigny, 1839)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/p4e-wyp-v0q
title: Spirorutilus carinatus (d'Orbigny, 1846)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4fj-xp7-3wy
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/q9e-zpg-szz
title: Guttulina irregularis (d'Orbigny, 1846)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/55d-a8e-1xg
title: †Coleites reticulosus (Plummer, 1927)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/65e-fz9-9wa
title: Operculina complanata (Defrance in Blainville, 1822)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/04d-9wb-m6e
title: Cytherura Sars, 1866

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/82p-k6k-y3v
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ebb-j12-8ra
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cqm-434-x2l
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/w5p-xrv-as2
title: Lacertidae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cb9-6ha-xvm
title: Lenticulina antillea (Cushman, 1923)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/nz5-p6k-dhv
title: Lenticulina atlantica (Barker, 1960)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/52p-588-f5m
title: Rosalina d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/j0v-dl6-y75
title: Triloculina tricarinata d'Orbigny in Deshayes, 1832

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6bc-60n-gcs
title: Lamarckina excavata (d'Orbigny, 1839)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cph-jdq-pkl
title: Lacertidae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vkk-6pa-fyc
title: Lamarckina excavata (d'Orbigny, 1839)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6t2-7kn-5w3
title: Lenticulina Lamarck, 1804

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/fg3-0xw-p7q
title: Sigmomorphina Cushman & Ozawa, 1928

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8p1-1tn-baj
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vcj-31d-00c
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/2cx-8kg-bhp
title: Lacroixilepis Keith, 2007

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rmb-zar-4j9
title: Favulina melo (d'Orbigny, 1839)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1l7-fj3-hrl
title: Guttulina communis (d'Orbigny, 1826)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/826-8ac-l5j
title: Cassidulina tortuosa Cushman & Hughes, 1925

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/dzv-c67-qbs
title: Globulina gibba (d'Orbigny in Deshayes, 1832)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wj4-4cr-5gb
title: Calcarina spengleri (Gmelin, 1791)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ft7-zfe-e3v
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/v8e-tyb-bn4
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mnr-1p3-cmf
title: Bulimina denudata Cushman & Parker, 1938

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/083-gy8-qt8
title: †Vacuovalvulina keijzeri (van Bellen, 1946)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5la-2hq-q6x
title: Stomatorbina concentrica (Parker & Jones, 1864)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9s1-shn-cyr
title: Laevidentalina communis (d'Orbigny, 1826)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/s1s-62m-xyb
title: Pseudopus

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9dv-z9h-gzx
title: †Nonion granulosum Ten Dam & Reinhold, 1941

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1d5-6yr-p9k
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7c1-1m1-62y
title: Bivalvia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7ee-3my-1qt
title: Acanthocythereis ornata (Müller, 1894)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ald-s1b-10d
title: Ammonia Brünnich, 1771

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.14288/1.0438691
title: Functional traits and size interact to influence growth and carbon sequestration among trees in urban greenspaces

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;ol&gt; &lt;li&gt;There is persistent uncertainty about how integrated plant functions, like growth, are mechanistically constrained and practically predicted by functional traits. For trees, these knowledge gaps persist for two reasons: first, studies of ‘natural’ forests are observational, with highly variable and confounding resource limitation and competition; second, most studies investigate only a few popular traits and ignore context-dependencies in trait-effects on growth (e.g., trait-environment or trait-ontogeny interactions).&lt;/li&gt; &lt;li&gt;We assessed 17 traits as predictors of radial growth and aboveground carbon sequestration for 182 trees, including individuals of 42 species common to temperate cities. By focusing exclusively on planted trees growing in isolation, our unique study is a pseudo-experiment that spans a large range of taxonomic and trait variability and minimizes confounding effects of environmental heterogeneity (e.g., shifts in light availability with tree size). Focal traits included not only commonly measured traits related to leaf economics and plant size, but also wood traits and whole-plant phenology.&lt;/li&gt; &lt;li&gt;Models with indices of tree ontogeny (size) and traits explained 80% and 72% of variability in relative growth and carbon sequestration, respectively, and traits accounted for ~20% of the variation. Traits related to said tree functions included leaf dry matter content (LDMC), leaf N content, mature height, wood anatomy, and phenology. LDMC was positively correlated with wood growth and C sequestration across all size classes, while the positive effects of leaf N, mature height, and wood density were only apparent for smaller trees. Ring-porous species had higher rates of growth and C sequestration than diffuse-porous species.&lt;/li&gt; &lt;li&gt;Consistent with recent theory, growth rates of isolated, urban trees vary as a function of simple and interactive effects of traits and size. Our findings are useful for optimizing reforestation efforts in temperate cities, where planners and land managers can select species for rapid growth and C sequestration using freely available data for the 'effect' traits we identified, including wood anatomy and density, leaf N, and LDMC. Lastly, the trait-growth relationships we describe here may reflect those of ‘naturally’ isolated trees growing in savannas and/or woodlands and provide an insightful frame of reference for trees in closed-canopy forests.&lt;/li&gt; &lt;/ol&gt;
DOI: 10.14288/1.0438628
title: Combining camera trap surveys and IUCN range maps to improve knowledge of species distributions

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;&lt;span lang="EN-US"&gt;Reliable maps of species distributions are fundamental for biodiversity research and conservation. Range maps created by the International Union for Conservation of Nature (IUCN) Red List are often considered authoritative but may not match species occurrence data. We tested concordance between occurrences from camera trap surveys and predicted occurrence from IUCN maps for 510 medium- to large-bodied mammalian species in 80 camera-trap sampling areas. Across all areas, cameras detected 39% of the species that were expected to occur based on IUCN ranges.  The probability of mismatches between camera traps and IUCN range maps was significantly higher for smaller-bodied mammals and habitat specialists in the Neotropics and Indomalaya, and in areas with shorter canopy forests. Our results indicate that in many areas within their range map distributions species may be rare or absent. We suggest that combining range map data with accumulating data from ground-based biodiversity sensors, such as camera traps, acoustic recorders, and eDNA surveys, provides a richer knowledge base for conservation mapping and planning.&lt;/span&gt;&lt;/p&gt;
DOI: 10.15468/dl.dvjz5v
title: Occurrence Download

description: A dataset containing 3990 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Herpetofauna y avifauna de los municipios de Villeta y Guaduas (Cundinamarca), en el contexto de la vulnerabilidad del territorio al cambio climático"
 ]
}

 The dataset includes 3990 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000509-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.14288/1.0438629
title: Demographic mechanisms and anthropogenic drivers of contrasting population dynamics of hummingbirds

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p id="docs-internal-guid-166be8cf-7fff-07d1-d701-4946a923cb3f" dir="ltr"&gt;Conserving species requires knowledge of demographic rates (survival, recruitment) that govern population dynamics to allow the allocation of limited resources to the most vulnerable stages of target species' life cycles. Additionally, quantifying drivers of demographic change facilitates the enactment of specific remediation strategies. However, knowledge gaps persist in how similar environmental changes lead to contrasting population dynamics through demographic rates. For sympatric hummingbird species, the population of urban-associated partial-migrant Anna's hummigbird (&lt;em&gt;Calypte anna&lt;/em&gt;) has increased, yet the populations of Neotropical migrants including rufous, calliope, and black-chinned hummingbirds have decreased. Here, we developed an integrated population model to jointly analyze 25 years of mark-recapture data and population survey data for these four species. We examined the contributions of demographic rates on population growth and evaluated the effects of anthropogenic stressors including human population density and crop cover on demographic change in relation to species' life histories. While recruitment appeared to drive the population increase of urban-associated Anna's hummingbirds, decreases in juvenile survival contributed most strongly to population declines of Neotropical migrants and highlight a potentially vulnerable phase in their life-history. Moreover, rufous hummingbird adult and juvenile survival rates were negatively impacted by human population density. Mitigating threats associated with intensively modified anthropogenic environments is a promising avenue for slowing further hummingbird population loss. Overall, our model grants critical insight into how anthropogenic modification of habitat affects the population dynamics of species of conservation concern.&lt;/p&gt;
DOI: 10.14288/1.0447402
title: Data and Code for "Estimating whole-body centre of mass sway during quiet standing with inertial measurement units"

description: Includes 1) code to estimate centre of mass displacement using inertial measurement data and 2) code and data to replicate figures from "Estimating whole-body centre of mass sway during quiet standing with inertial measurement units".
DOI: 10.14288/1.0445570
title: Scaling of the extended phenotype: convergent energetics from diverse spider web geometries.

description: &lt;b&gt;Abstract&lt;/b&gt; &lt;br&gt; Capturing enough energy to support growth, survival, and reproduction is the main challenge organisms face. Metabolic theory predicts that larger multicellular organisms require less energy per unit time and mass than smaller ones. Structures used to capture energy thus need not scale isometrically with body size. Web-building spiders rely on extended phenotypes in the form of silk webs to capture energy. Webs tend to be phylogenetically constrained composite traits, being two-dimensional, typically in the shape of orbs in some spider families, or three-dimensional, in the shape of a tangle or a sheet-and-tangle, in others. We show that the mass-specific prey-capture surface area of webs with different geometries scales in taxon-specific ways with spider body size, including hollowing of sheet-and-tangle webs to maintain isometry. The mass-specific energy consumption rate, however, scaled hypometrically with identical slopes and intercepts across all three web geometries. Although an allometric relationship between energy acquisition and body size has been shown repeatedly across metazoans, no previous studies have shown such a relationship mediated by a diverse set of extended phenotypes. Our findings support the most general trend predicted by metabolic theory while illustrating how the extended phenotypes spiders build meet their bodies’ energetic demands in diverse ways. &lt;br&gt; &lt;br&gt; &lt;b&gt;Usage notes&lt;/b&gt; &lt;br&gt; This dataset contains the data (i.e., Trait_data.csv, Bodylength_data.csv, and Wheeler.tre) and code (i.e., Whole_analysis_models_1-2.R, Whole_analysis_models_4-9.R, Ratio_analysis_models_1-2.R, Ratio_analysis_models_4-9.R, PGLS_analysis_model_3.R, and BodyLength_analysis.R) used to generate the results and figures for the paper titled ‘Scaling of the extended phenotype: convergent energetics from diverse spider web geometries’. The files Ratio_analysis_models_1-2.R, Ratio_analysis_models_4-9.R, PGLS_analysis_model_3.R, and BodyLength_analysis.R contain the code used to generate the graphs featured in the paper. The definitions for all columns (including units) for Trait_data.csv and Bodylength_data.csv are included in the ReadMe file. The Wheeler.tre file is used to create the phylogenetic tree used in the PGLS analysis. All analyses and graphs were done in R version 4.0.2.