cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28563717.v2
title: Evidence of Mpox clade IIb infection in primary human alveolar epithelium

description: Monkeypox virus (Mpox) has been recognized for causing distinct skin lesions and is primarily transmitted through skin and sexual contact. To date, the transmissibility and pathogenesis of the Mpox virus in distal human lung has never been completely explored. Here the transmission pathways and Mpox tropism on patient-derived air-liquid epithelium (ALE) model fabricated using isolated primary human alveolar epithelial cells (hAECs) were investigated. hAECs were cultured and exposed to the Mpox virus clade IIb isolated from the patient. DNA, proteins, and the tropism were elucidated using polymerase chain reaction (PCR), Western blot, and high-content fluorescent imaging. Transmission electron microscopy (TEM) was employed to systematically observe the cellular distribution of viral particles. Viral titres were determined by TCID<sub>50</sub> assay. Innate immune response and inflammatory mediators were measured using Milliplex® multiplex and ELISA analysis. Pathology at alveolar barrier integrity was determined using transepithelial electrical resistance (TEER) analysis. The study included mock-infected cells as control. Mpox virus significantly infected 42.82% of total hAEC populations. The prominent observed pathology included a significant reduction in TEER values, loss of tight junction protein, presence of tunnelling nanotubes (TNTs), and syncytium morphology. Four stages of Mpox biogenesis were clearly observed without significant activation of IL-6, MIP1alpha, TNF-α, and Galectin-9, although IL-1β were subtly promoted. The developed patient-derived ALE is a versatile model for Mpox virus clade IIb infection reflecting respiratory transmission competence of the Mpox. Postinfection lung pathogenesis demonstrated alveolar barrier damage without significant inflammation, raising concerns about possible immune evasion by the virus.
DOI: 10.6084/m9.figshare.30361683
title: Whole genome sequencing reveals significant intra-hospital clonal transmission and a potential multidrug resistant and hypervirulent sequence cluster of <i>Corynebacterium striatum</i>

description: With increasing reports about <i>Corynebacteritum straitum</i>, its role as an emerging human pathogen is been recognized. However, few studies have explored the genomic epidemiology of <i>C</i>. <i>straitum</i> in China. A total of 263 isolates collected in various specimens from 2021 to 2022 were analyzed from a tertiary hospital in China. Nearly all isolates (98.5%, 259/263) were multidrug resistant (MDR). The highest resistance was observed for clindamycin (96.5%), followed by ciprofloxacin (95.0%) and erythromycin (93.5%). Genome sequencing indicated a significant prevalence of intra-hospital clonal transmission, involving six distinct clones (clone one-six). An average of 7.35 antimicrobial resistance genes and 10.65 virulence genes were identified in each strain. Genomic analysis identified a potentially hypervirulent sequence cluster (designated SC3) exhibiting near-universal carriage of four pilus assembly genes (<i>spaH</i>, <i>spaI</i>, <i>srtD</i>, and <i>srtE</i>), whereas these genes occurred at significantly lower frequencies in other sequence clusters. Further analysis estimated the emergence of SC3 strains around 1929.56 (95% HPD: 1863.41-1995.71). Phenotypic virulence assays demonstrated that <i>C. straitum</i> strains carrying the <i>spaH</i>, <i>spaI</i>, <i>srtD</i>, and <i>srtE</i> genes exhibited significantly higher virulence compared to strains lacking these genes. Our results revealed that multiple MDR <i>C</i>. <i>straitum</i> colones were circulating in the hospital. A suggestive MDR and hypervirulent SC3 was identified with potential evolutionary advantage and enhanced transmission capability.
DOI: 10.6084/m9.figshare.30361683.v1
title: Whole genome sequencing reveals significant intra-hospital clonal transmission and a potential multidrug resistant and hypervirulent sequence cluster of <i>Corynebacterium striatum</i>

description: With increasing reports about <i>Corynebacteritum straitum</i>, its role as an emerging human pathogen is been recognized. However, few studies have explored the genomic epidemiology of <i>C</i>. <i>straitum</i> in China. A total of 263 isolates collected in various specimens from 2021 to 2022 were analyzed from a tertiary hospital in China. Nearly all isolates (98.5%, 259/263) were multidrug resistant (MDR). The highest resistance was observed for clindamycin (96.5%), followed by ciprofloxacin (95.0%) and erythromycin (93.5%). Genome sequencing indicated a significant prevalence of intra-hospital clonal transmission, involving six distinct clones (clone one-six). An average of 7.35 antimicrobial resistance genes and 10.65 virulence genes were identified in each strain. Genomic analysis identified a potentially hypervirulent sequence cluster (designated SC3) exhibiting near-universal carriage of four pilus assembly genes (<i>spaH</i>, <i>spaI</i>, <i>srtD</i>, and <i>srtE</i>), whereas these genes occurred at significantly lower frequencies in other sequence clusters. Further analysis estimated the emergence of SC3 strains around 1929.56 (95% HPD: 1863.41-1995.71). Phenotypic virulence assays demonstrated that <i>C. straitum</i> strains carrying the <i>spaH</i>, <i>spaI</i>, <i>srtD</i>, and <i>srtE</i> genes exhibited significantly higher virulence compared to strains lacking these genes. Our results revealed that multiple MDR <i>C</i>. <i>straitum</i> colones were circulating in the hospital. A suggestive MDR and hypervirulent SC3 was identified with potential evolutionary advantage and enhanced transmission capability.
DOI: 10.15468/dl.3vnskc
title: Occurrence Download

description: A dataset containing 3731 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Acacia confusa",
 "Year 1980-2026"
 ]
}

 The dataset includes 3731 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001219-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.tq76n
title: Data from: Ecological opportunity and ecomorphological convergence in Australasian robins (Petroicidae)

description: Ecological theories of adaptive radiation predict that ecological
 opportunity (EO) stimulates cladogenesis through entry into a novel
 environment and/or release of competition pressures. Due to its dynamic
 paleoclimatic and geological history, the Australo-Papuan region
 constitutes an opportune scenario to study patterns of diversification in
 relation to the colonization of new ecological niches. Here, we employ a
 comparative framework using the Australasian robins (Petroicidae) as a
 model system to test whether the diversification of this bird family
 fulfils a niche-filling process as predicted by the EO model, and to test
 whether the observed morphological similarity is described by a pattern of
 phylogenetic niche conservatism (PNC) or convergence. Although we detected
 an early-burst, we did not find a slowdown in speciation or morphological
 evolution as expected in a niche-filling scenario. Divergence in tarsus
 length and tail length (PC1) was consistent with a multi-peak model, in
 which PC1 represents a convergent trait among distantly related clades
 sharing the same foraging strategy. Our study thus shows that convergence
 rather than PNC seems to explain the existence of morphological similarity
 across independent lineages in the Petroicidae. We also found a low level
 of PNC regarding annual variations in temperature and precipitation, which
 is in agreement with the hypothesis that diversification within the
 Petroicidae involved repeated radiations. We suggest two non-mutually
 exclusive hypotheses to explain the overall lack of density-dependent
 cladogenesis. First, the extreme spatial and temporal heterogeneity of
 this region may have generated a pattern of repeated ecological
 opportunity over time and, second, this family may not yet have reached
 equilibrium diversity.
description: Petroicidae dataset
 (morfological and ecological measures)Morfological and
 ecological traits employed in the studyPetroicidaeData.csv.xlsx
DOI: 10.5061/dryad.r17n5
title: Data from: Separating mortality and emigration: modelling space use, dispersal and survival with robust-design spatial-capture-recapture data

description: 1. Capture-recapture (CR) techniques are commonly used to gain information
 about population dynamics, demography and life-history traits of
 populations. However, traditional CR models cannot separate mortality from
 emigration. Recently developed spatial-capture-recapture (SCR) models
 explicitly incorporate spatial information into traditional CR models,
 thus allowing for individuals’ movements to be modelled explicitly. 2. In
 this paper, we extend SCR models using robust-design data to allow for
 both processes in which individuals can disappear from the population,
 mortality and dispersal, to be estimated separately. We formulate a
 general robust-design spatial capture-recapture (RD-SCR) model, explore
 the properties of the model in a simulation study, and compare the results
 to a Cormack-Jolly-Seber model and a non-spatial robust-design model with
 temporary emigration. In the case study, we fit several versions of the
 general model to data on field voles (Microtus agrestis) and compare the
 results with those from the non-spatial models fitted to the same data. We
 also evaluate assumptions of the fitted models with a series of
 simulation-based posterior predictive goodness-of-fit checks that are
 applicable to SCR models in general and the RD-SCR model in particular. 3.
 The simulation results show that the model preforms well under a wide
 range of dispersal distances. Our model outperforms the traditional CR
 models in terms of both accuracy and precision for survival. The case
 study showed that adult females have an approximately 3.5 times higher
 mortality rate than adult males. Males have larger home-ranges and
 disperse longer distances than females, but both males and females mostly
 move their activity centres within their previous home-range between
 trapping sessions at three week intervals. 4. Our RD-SCR model has several
 advantages compared to other approaches to estimate “true” survival
 instead of only “apparent” survival. Additionally, the model extracts
 information about space use and dispersal distributions that are relevant
 for behavioural studies as well as studies of life-history variation,
 population dynamics and management. The model can be widely applied due to
 the flexible framework, and other variations of the model could easily be
 implemented.
description: Case study data on field
 volesThis file is an ASCII
 text representation of an R list object created by the ‘dput’ function in
 R. It can be read into R by the ‘dget’ function. Please see the README.txt
 file for a description of the list elements. See Appendix S2 of the paper
 for detailed information about the data. The data have the same structure
 as the data that can be simulated and fit to the RD-SCR model provided in
 Appendix S3 of the paper.ErgonAndGardner2013.rdat
DOI: 10.15468/dl.n6whvj
title: Occurrence Download

description: A dataset containing 503 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bejaria sprucei",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 503 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001220-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1900s
title: Data from: A trade-off between reproductive investment and maternal cerebellum size in a precocial bird

description: Natural selection favours increased investment in reproduction, yet
 considerable variation in parental investment is observed in natural
 populations. Life-history theory predicts that this variation is
 maintained by a trade-off between the benefits of increased reproductive
 investment and its associated costs for the parents. The nature of these
 costs of reproduction, however, remains poorly understood. The brain is an
 energetically highly expensive organ and increased reproductive investment
 may, therefore, negatively affect brain maintenance. Using artificial
 selection lines for high and low prenatal maternal investment in a
 precocial bird, the Japanese quail (Coturnix japonica), we provide
 experimental evidence for this hypothesis by showing that increased
 prenatal provisioning negatively affects the size of a particular brain
 region of the mother, the cerebellum. Our finding suggests that cognitive
 demands may constrain the evolution of parental investment, and vice
 versa, contributing to the maintenance of variation in reproductive
 behaviour in animal populations.
description: Data_QuailbrainBrain data from Japanese quail artificially selected for high or low maternal investment.data_Quailbrain.xlsx
DOI: 10.5061/dryad.cj030
title: Data from: How embryos escape from danger: the mechanism of rapid, plastic hatching in red-eyed treefrogs

description: Environmentally cued hatching allows embryos to escape dangers and exploit
 new opportunities. Such adaptive responses require a flexibly regulated
 hatching mechanism sufficiently fast to meet relevant challenges. Anurans
 show widespread, diverse cued hatching responses, but their described
 hatching mechanisms are slow, and regulation of timing is unknown.
 Arboreal embryos of red-eyed treefrogs, Agalychnis callidryas, escape from
 snake attacks and other threats by very rapid premature hatching. We used
 videography, manipulation of hatching embryos, and electron microscopy to
 investigate their hatching mechanism. High-speed video revealed three
 stages of the hatching process: pre-rupture shaking and gaping, vitelline
 membrane rupture near the snout, and muscular thrashing to exit through
 the hole. Hatching took 6.5-49 s. We hypothesized membrane rupture to be
 enzymatic, with hatching enzyme released from the snout during shaking. To
 test this, we displaced hatching embryos to move their snout from its
 location during shaking. The membrane ruptured at the original snout
 position and embryos became trapped in collapsed capsules; they either
 moved repeatedly to relocate the hole or shook again and made a second
 hole to exit. Electron microscopy revealed that hatching glands are
 densely concentrated on the snout and absent elsewhere. They are full of
 vesicles in embryos and release most of their contents rapidly at
 hatching. Agalychnis callidryas' hatching mechanism contrasts with
 the slow process described in anurans to date and exemplifies one way
 embryos can achieve rapid, flexibly timed hatching to escape from acute
 threats. Other amphibians with cued hatching may also have novel hatching
 mechanisms.
description: High speed video
 dataThese are the data from
 high speed video of Agalychnis callidryas embryos
 hatching.CohenSeidWarkentin-HSVideoData.xlsxEmbryo displacement dataThese data are from the embryo displacement experiment. They are related to the timing of hatching events for rotation control and displaced embryos.CohenSeidWarkentin-embryo_displacement.csv
DOI: 10.5061/dryad.m8jr7
title: Data from: Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis

description: Deep sequencing of ribosome footprints (ribosome profiling) maps and
 quantifies mRNA translation. Because ribosomes decode mRNA every 3 nt, the
 periodic property of ribosome footprints could be used to identify novel
 translated ORFs. However, due to the limited resolution of existing
 methods, the 3-nt periodicity is observed mostly in a global analysis, but
 not in individual transcripts. Here, we report a protocol applied to
 Arabidopsis that maps over 90% of the footprints to the main reading frame
 and thus offers super-resolution profiles for individual transcripts to
 precisely define translated regions. The resulting data not only support
 many annotated and predicted noncanonical translation events but also
 uncover small ORFs in annotated noncoding RNAs and pseudogenes. A
 substantial number of these unannotated ORFs are evolutionarily conserved,
 and some produce stable proteins. Thus, our study provides a valuable
 resource for plant genomics and an efficient optimization strategy for
 ribosome profiling in other organisms.
description: for_dryadUsing ribosome profiling, we identified novel translated ORFs in annotated ncRNAs and pseudogenes in Arabidopsis thaliana. We searched other 15 plant genomes to examine if the novel protein sequences are conserved. The 19 fasta files contain amino acid sequence alignments of each novel ORF and their homologs. The distance.py file is a python script file for calculation of sequence identity among the homologs.
DOI: 10.5061/dryad.f6p6n
title: Data from: Eating up the world's food web and the human trophic level

description: Trophic levels are critical for synthesizing species’ diets, depicting
 energy pathways, understanding food web dynamics and ecosystem
 functioning, and monitoring ecosystem health. Specifically, trophic levels
 describe the position of species in a food web, from primary producers to
 apex predators (range, 1–5). Small differences in trophic level can
 reflect large differences in diet. Although trophic levels are among the
 most basic information collected for animals in ecosystems, a human
 trophic level (HTL) has never been defined. Here, we find a global HTL of
 2.21, i.e., the trophic level of anchoveta. This value has increased with
 time, consistent with the global trend toward diets higher in meat.
 National HTLs ranging between 2.04 and 2.57 reflect a broad diversity of
 diet, although cluster analysis of countries with similar dietary trends
 reveals only five major groups. We find significant links between
 socio-economic and environmental indicators and global dietary trends. We
 demonstrate that the HTL is a synthetic index to monitor human diets and
 provides a baseline to compare diets between countries.
description: Data and scripts for the
 paperScripts and all data
 necessary to run the analyses and redo the figures. A detailed script
 "main.R" describes data processing.BonhDubr2013.zip
DOI: 10.5281/zenodo.18384356
title: Oxidative Stress-Induced Hepatic and Renal Toxicity of Intravenously Injected Iron Oxide Nanoparticles in Male Wistar Rats
DOI: 10.5281/zenodo.18384357
title: Oxidative Stress-Induced Hepatic and Renal Toxicity of Intravenously Injected Iron Oxide Nanoparticles in Male Wistar Rats
DOI: 10.5061/dryad.4966m
title: Data from: Nitrogen loads influence trophic organization of estuarine fish assemblages

description: Nutrient (N and P) loading may affect functioning in aquatic ecosystems by
 restructuring producer assemblages with flow-on effects to consumers.
 Trophic niche occupancy and trophic organization of consumers are key
 components of ecosystem function that have been increasingly investigated
 using quantitative isotopic niche indices. These indices are based on the
 premise that the isotopic values of consumer tissues indicate their
 assimilated diet. Typically, isotopic niche indices are calculated using
 only consumer isotope data, which limit their application for spatial and
 temporal comparisons because consumer isotopic niches depend on isotopic
 variability of available autotrophs. We used measures of isotopic
 variability of autotrophs to standardize isotopic niche indices, which
 enabled us to compare trophic organization of fish assemblages in nine
 estuaries spanning a broad range of nutrient loading. We related
 standardized isotopic niche indices of fish assemblages to nitrogen and
 phosphorous loads and hydrological flushing of the estuaries in autumn and
 spring. The estuarine fish assemblages studied here showed greater trophic
 diversity and less redundancy given moderate to high inorganic nitrogen
 loading. Taxonomic richness partly influenced three isotopic niche indices
 measuring trophic diversity, but not measures of redundancy. Similar
 patterns may occur in other systems in which nitrogen loads have increased
 but the diversity of primary producers has not been reduced to a single
 dominant source. Our results demonstrate bottom-up controls of estuarine
 food webs. Effects of inorganic nitrogen loading were transmitted upwards
 through the food web to affect the trophic organization of higher trophic
 levels, demonstrating the crucial role of nitrogen for estuarine trophic
 dynamics.
description: Isotopic niche indices
 for estuarine fishIsotopic niche indices
 for the fish and source assemblages of 9 Australian estuaries. Indices
 were calculated using bayesian methods of Jackson et al. (2011). Predictor
 variables are also included.Warry_et_al_FE_2016.xlsx
DOI: 10.15468/dl.jk3cbj
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Roscoea humeana"
 ]
}

 The dataset includes 47 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001221-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.