cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5q449h5
title: Role of an ABA receptor SlPYL9 in tomato fruit ripening

description: Abstract Abscisic acid (ABA) regulates fruit ripening, yet little is known
 about the exact roles of ABA receptors in fruit. In this study, we
 revealed the role of SlPYL9, a tomato PYR (pyrabactin resistance) / PYL
 (pyrobactin resistance-like) / RCAR (regulatory component of ABA
 receptors) ABA receptor, as a positive regulator of ABA signaling and
 fruit ripening. SlPYL9 inhibited protein phosphatase-type 2C (PP2C2/6) in
 ABA dose-dependent way, and it interacts physically with SlPP2C 2 / 3 / 4
 / 5 in an ABA-dependent manner. Expression of SlPYL9 was observed in the
 seeds, flowers and fruit. Overexpression and suppression of SlPYL9 induced
 a variety of phenotypes via altered expression of ABA signaling genes
 (SlPP2C1/2/9, SlSnRK2.8, SlABF2), thereby affecting expression of
 ripening-related genes involved in ethylene release and cell wall
 modification. SlPYL9-OE / RNAi plants showed a typical ABA hyper- /
 hypo-sensitive phenotype in terms of seed germination, primary root growth
 and the response to drought. Fruit ripening was significantly accelerated
 in SlPYL9-OE by 5-7 days as a result of increased endogenous ABA
 accumulation and advanced release of ethylene compared with the wild-type
 (WT). Meanwhile, in the SlPYL9-RNAi lines, fruit ripening was delayed,
 mesocarp thickness was enhanced, and the petals did not abscise as timely
 as the WT, resulting in conical / oblong and gourd-shaped fruit. These
 results suggest that SlPYL9 is involved in ABA signaling, thereby playing
 a role in the regulation of flower abscission and fruit ripening in
 tomato.
description: Data set 1
 (transcriptome of PYL9-OE:Ri) Data set 1. The
 expression of fruit ripening-related genes in fruits at the breaker stage
 detected by RNA-seq.   Data set 2
 (Differentially expressed genes) Data set 2.
 Differentially expressed genes in the WT and transgenic fruits at breaker
 stage detected by RNA-seq.   
 
 Data set 3 (Total
 gene numbers in the WT and SlPYL9-OE/Ri fruits) Data set 3. Total gene
 numbers in the WT and transgenic fruits at the breaker stage detected by
 RNA-seq.
DOI: 10.5061/dryad.v50tm7m
title: Data from: Repertoire-wide gene structure analyses: a case study comparing automatically predicted and manually annotated gene models

description: The location and modular structure of eukaryotic protein-coding genes in
 genomic sequences can be automatically predicted by gene annotation
 algorithms. These predictions are often used for comparative studies on
 gene structure, gene repertoires, and genome evolution. However, automatic
 annotation algorithms do not yet correctly identify all genes within a
 genome, and manual annotation is often necessary to obtain accurate gene
 models and gene sets. As manual annotation is time-consuming, only a
 fraction of the gene models in a genome is typically manually annotated,
 and this fraction often differs between species. To assess the impact of
 manual annotation efforts on genome-wide analyses of gene structural
 properties, we compared the structural properties of protein-coding genes
 in seven diverse insect species sequenced by the i5k initiative. Our
 results show that the subset of genes chosen for manual annotation by a
 research community (3.5-7% of gene models) may have structural properties
 (e.g., lengths and exon counts) that are not necessarily representative
 for a species’ gene set as a whole. Nonetheless, the structural properties
 of automatically generated gene models are only altered marginally (if at
 all) through manual annotation. Major correlative trends, for example a
 negative correlation between genome size and exonic proportion, can be
 inferred from either the automatically predicted or manually annotated
 gene models alike. Vice versa, some previously reported trends did not
 appear in either the automatic or manually annotated gene sets, pointing
 towards insect-specific gene structural peculiarities. In our analysis of
 gene structural properties, automatically predicted gene models proved to
 be sufficiently reliable to recover the same gene-repertoire-wide
 correlative trends that we found when focusing on manually annotated gene
 models only. We acknowledge that analyses on the individual gene level
 clearly benefit from manual curation. However, as genome sequencing and
 annotation projects often differ in the extent of their manual annotation
 and curation efforts, our results indicate that comparative studies
 analyzing gene structural properties in these genomes can nonetheless be
 justifiable and informative.
description: Wilbrandt et al. (2019)
 Additional File 3: COGNATE resultsPlease find descriptive
 information in the attached README.Wilbrandt-et-al_2019_Additional_File_3_COGNATE-results.zip
DOI: 10.5061/dryad.8m63m78
title: Data from: Habitat-dependent occupancy and movement in a migrant songbird highlights the importance of mangroves and forested lagoons in Panama and Colombia

description: Climate change is predicted to impact tropical mangrove forests due to
 decreased rainfall, sea-level rise, and increased seasonality of flooding.
 Such changes are likely to influence habitat quality for migratory
 songbirds occupying mangrove wetlands during the tropical dry season.
 Overwintering habitat quality is known to be associated with fitness in
 migratory songbirds, yet studies have focused primarily on territorial
 species. Little is known about the ecology of non-territorial species that
 may display more complex movement patterns within and among habitats of
 differing quality. In this study, we assess within season survival and
 movement at two spatio-temporal scales of a non-territorial overwintering
 bird, the prothonotary warbler (Protonotaria citrea), that depends on
 mangroves and tropical lowland forests. Specifically, we (1) estimated
 within-patch survival and persistence over a six-week period using
 radio-tagged birds in central Panama and (2) modelled abundance and
 occupancy dynamics at survey points throughout eastern Panama and northern
 Colombia as the dry season progressed. We found that site persistence was
 highest in mangroves; however, the probability of survival did not differ
 among habitats. The probability of warbler occupancy increased with canopy
 cover, and wet habitats were least likely to experience local extinction
 as the dry season progressed. We also found that warbler abundance is
 highest in forests with the tallest canopies. This study is one of the
 first to demonstrate habitat-dependent occupancy and movement in a
 non-territorial overwintering migrant songbird, and our findings highlight
 the need to conserve intact, mature mangrove and lowland forests.
description: Prothonotary warbler
 nonbreeding occupancy and movementThis zipped file
 contains subfolders with data used in each analysis. The subfolder names
 are as follows: (1) Data for abundance models, (2) Data for occupancy
 models, (3) Data for movement models, and (4) Data for site persistence
 and survivalData for
 Dryad-20190807T141519Z-001.zip
DOI: 10.5061/dryad.07sj8sq
title: Data from: Eulerian videography technology improves classification of sleep architecture in primates

description: Sleep is a critically important dimension of primate behavior, ecology,
 and evolution, yet primate sleep is under-studied because current methods
 of analyzing sleep are expensive, invasive, and time-consuming. In
 contrast to electroencephalography (EEG) and actigraphy, videography is a
 cost-effective and non-invasive method to study sleep architecture in
 animals. With video data, however, it is challenging to score subtle
 changes that occur in different sleep states, and technology has lagged
 behind innovations in EEG and actigraphy. Here, we applied Eulerian
 videography to magnify pixels relevant to scoring sleep from video, and
 then compared these results to analyses based on actigraphy and standard
 infrared videography. We studied four species of lemurs (Eulemur
 coronatus, Lemur catta, Propithecus coquereli, Varecia rubra) for 12-hour
 periods per night, resulting in 6,480 one-minute epochs for analysis.
 Cramer’s V correlation between actigraphy-classified sleep and infrared
 videography-classified sleep revealed consistent results in 8 out of 9 of
 the 12 h videos scored. A sample of the infrared videography was then
 processed by Eulerian videography for movement magnification and re-coded.
 A second Cramer’s V correlation analysis, between two independent scorers
 coding the same Eulerian-processed video, found that inter-observer
 agreement among Eulerian videography increased sleep vs. awake, NREM, and
 REM classifications by 7.1%, 46.7%, and 34.3%, respectively. Furthermore,
 Eulerian videography was more strongly correlated with actigraphy data
 when compared to results from standard infrared videography. The increase
 in agreement between the two scorers indicates that Eulerian videography
 has the potential to improve the identification of sleep states in lemurs
 and other primates, and thus to expand our understanding of sleep
 architecture without the need for EEG.
description: Comparison between
 Infrared and Eulerian VideoThis video provides a
 side-by-side comparison of the original infrared video and the novel
 Eulerian video to provide a visual demonstration of the spatial
 magnification.Infrared Eulerian Video
 Comparison.m4v
DOI: 10.5061/dryad.5d3s2vg
title: Data from: A systematic review of comorbidities and outcomes of adult patients with pleural infection

description: Background Pleural infection remains an important cause of mortality. This
 study aimed to investigate worldwide patterns of pre-existing
 comorbidities and clinical outcomes of patients with pleural infection.
 Methods Studies reporting on adults with pleural infection between
 2000-2017 were identified from a search of Embase and Medline. Papers
 reporting exclusively on tuberculous, fungal or post pneumonectomy
 infection were excluded. Two reviewers assessed 20980 records for
 eligibility. Results 211 studies met the inclusion criteria. 134 papers
 (227,898 patients, mean age 52.8 years) reported comorbidity and/or
 outcome data. The majority of studies were retrospective observational
 cohorts (n=104, 78%) and the most common region of reporting was East Asia
 (n=33, 24%) followed by North America (n=27, 20%). 85 papers (50,756
 patients) reported comorbidity. The median percentage prevalence of any
 comorbidity was 72% (IQR 58-83%), with respiratory illness (20%, 16-32%)
 and cardiac illness (19%, 15-27%) most commonly reported. 125 papers
 (192,298 patients) reported outcome data. The median length of stay was 19
 days (IQR 13-27) and median in-hospital or 30-day mortality was 4% (IQR
 1-11%). In regions with high-income economies (n=100, 74%) patients were
 older (mean 56.5 vs. 42.5 years, p&lt;0.0001), but there were no
 significant differences in prevalence of pre-existing comorbidity nor in
 length of hospital stay or mortality. Conclusion Patients with pleural
 infection have high levels of comorbidity and long hospital stays. Most
 reported data are from high-income economy settings. Data from
 lower-income regions is needed to better understand regional trends and
 enable optimal resource provision going forward.
description: Data extraction for: A
 systematic review of comorbidities and outcomes of adult patients with
 pleural infection.Sheet 1: Codes. Sheet 2:
 Cormorbidity data from all included studies. Sheet: Outcome data from all
 included studies.Dryad_upload_ERJ.xlsx
DOI: 10.5061/dryad.585581j
title: Cortical microstructural correlates of astrocytosis in autosomal dominant Alzheimer disease

description: Objective To study the macrostructural and microstructural MRI
 correlates of brain astrocytosis, measured
 with 11C-deuterium-L-deprenyl (11C-DED)–PET, in familial
 autosomal dominant Alzheimer disease (ADAD). Methods The total
 sample (n = 31) comprised ADAD mutation carriers (n = 10 presymptomatic,
 39.2 ± 10.6 years old; n = 3 symptomatic, 55.5 ± 2.0 years old) and
 noncarriers (n = 18, 44.0 ± 13.7 years old) belonging to families with
 mutations in either the presenilin-1 or amyloid precursor protein genes.
 All participants underwent structural and diffusion MRI and
 neuropsychological assessment, and 20 participants (6 presymptomatic and 3
 symptomatic mutation carriers and 11 noncarriers) also
 underwent 11C-DED-PET. Results Vertex-wise interaction
 analyses revealed a differential relationship between carriers and
 noncarriers in the association between 11C-DED binding and
 estimated years to onset (EYO) and between cortical mean diffusivity (MD)
 and EYO. These differences were due to higher 11C-DED binding in
 presymptomatic carriers, with lower binding in symptomatic carriers
 compared to noncarriers, and to lower cortical MD in presymptomatic
 carriers, with higher MD in symptomatic carriers compared to noncarriers.
 Using a vertex-wise local correlation approach, 11C-DED binding
 was negatively correlated with cortical MD and positively correlated with
 cortical thickness. Conclusions Our proof-of-concept study is the
 first to show that microstructural and macrostructural changes can reflect
 underlying neuroinflammatory mechanisms in early stages of Alzheimer
 disease (AD). The findings support a role for neuroinflammation in AD
 pathogenesis, with potential implications for the correct interpretation
 of neuroimaging biomarkers as surrogate endpoints in clinical trials.
description: Supplementary tables e-1
 to e-6, and figures e-1 and e-2Vilaplana_et_al_Supplement.pdf
DOI: 10.5061/dryad.b75g05b
title: Data from: How the thermal environment shapes the structure of termite mounds

description: A computational model has been developed to predict the role of
 environment in the forms and functions of termite mounds. The proposed
 model considers the most relevant forces involved in the heat transfer
 process of termite mounds, while also reflects their gasexchange function.
 The method adopts a system configuration procedure to determine thermally
 optimized mound structures. The model successfully predicts the main
 architectural characteristics of typical Macrotermes michaelseni mounds
 for the environmental conditions they live in. The results indicate that
 the mound superstructure and internal condition strongly depend on the
 combined effect of environmental forces. It is noted that mounds being
 exposed to higher solar irradiances develop intricate lateral channels,
 inside, and taller and more pronounced spire tilt towards the sun,
 outside. It is also found that the mounds’ spire tilt angle depends on the
 geographical location, following the local average solar zenith angle for
 strong irradiances. Although wind does not influence the overall
 over-ground mound shape, it significantly affects the mound internal
 condition. The results of this study resonate with what is seen in nature.
 The proposed approach provides a broader view of the factors that are
 effective in the form and function of a naturally made structure.
description: MatlabCodesMatlab codes used for optimization procedure
DOI: 10.5061/dryad.gv5qp70
title: Data from: Multi-scale spatial genetic structure within and between populations of wild cherry trees in nuclear genotypes and chloroplast haplotypes

description: Spatial genetic structure (SGS) of plants mainly depends on the effective
 population size and gene dispersal. Maternally inherited loci are expected
 to have higher genetic differentiation between populations and more
 intensive SGS within populations than biparentally inherited loci because
 of smaller effective population sizes and fewer opportunities of gene
 dispersal in the maternally inherited loci. We investigated biparentally
 inherited nuclear genotypes and maternally inherited chloroplast
 haplotypes of microsatellites in 17 tree populations of three wild cherry
 species under different conditions of tree distribution and seed
 dispersal. As expected, inter-population genetic differentiation was 6–9
 times higher in chloroplast haplotypes than in nuclear genotypes. This
 difference indicated that pollen flow 4–7 times exceeded seed flow between
 populations. However, no difference between nuclear and chloroplast loci
 was detected in within-population SGS intensity due to their substantial
 variation among the populations. The SGS intensity tended to increase as
 trees became more aggregated, suggesting that tree aggregation biased
 pollen and seed dispersal distances toward shorter. The loss of effective
 seed dispersers, Asian black bears, did not affect the SGS intensity
 probably because of mitigation of the bear loss by other vertebrate
 dispersers and too few tree generations after the bear loss to alter SGS.
 The findings suggest that SGS is more variable in smaller spatial scales
 due to various ecological factors in local populations.
description: DataS1Locations, tree sizes,
 and microsatellites (nuclear multilocus genotypes and chloroplast
 haplotypes) of sampled trees in populations of cherry species in study
 sites
DOI: 10.5281/zenodo.18332183
title: Precision Cascade Engine — Insurance Evidence Module v1.0.1 (Audit‑Certified Reproducibility Archive)

description: Abstract

 

This record releases the Precision Cascade Insurance Module v1.0.1: an audit‑certified, deterministic reproducibility archive that adapts the Precision Cascade Engine to insurance evidence across underwriting, broking, claims, and audit functions.

 

The module standardises insurance evidence handling by converting raw submissions, logs, engineering reports, and policy documents into canonical, reproducible truth objects governed by explicit validation, provenance, and integrity rules. The system enforces deterministic execution, golden‑output validation, cryptographic sealing, and independent auditability.

 

The module governs evidential truth only. It does not perform pricing, capacity allocation, underwriting decisions, or commercial optimisation. All market judgment remains external to the engine.

 

Description

 

Overview

 

This archive provides a complete, executable insurance evidence infrastructure built on the Precision Cascade Engine. It demonstrates how insurance evidence can be handled in a deterministic, audit‑grade manner prior to commercial interpretation.

 

Scope

 

The module supports:

 

• underwriting

• claims handling

• delegated authority

• exposure analysis

• compliance and audit

across all major classes of business.

 

Architecture

 

The archive includes:

 

• an Insurance Adapter

• an Insurance Governance Profile

• two fully audited reference cases (cyber claim, energy underwriting)

• deterministic pipelines

• integrity sealing and replication kits

 

Relationship to the Core Engine

 

This module is derived from, but does not alter, the Precision Cascade Cosmology Engine. It represents a domain adaptation, not a modification. No scientific content from the cosmology engine is reused; only the evidence architecture is inherited.
DOI: 10.5061/dryad.q7f3v12
title: Data from: A case of Hashimoto’s thyroiditis with multiple drug resistance and high expression of efflux transporters

description: Context Hashimoto’s thyroiditis is the most common cause of
 hypothyroidism. Patients usually respond well to oral synthetic thyroxine
 (levothyroxine); however, for unknown reasons some individuals present
 with treatment-resistant Hashimoto thyroiditis. In cases of cancer and
 certain infectious diseases, the ATP binding cassette (ABC) transporters
 have been implicated in multidrug resistance, and we hypothesized and
 investigated a role of ABC transporters in drug-resistant Hashimoto’s
 thyroiditis. Case Description The patient whose case we report had a
 history of Hashimoto’s thyroiditis, immune thrombocytopenia, and
 refractory hypertension, with varying treatment resistance to the oral
 medications prescribed for each condition. In order to establish or
 exclude a genetic basis for her illness, we examined the patient’s gene
 expression profiles using peripheral blood leukocytes, and found
 that ABCG2/BCRPexpression was significantly high compared with
 healthy volunteers. Also, the increased daunomycin efflux capacity of our
 patient’s lymphocytes was successfully inhibited by fumitremorgin C, a
 specific ABCG2/BCRP inhibitor, and the patient’s level of
 thyroid-stimulating hormone increased by 248.6% after administration of
 intact levothyroxine tablets but decreased by 45.1% when tablets were
 crushed. Her average blood pressure decreased from 166.3/108.5 mmHg to
 125.9/78.8 mmHg when switching from intact to crushed losartan tablets.
 Conclusions High expression and accelerated efflux transporter activity of
 ABCG2/BCRP in the small intestine are expected to contribute to the
 ineffectiveness of orally administered intact tablets in cases with
 treatment-resistant Hashimoto’s thyroiditis, and crushed tablets can be
 more effective for some of these patients.
description: H-Thyroiditis_Suppl_Fig1H-Thyroiditis_Supplemental_Figure_1H-Thyroiditis_Suppl_Fig2H-Thyroiditis_Suppl_Table_1H-Thyroiditis_Supplemental_Table_1.pdf
DOI: 10.5061/dryad.bg44d2k
title: Data from: Plants are more likely to be spiny at mid-elevations in the Qinghai-Tibetan Plateau, south-western China

description: Aim: We tested the elevational herbivory defence hypothesis, which
 predicts that plants from low elevations are better defended than plants
 from higher elevations. Location: The Qinghai-Tibetan Plateau in
 south-western China - the world’s highest plateau. Major taxa studied:
 Angiosperms. Methods: We collated binary spinescence data for 10,622
 angiosperm species ranging from 600 to 6,000 m a.s.l. Logistic regression
 was used to quantify the elevational pattern in spinescence. Because
 spinescence is thought to be especially effective against mammalian
 herbivores, we also quantified the association between spinescence and
 mammalian herbivore richness. Results: We found a unimodal relationship
 between elevation and spinescence, with the highest proportion of
 spinescent species occurring at mid-elevations. This unimodal relationship
 was present in perennial herbs, shrubs and trees, but not in annual herbs.
 Herbivorous mammal richness also showed a unimodal elevational pattern. A
 positive association between herbivorous mammal richness and the incidence
 of spinescent species suggests that elevational variation in herbivore
 pressure from mammals might drive elevational variation in spinescence.
 Main conclusions: Our findings further call into question the elevational
 herbivory defence hypothesis and shed new light on the potential causes of
 elevational gradients in plant diversity.
description: List of angiosperms in
 the Qinghai-Tibetan PlateauWe compiled a list of
 all of the angiosperm species present in the study area, based on Wu
 (2008), Flora of Tibet, Flora of Qinghai and Flora of Yunnan, and Wang
 (1993, 1994).The elevational range for each species from the data sources
 above, complemented by data from the Chinese Virtual Herbarium, published
 papers, investigation reports of nature reserves and personal
 communications with experts.Song_et_al_Readme.txt