cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m453vh1
title: Data from: Simultaneous radiation of bird and mammal lice following the K-Pg boundary

description: The diversification of parasite groups often occurs at the same time as
 the diversification of their hosts. However, most studies demonstrating
 this concordance only examine single host-parasite groups. Multiple
 diverse lineages of ectoparasitic lice occur across both birds and
 mammals. Here we describe the evolutionary history of lice based on
 analyses of 1,107 single copy orthologous genes from sequenced genomes of
 46 species of lice. We identify three major diverse groups of lice: one
 exclusively on mammals, one almost exclusively on birds, and one on both
 birds and mammals. Each of these groups radiated just after the
 Cretaceous-Paleogene (K-Pg) boundary, the time of the mass extinction
 event of the dinosaurs and rapid diversification of most of the modern
 lineages of birds and mammals.
description: Supporting data for
 "Simultaneous radiation of bird and mammal lice following the K-Pg
 boundary"This zip file contains
 the supporting alignments and trees for the publication "Simultaneous
 radiation of bird and mammal lice following the K-Pg boundary" by
 Johnson, Kevin, Nguyen, Nam-phuong, Sweet, Andrew, Boyd, Bret, Warnow,
 Tandy, Allen, Julie. The files are: initial.fasta - The concatenated
 alignment of the 1st and 2nd codon positions of 1,107 single copy genes,
 grouped by the partitions from the GTR+alpha rate parameters.
 initial.partition - The partitions of the initial.fasta alignment.
 RAxML_bipartitions.RAXML.BOOTSTRAP - The RAxML tree estimated from the
 partitioned concatenated alignment, with bootstrap support. genes.zip - An
 archive containing the individual gene alignments used to create the
 concatenated alignment, where each folder is a gene, and the contents are:
 FNA2AA.fasta - The UPP alignment after translating AA coding sequences
 into nucleotides FNA2AA.no3rd.fasta - The UPP alignment after removing 3rd
 codon positions. astral/astral.tree - The ASTRAL tree estimated from the
 RAxML gene trees astral/raxml.ml.trees - The RAxML trees estimated from
 the individual gene alignmentsdata.zip
DOI: 10.5061/dryad.mj2j4v2
title: Data from: Serial homology and correlated characters in morphological phylogenetics: modeling the evolution of dental crests in placentals

description: Accurate modeling of the complexity of morphological evolution is crucial
 for morphological phylogenetics and for performing tests on a wide variety
 of evolutionary scenarios. In this context, morphological integration and
 the problem of correlated categorical characters represent a major
 challenge. In particular, the magnitude and implications of correlations
 among serially homologous structures such as teeth have been much debated
 but were never tested statistically within a broad phylogenetic context.
 Here, we present a large-scale empirical study analyzing the serial
 variation of cingular crests on successive molars (M1, M2 and M3) of 274
 placental species in a phylogenetic context. Both likelihood analyses and
 analysis of phylogenetic co-distributions demonstrated highly correlated
 evolution in the entire sample and thus the non-independence of these
 serial features at a macroevolutionary scale. Likelihood analyses show
 that their serial variation should be better scored within a single
 composite character model with constrained paths for transitions enabling
 simultaneous changes on all three molars, which suggests a strong
 developmental or genetic integration. These results are congruent with
 current molecular and developmental knowledge related to dental
 morphological variation and call into question the frequent use of
 separate characters scored on serially homologous structures of the
 dentition in phylogenetic analyses. Overall, they provide long-overdue and
 clear empirical evidence that in-depth studies of patterns of integration
 constitute an essential step towards more realistic character construction
 and modeling. This approach is critical for more accurate morphological
 phylogenetics and, more generally, for testing macroevolutionary scenarios
 on groups of correlated characters.
description: Online Appendix
 4_Specimen_List_&_ObservationsOnline Appendix 4 - List
 of specimens and observations of cingulum distribution, Excel
 fileOnline Appendix
 5_Tree_nodes_numberedOnline Appendix 5 -
 Dated tree with node/taxa numbers, PDF fileOnline Appendix
 1_Cingulum_Observation_&_Tree_ConstructionOnline Appendix 1 -
 Details on cingulum observation and tree construction, Word
 documentOnline Appendix
 2_Ages_Divergences_Used_TreeOnline Appendix 2 -
 Details on Ages used for divergences, Excel file.Online Appendix
 3_Results-Likelihood_ModelsOnline Appendix 3 - ML
 results, Excel file.Online Appendix
 6_Details_Node_PositioningOnline Appendix 6 -
 Illustration of methodology for node positioning on the analyzed tree, PDF
 file.Online_Appendix_7_Matrices_QOnline Appendix 7 - Illustration of matrices used for likelihood tests of character models, PDF file.Online_Appendix_8_Results_Rates_models_EntireSampleOnline Appendix 8 - Excel sheets with the estimated transition rates for all models for the anterior and posterior cingula in the entire sample (Placentalia)
DOI: 10.5061/dryad.5jp0bq3
title: Data from: Along the speciation continuum: quantifying intrinsic and extrinsic isolating barriers across five million years of evolutionary divergence in California jewelflowers

description: Understanding the relative roles of intrinsic and extrinsic reproductive
 barriers, and their interplay within the geographic context of diverging
 taxa, remains an outstanding challenge in the study of speciation. We
 conducted a comparative analysis of reproductive isolation in California
 Jewelflowers (Streptanthus, s.l., Brassicaceae) by quantifying potential
 barriers to gene flow at multiple life history stages in 39 species pairs
 spanning five million years of evolutionary divergence. We quantified nine
 potential pre- and postzygotic barriers and explored patterns of
 reproductive isolation in relation to genetic distance. Intrinsic
 postzygotic isolation was initially weak, increased at intermediate
 genetic distances, and reached a threshold characterized by complete
 genetic incompatibility. Climatic niche differences were strong at shallow
 genetic distances, and species pairs with overlapping ranges showed slight
 but appreciable phenological isolation, highlighting the potential for
 ecological barriers to contribute to speciation. Geographic analyses
 suggest that speciation is not regionally allopatric in the California
 Jewelflowers, as recently diverged taxa occur in relatively close
 proximity and display substantial range overlap. Young pairs are
 characterized by incomplete intrinsic postzygotic isolation, suggesting
 that extrinsic barriers or fine-scale spatial segregation are more
 important early in the divergence process than genetic incompatibilities.
description: Data_01_Geographic_coordinates_CA_consortium_and_GBIF_coordinates_cleanedGeographic coordinates of collection records from the California Consortium of Herbaria and GBIF. Data used for geographic analyses, and climatic niche modeling.Data_02_Phenology_hebarium_records_cleanedHerbarium records from California Consortium of Herbaria and GBIF, with collection date. Data used for phenological analyses.Data_03_Floral_morphology_traits_TJM2Floral morphology data extracted from The Jepson Manual 2. Data used for floral morphology analyses.Data_04_All_crossing_dataExperimental crossing data.Data_05_F1_germination_and_survivalExperimental data on F1 germination and survival to flowering.Data_06_F1_pollen_viabilityExperimental data on pollen viability in F1s.Fig1_pruned_strep_treePruned phylogeny from Cacho et al. 2014, "Novel nuclear markers inform the systematics and the evolution of serpentine use in Streptanthus and allies (Thelypodieae, Brassicaceae)"Fig1_species_and_site_coordinatesSeed collection locations.
DOI: 10.5061/dryad.ms7q2q4
title: Data from: Tuatara and a new morphometric dataset for Rhynchocephalia: comments on Herrera‐Flores et al

description: It has recently been suggested that a ‘living fossil’ can be identified
 because it is both morphologically conservative and exhibits a
 significantly slower rate of morphological evolution compared to related
 lineages (Herrera-Flores et al. 2017). As an exemplar, variation among
 known rhynchocephalians was investigated, and it was concluded that the
 New Zealand tuatara Sphenodon punctatus Gray, 1831 is a living fossil
 species (Herrera-Flores et al. 2017). In addition to the dubious
 biological meaning and basis of describing a ‘living fossil’ (Grandcolas
 et al. 2014; Grandcolas and Trewick 2016), we find major flaws in the
 methods used to investigate morphological conservatism among
 rhynchocephalians. To assist future studies of dentary shape variation
 among rhynchocephalians and morphological conservatism, we provide a
 geometric morphometric dataset for tuatara.
description: Tutara
 samplingPhotographic and
 digitisation sampling of tuatara dentary bones for this study. File
 includes provenance and museum collection information.tuatara-sampling.xlsxTuatara morphometric datasetProcrustes coordinates and centroid size values for digitised tuatara dentary bones. File can be easily modified (instructions included) for conversion into .csv file for input into the geometric morphometric software MorphoJ. File includes keys for the classifier strings used in specimen IDs to classify specimens into groups (e.g. regions, left or right, living or fossil).tuatara-morpho-dataset.xlsxSupporting MaterialSupporting Tables and FiguresSUPPORTING.docxSupplementary Figure 1Supplementary Figure 1SUPFIG1.tifSupplementary Figure 2Supplementary Figure 2SUPFIG2.tifSupplementary Figure 3Supplementary Figure 3SUPFIG3.tifSupplementary Figure 4Supplementary Figure 4SUPFIG4.tifSupplementary Table 1Supplementary Table 1SUPTABLE1.docx
DOI: 10.5061/dryad.4jb32s2
title: Data from: Drivers of power line use by white storks: a case study of birds nesting on anthropogenic structures

description: 1. Anthropogenic structures are mainly known to have negative impacts on
 wildlife populations but sometimes arethey can be beneficial. Power lines
 are a main driver of bird mortality through collision or electrocution,
 but electricity pylons are also commonly used for nest building by some
 species. Birds and nests cause power outages that need to be tackled by
 electricity companies. However, the use of pylons by threatened species
 provides an opportunity for conservation purposes. 2. In this study, we
 described an empirical modelling approach to predict the circumstances
 under which circumstances nesting birds use electricity pylons are used by
 nesting birds. We focused on white storks Ciconia ciconia, a species that
 has been increasingly using electricity pylons for nesting across Europe.
 3. In a country-level census in Portugal, we found a total of 1348 white
 stork nests in 668 of the 8680 very high-tension power line pylons
 occurring in the distribution range of this colonial species, with spatial
 clustering in pylon occupation up to a distance of 30 km. The number of
 nests in each used pylon ranged from 1 to 21 (mean±SD= 2.2±2.06). 4. The
 main drivers of pylon use by nesting storks were distance to major feeding
 areas (rice fields, landfills and large wetlands), with more intensive use
 closer to these features, followed by land cover type surrounding each
 pylon. Pylon type and age, and stork population density in the region, had
 comparatively less importance. 5. Synthesis and applications. Our approach
 can be used to plan both for species conservation and minimising damage to
 infrastructures. For power lines, we outline: (i) planning power line
 routes to take account of the probability of pylon use; (ii) applying
 nesting deterrent devices (to reduce bird mortality and power outage risk)
 and providing nesting platforms (to promote bird use) on suitable pylons;
 and (iii) selecting adequate pylon types to promote or inhibit nesting.
description: White stork nests in
 power line pylons and associated variablesNumber of nests of white
 storks in very high tension power line pylons in Portugal, in 2007, and
 associated variables to model the drivers of pylon use. Information on
 nest occurrence collected in the field, through aerial surveys.
 Explanatory variables from land cover information data, stork censuses and
 information provided by the power line company (REN).Data for storks
 paper.xlsx
DOI: 10.6084/m9.figshare.31157836
title: Supplementary Material for: A CASE OF BRANCH RETINAL ARTERIOLE OCCLUSION AND PARACENTRAL ACUTE MIDDLE MACULOPATHY AFTER COVID-19 INFECTION

description: Introduction
To report a case of segmental deep capillary plexus ischemic injury after COVID-19 infection in a vaccinated otherwise healthy male.
Case Presentation
A healthy 38-year-old male presented with a complaint of not being able to see above his fixation point in the left eye. He had developed a positive scotoma two weeks after a COVID-19 infection. Examination showed a branch retinal arteriole occlusion in the inferotemporal quadrant with an area of subtle arcuate retinal whitening inferior to the fovea. Systemic workup was unremarkable. His vision remained 20/20, with a persistent scotoma over two months. Severe thinning of the inner nuclear layer and marked attenuation of the outer plexiform layer in an arcuate segment inferior to the fovea were detected with OCT. OCTA revealed a flow void in the deep capillary plexus inferior to the fovea and cessation of the blood flow distal to the occluded retinal arteriole. 
Conclusion
This case highlights the deep capillary plexus's unique vulnerability to COVID-19-related occlusion, likely due to its high autoregulatory demand and dense vascular architecture. It emphasizes the need for further investigation into retinal microvascular complications of the disease.
DOI: 10.6084/m9.figshare.31157836.v1
title: Supplementary Material for: A CASE OF BRANCH RETINAL ARTERIOLE OCCLUSION AND PARACENTRAL ACUTE MIDDLE MACULOPATHY AFTER COVID-19 INFECTION

description: Introduction
To report a case of segmental deep capillary plexus ischemic injury after COVID-19 infection in a vaccinated otherwise healthy male.
Case Presentation
A healthy 38-year-old male presented with a complaint of not being able to see above his fixation point in the left eye. He had developed a positive scotoma two weeks after a COVID-19 infection. Examination showed a branch retinal arteriole occlusion in the inferotemporal quadrant with an area of subtle arcuate retinal whitening inferior to the fovea. Systemic workup was unremarkable. His vision remained 20/20, with a persistent scotoma over two months. Severe thinning of the inner nuclear layer and marked attenuation of the outer plexiform layer in an arcuate segment inferior to the fovea were detected with OCT. OCTA revealed a flow void in the deep capillary plexus inferior to the fovea and cessation of the blood flow distal to the occluded retinal arteriole. 
Conclusion
This case highlights the deep capillary plexus's unique vulnerability to COVID-19-related occlusion, likely due to its high autoregulatory demand and dense vascular architecture. It emphasizes the need for further investigation into retinal microvascular complications of the disease.
DOI: 10.5061/dryad.77vq6gs
title: Data from: Topographic mapping of the interfaces between human and aquatic mosquito habitats to enable barrier-targeting of interventions against malaria vectors

description: Geophysical topographic metrics of local water-accumulation potential are
 freely available and have long been known as high resolution predictors of
 where aquatic habitats for immature Anopheles mosquitoes are most
 abundant, resulting in elevated densities of adult malaria vectors and
 human infection burden. Using existing entomological and epidemiological
 survey data, here we illustrate how topography can also be used to map out
 the interfaces between wet, unoccupied valleys and dry, densely populated
 uplands, where malaria vector densities and infection risk are focally
 exacerbated. These topographically identifiable geophysical boundaries
 experience disproportionately high vector densities and malaria
 transmission risk because this is where Anopheles mosquitoes first
 encounter humans when they search for blood after emerging or ovipositing
 in the valleys. Geophysical topographic indicators accounted for 67% of
 variance for vector density but only 43% for infection prevalence, so they
 could enable very selective targeting of interventions against the former
 but not the latter (targeting ratios of 9.0 versus 1.5 to 1,
 respectively). So in addition to being useful for targeting larval source
 management to wet valleys, geophysical topographic indicators may also be
 used to selectively target adult Anopheles mosquitoes with insecticidal
 residual sprays, fencing, vapour emanators or space sprays to barrier
 areas along their fringes.
description: Anopheles gambiae
 datasetThe dataset contains
 densities of mosquito vector collected in different locations in Dar es
 Salaam cityMalaria prevalence
 dataThe dataset contains
 malaria positivity as it was tested in Dar es Salaam
 city.Prevalence
 data.xlsGeophysical
 variablesThis file provides
 topographic hydrological variables used in the analysis. the variables
 were derived from a 10m resolution digital elevation model of Dar es
 Salaam city.
DOI: 10.6084/m9.figshare.31157839
title: Supplementary Material for: Clinical Prognostic Significance of LRG1 in Metastatic Breast Cancer

description: Background & objective: Leucine-rich α-2 glycoprotein 1 (LRG1) is a multifunctional pro-inflammatory signaling molecule that has been proposed as a promising biomarker and potential therapeutic target across various types of cancer. Prospective studies investigating LRG1 in breast cancer patients are scarce. The purpose of this study was to investigate whether circulating LRG1 levels are associated with overall survival in patients with metastatic breast cancer. 
Methods: The present study encompassed 47 individuals with ER-positive/HER2-negative metastatic breast cancer who were scheduled to receive treatment with CDK4/6 inhibitors in combination with endocrine therapy as a first or second line of treatment. The primary endpoint was three-year overall survival. Plasma LRG1 levels were measured using an enzyme-linked immunosorbent assay.
Results: LRG1 levels were significantly associated with advanced age, C-reactive protein, invasive lobular carcinoma, and the presence of lung metastases. During the three-year follow-up period, 30% of participants died. Kaplan–Meier analysis based on the optimal cutoff indicated that patients with elevated LRG1 levels had a significantly higher risk of mortality compared to those with lower concentrations (log-rank p = 0.008), with a hazard ratio (HR) of 3.22 [95% CI: 1.32–11.05]; P = 0.013. This association remained significant after adjustment for potential confounders. Similarly, when modeled as a log₂-transformed continuous variable, LRG1 levels were also significantly associated with overall survival (HR per doubling = 5.82 [95% CI: 1.35–25.13]; P = 0.018).
Conclusions: LRG1 significantly predicted three-year overall survival in patients with metastatic breast cancer, supporting its potential as a prognostic biomarker.
DOI: 10.6084/m9.figshare.31157839.v1
title: Supplementary Material for: Clinical Prognostic Significance of LRG1 in Metastatic Breast Cancer

description: Background & objective: Leucine-rich α-2 glycoprotein 1 (LRG1) is a multifunctional pro-inflammatory signaling molecule that has been proposed as a promising biomarker and potential therapeutic target across various types of cancer. Prospective studies investigating LRG1 in breast cancer patients are scarce. The purpose of this study was to investigate whether circulating LRG1 levels are associated with overall survival in patients with metastatic breast cancer. 
Methods: The present study encompassed 47 individuals with ER-positive/HER2-negative metastatic breast cancer who were scheduled to receive treatment with CDK4/6 inhibitors in combination with endocrine therapy as a first or second line of treatment. The primary endpoint was three-year overall survival. Plasma LRG1 levels were measured using an enzyme-linked immunosorbent assay.
Results: LRG1 levels were significantly associated with advanced age, C-reactive protein, invasive lobular carcinoma, and the presence of lung metastases. During the three-year follow-up period, 30% of participants died. Kaplan–Meier analysis based on the optimal cutoff indicated that patients with elevated LRG1 levels had a significantly higher risk of mortality compared to those with lower concentrations (log-rank p = 0.008), with a hazard ratio (HR) of 3.22 [95% CI: 1.32–11.05]; P = 0.013. This association remained significant after adjustment for potential confounders. Similarly, when modeled as a log₂-transformed continuous variable, LRG1 levels were also significantly associated with overall survival (HR per doubling = 5.82 [95% CI: 1.35–25.13]; P = 0.018).
Conclusions: LRG1 significantly predicted three-year overall survival in patients with metastatic breast cancer, supporting its potential as a prognostic biomarker.
DOI: 10.5281/zenodo.18388198
title: Ethical Evaluation Indicators

description: Data from Delphi Expert Consultation and Analytic Hierarchy Process in the Process of Constructing Ethical Evaluation Indicators
DOI: 10.5281/zenodo.18388199
title: Ethical Evaluation Indicators

description: Data from Delphi Expert Consultation and Analytic Hierarchy Process in the Process of Constructing Ethical Evaluation Indicators
DOI: 10.6084/m9.figshare.31157842
title: Supplementary Material for: Use of the Loop Open-Source Automated Insulin Delivery System in Children with Type 1 Diabetes: Six-Month Results from a Single Center

description: Introduction: As an alternative to commercial automated insulin delivery (AID) systems open-source AID (OS-AID) technologies such as Loop had growing interest among people with type 1 diabetes (T1D). This study aims to evaluate the six-month glycemic outcomes of children using the Loop iOS.3 system.
Methods: A total of fifty children aged 2–18 years with a minimum 6-month T1D duration, initiated Loop OS-AID between May 2023 and May 2024. Data from continuous glucose monitoring and insulin delivery were collected and analyzed at baseline, 3 months, and 6 months. Primary outcomes included time in range (TIR, 3.9 – 10mmol/L [70–180 mg/dL]), time above range (TAR), time below range (TBR), glucose management indicator (GMI), and HbA1c.
Results: TIR improved significantly from 68.3% at baseline to 72.7% at 6 months (p=0.003). The proportion of participants with TIR &gt;70% increased from 46% to 66% (p=0.012). The mean HbA1c value showed a significant decrease from baseline to month 6 (53 mmol/mol [7.0%] vs. 49 mmol/mol [6.6%], p=0.006), although HbA1c measurements were available for a limited number of participants. TAR1 &gt; 10mmol/L (180 mg/dL) decreased (2 vs 17.1 p &lt;0.001), while TAR2 &gt;13.8mmol/L (250mg/dl) showed a slight, non-significant reduction (5 vs 4 p=0.363). TBR1 &lt;3.9mmol/L (70mg/dL) and TBR2 &lt;3mmol/L (54mg/dL) remained stable (3 vs 3, p1=0.474; 0.7 vs 0.9, p2=0.560). The basal insulin ratio dropped significantly (40.3% vs 19.7%, p &lt;0.001), suggesting a shift in dosing dynamics due to the algorithm’s automatic correction bolus strategy. 
Conclusion: Use of the Loop OS-AID system resulted in improved glycemic outcomes without increased risk of hypoglycemia or DKA (Diabetic ketoacidosis). These findings support Loop as a safe and effective alternative for pediatric T1D management. Further large-scale and longer-term studies are warranted.