cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.db8hd
title: Data from: Number of alleles as a predictor of the relative assignment accuracy of STR and SNP baselines for chum salmon

description: Short tandem repeat (STR) markers, which exhibit many alleles per locus,
 are commonly used to assign fish to their populations of origin. Single
 nucleotide polymorphisms (SNPs), which have many technical advantages over
 STRs, typically exhibit only two alleles per locus. Simulation studies
 have indicated that number of independent alleles is a good predictor of
 accuracy of genetic markers for fishery applications. Extant STR baselines
 for salmon contain hundreds of alleles, and it has been extrapolated that
 hundreds of SNP markers need to be developed before SNP baselines will
 compare to these STR baselines. We compared 15 STRs exhibiting 349
 independent alleles to 61 SNP assays exhibiting 66 independent alleles for
 accuracy in assigning to closely related populations of chum salmon. The
 SNP baseline yielded slightly higher mean accuracies for proportional
 assignment and comparable accuracies for individual assignment. Overall
 the SNP baseline performed considerably better, relative to the
 microsatellite baseline, than predicted based on the number of independent
 alleles in each baseline. We suggest that this discrepancy is due to the
 fact that the simulation studies do not capture the impacts of the
 different strategies commonly employed for discovering and selecting STR
 and SNP markers.
description: convert
 input3MSATShort tandem repeat
 (STR) genotype data in CONVERT formatconvert
 input3SNPSingle nucleotide
 polymorphism (SNP) genotype data in CONVERT format. Includes all loci in
 raw format.snp4b convert
 inputsingle nucleotide
 polymorphism (SNP) genotype data in CONVERT format. Linked SNPs converted
 to haplotypes and uninformative SNPs removed (as described in
 paper).
DOI: 10.5061/dryad.k30c2n0
title: Data from: Static dental disparity and morphological turnover in sharks across the end-Cretaceous mass extinction

description: The Cretaceous–Palaeogene (K–Pg) mass extinction profoundly altered
 vertebrate ecosystems and prompted the radiation of many extant clades [1,
 2]. Sharks (Selachimorpha) were one of the few larger-bodied marine
 predators that survived the K–Pg event and are represented by an
 almost-continuous dental fossil record. However, the precise dynamics of
 their transition through this interval remain uncertain [3]. Here, we
 apply 2D geometric morphometrics to reconstruct global and regional dental
 morphospace variation among Lamniformes (Mackerel sharks) and
 Carcharhiniformes (Ground sharks). These clades are prevalent predators in
 today’s oceans, and were geographically widespread during the late
 Cretaceous–early Palaeogene. Our results reveal a decoupling of
 morphological disparity and taxonomic richness. Indeed, shark disparity
 was nearly static across the K–Pg extinction, in contrast to abrupt
 declines among other higher-trophic-level marine predators [4, 5].
 Nevertheless, specific patterns indicate that an asymmetric extinction
 occurred among lamniforms possessing low-crowned/triangular teeth and that
 a subsequent proliferation of carcharhiniforms with similar tooth
 morphologies took place during the early Paleocene. This compositional
 shift in post-Mesozoic shark lineages hints at a profound and persistent
 K–Pg signature evident in the heterogeneity of modern shark communities.
 Moreover, such wholesale lineage turnover coincided with the loss of many
 cephalopod [6] and pelagic amniote [5] groups, as well as the explosive
 radiation of middle trophic-level teleost fishes [1]. We hypothesize that
 a combination of prey availability and post-extinction trophic cascades
 favored extant shark antecedents and laid the foundation for their
 extensive diversification later in the Cenozoic [7, 8, 9, 10].
description: R source
 codeProgramming commands
 essential for replicating our geometric morphometric and statistical
 analyses are here given. The main source code (Bazzi et
 al_Dryad_MasterRScript) is accompanied by separate R scripts (functions
 and analytical loops) which can be sourced directly provided the working
 directory has been set.R
 Scripts.zipBazzi et
 al_Data_Dryad_Supplementary_File_1Extended experimental
 procedures, results, and discussion.Bazzi et
 al_Data_Dryad_Supplementary_File_2Original occurrence
 dataset (metadata).Bazzi et
 al_Data_Dryad_Supplementary_File_3Tps file containing
 two-dimensional landmark data.Bazzi et
 al_Data_Dryad_Supplementary_File_4Sliders
 file.
DOI: 10.5061/dryad.2r4gj
title: Data from: Phenotypic assortment mediates the effect of social selection in a wild beetle population

description: Social interactions often have major fitness consequences, but little is
 known about how specific interacting phenotypes affect the strength of
 natural selection. Social influences on the evolutionary process can be
 assessed using a multilevel selection approach that partitions the effects
 of social partner phenotypes on fitness (referred to as social or group
 selection) from those of the traits of a focal individual (nonsocial or
 individual selection). To quantify the contribution of social selection to
 total selection affecting a trait, the patterns of phenotypic association
 among interactants must also be considered. We estimated selection
 gradients on male body size in a wild population of forked fungus beetles
 (Bolitotherus cornutus). We detected positive nonsocial selection and
 negative social selection on body size operating through differences in
 copulation success, indicating that large males with small social partners
 had highest fitness. In addition, we found that, in low-density demes, the
 phenotypes of focal individuals were negatively correlated with those of
 their social partners. This pattern reversed the negative effect of group
 selection on body size and led to stronger positive selection for body
 size. Our results demonstrate multilevel selection in nature and stress
 the importance of considering social selection whenever conspecific
 interactions occur nonrandomly.
description: deme-statsData used to generate Figure 3 and related statistics. Data collected from the wild and managed with JMP V.7male-male-interactionsFile used to calculate covariances, described as Cii and Cii (prime). Data collected in the wild and managed with JMP v7. Data used to generate figure Table 2 and used in calculation of Table 5.Social-selection-gradientData collected in the wild and managed with JMP v7. Data used in the calculation of Table 3, Table 4, and Table 5. These are the data used to calculate selection gradients. Also used to generate Figure 4.
DOI: 10.5061/dryad.4hv2b38
title: Data from: Locality or habitat? Exploring predictors of biodiversity in Amazonia

description: Amazonia is an environmentally heterogeneous and biologically megadiverse
 region, and its biodiversity varies considerably over space. However,
 existing knowledge on Amazonian biodiversity and its environmental
 determinants stems almost exclusively from studies of macroscopic
 above‐ground organisms, notably vertebrates and trees. In contrast,
 diversity patterns of most other organisms remain elusive, although some
 of them, for instance microorganisms, constitute the overwhelming majority
 of taxa in any given location, both in terms of diversity and abundance.
 Here, we use DNA metabarcoding to estimate prokaryote and eukaryote
 diversity in environmental soil and litter samples from 39 survey plots in
 a longitudinal transect across Brazilian Amazonia using 16S and 18S gene
 sequences, respectively. We characterize richness and community
 composition based on operational taxonomic units (OTUs) and test their
 correlation with longitude and habitat. We find that prokaryote and
 eukaryote OTU richness and community composition differ significantly
 among localities and habitats, and that prokaryotes are more strongly
 structured by locality and habitat type than eukaryotes. Our results (1)
 provide a first large‐scale mapping of Amazonian soil biodiversity,
 suggesting that OTU richness patterns might follow substantially different
 patterns from those observed for macro‐organisms; and (2) indicate that
 locality and habitat factors interact in determining OTU richness patterns
 and community composition. This study shows the potential of DNA
 metabarcoding in unveiling Amazonia's outstanding diversity, despite
 the lack of complete reference sequence databases for the organisms
 sequenced.
description: OTU table for
 16SOTU table for 16S: The
 number of OTUs by plot.Abundance16s_total.csvAbundance18s_totalOTU table with the number of OTU by plot for 18S.16S_taxTaxonomic table and sequences for 16S.18S_taxTaxonomic table and sequences for 18S.Ritter_et_al_2017R-script with all analysis
DOI: 10.5061/dryad.m8s3r88
title: Data from: An MRI measure of degenerative and cerebrovascular pathology in Alzheimer’s disease

description: Objective: To develop, replicate, and validate an MRI-based quantitative
 measure of both cerebrovascular and neurodegeneration in Alzheimer’s
 disease for clinical and potentially research purposes. Methods. We used
 data from a cross-sectional and longitudinal community-based study of
 Medicare-eligible residents in northern Manhattan followed every 18-24
 months (N=1,175, mean age=78 years). White matter hyperintensities,
 infarcts, hippocampal volumes, and cortical thicknesses were quantified
 from MRI and combined to generate an MRI measure associated with episodic
 memory. The combined MRI measure was replicated and validated using
 autopsy data, clinical diagnoses, and cerebrospinal fluid biomarkers and
 amyloid PET from the Alzheimer’s Disease Neuroimaging Initiative. Results.
 The quantitative MRI measure was developed in a group of community
 participants (n=690) and replicated in a similar second group (n=485).
 Compared with healthy controls, the quantitative MRI measure was lower in
 patients with mild cognitive impairment and lower still in those with
 clinically diagnosed Alzheimer’s disease. The quantitative MRI measure
 correlated with neurofibrillary tangles, neuronal loss, atrophy, and
 infarcts at postmortem in an autopsy subset and was also associated with
 PET amyloid imaging and cerebrospinal fluid levels of total tau, p-tau,
 and Aβ42. The MRI measure predicted conversion to MCI and clinical
 Alzheimer’s disease among healthy controls. Conclusions. We developed,
 replicated and validated an MRI measure of cerebrovascular and
 neurodegenerative pathologies that are associated with clinical and
 neuropathological diagnosis of Alzheimer’s disease and related to
 established biomarkers.
description: supplementary_file
DOI: 10.5061/dryad.sd660pm
title: Data from: Functional and mechanistic neurotoxicity profiling using human iPSC–derived neural 3D cultures

description: Neurological disorders affect millions of people worldwide and appear to
 be on the rise. While the reason for this increase remains unknown,
 environmental factors are a suspected contributor. Hence, there is an
 urgent need to develop more complex, biologically relevant, and predictive
 in vitro assays to screen larger sets of compounds with the potential for
 neurotoxicity. Here, we employed a human induced pluripotent stem cell
 (iPSC)-based 3D neural platform composed of mature cortical neurons and
 astrocytes as a model for this purpose. The iPSC-derived human 3D cortical
 neuron/astrocyte co-cultures (3D neural cultures) present spontaneous
 synchronized, readily detectable calcium oscillations. This advanced
 neural platform was optimized for high-throughput screening in 384-well
 plates and displays highly consistent, functional performance across
 different wells and plates. Characterization of oscillation profiles in 3D
 neural cultures was performed through multi-parametric analysis that
 included the calcium oscillation rate and peak width, amplitude, and
 waveform irregularities. Cellular and mitochondrial toxicity were assessed
 by high-content imaging. For assay characterization, we used a set of
 neuromodulators with known mechanisms of action. We then explored the
 neurotoxic profile of a library of 87 compounds that included
 pharmaceutical drugs, pesticides, flame retardants, and other chemicals.
 Our results demonstrated that 57% of the tested compounds exhibited
 effects in the assay. The compounds were then ranked according to their
 effective concentrations based on in vitro activity. Our results show that
 a human iPSC-derived 3D neural culture assay platform is a promising
 biologically-relevant tool to assess the neurotoxic potential of drugs and
 environmental toxicants.
description: Supplemental Figures and
 TablesSupplemental figures and
 tables for neurospheroid articles. Shows examples of primary data, images,
 also provides tables with correlation coefficientsSupplemental
 Figures.pdfSupplemental Table
 1Supplemental Table 1 for
 neurospheroid paper. Table contains the list of tested
 chemicals.Supplemental Table
 2Supplemental Table 2
 presents PRIMARY DATA for calcium oscillation and viability read-outs for
 effects of compounds from neurotoxicity librarySupplementaryTable 3.
 Benchmark ConcentrationsSupplementaryTable 3.
 Benchmark Concentrations.The table contains benchmark concentrations and
 other statistical data generated from the dataset presented in the
 Supplementary Table 2.Assay optimization
 data_Assay optimization data_
 the table contains optimization data for selected compounds and
 controls
DOI: 10.5061/dryad.gp864h7
title: Data from: Human activities and landscape features interact to closely define the distribution and dispersal of an urban commensal.

description: The rock pigeon, Columba livia, is a cosmopolitan human commensal,
 domesticated thousands of years ago. However, the human-mediated factors
 governing its distribution and dispersal are not well understood. In this
 study, we performed (1) hierarchical distance sampling on ~400 island-wide
 point transects, (2) a population genomic inquiry based on ~7000 SNPs from
 almost 150 individuals, and (3) landscape-genomic analyses on the basis of
 extensive ecological and social-economic databases to characterize the
 distribution and dispersal patterns of rock pigeons across Singapore. Our
 distance sampling results indicated that the volume of intentional ‘mercy
 feeding’ and availability of high-rise buildings are the most reliable
 predictors of high pigeon densities in Singapore. Genomic analyses
 demonstrated that rock pigeons in Singapore form a single population
 possibly derived from rapid expansion from a genetically homogenous group
 of founder individuals. Specifically, rock pigeons in Singapore lack
 sex-biased dispersal and are clustered with a genetic patch size of ~3km.
 Landscape genomic analyses of great precision pointed to the presence of
 dense trees as agents of resistance to dispersal whereas a high road
 density reduces this resistance. By pinpointing a range of ecological and
 socio-economic variables determining the distribution and dispersal of
 pigeons, our study provides urban planners with the tools for optimal
 management of this human commensal, such as a curtailment of the practice
 of mercy feeding and modifications to the urban landscape to reduce pigeon
 density and to lower the likelihood of repopulation by dispersal.
description: Information of distance
 sampling point transectsGeographical
 coordinates, environmental covariates at each distance sampling point
 transcet. Geographical coordinates are using WGS84
 system.Geo_points_cvt.csvDistance sampling data in unmarked input formatdistdata.csvSNPs used in the study7013 SNPs from 144 individuals (missing data, linkage disequilibrium filtered).7013_144.vcfLocality and sex information for the genetic samplesGeographical coordinates are using WGS84 system.Pigeon_Gen_info.csv
DOI: 10.13012/b2idb-6451062_v1
title: Data for Tracking the early spatio-temporal dynamics of phytoplasma multiplication within its leafhopper vector

description: Trivellone_etal_Full_PaperList_SystRev.xlsx: This dataset contains the list of peer-reviewed studies selected and critically appraised for a systematic review of quantitative PCR (qPCR) investigations tracking phytoplasma load dynamics in insect vectors. The dataset includes bibliographic information and selection status for each study, reflecting the inclusion and exclusion criteria applied during the review process. The literature search was completed on December 15, 2025. The list of inclusion and exclusion criteria are listed in the second spreadsheet.
Further methodological details, including search strategy, screening workflow, and appraisal criteria, are described in the associated paper, “Tracking the early spatio-temporal dynamics of phytoplasma multiplication within its leafhopper vector”, as well as in the Supplementary Materials (see below), by Valeria Trivellone, Francesca Canuto, Giulia Lucetti, Christopher H. Dietrich, Luciana Galetto, Cristina Marzachì.
DOI: 10.5281/zenodo.18299100
title: Critical Zone Observatory in Pianosa Island: meteorological data (01/01/2024-31/12/2024)

description: This dataset presents meteorological data collected, every 15 minutes, by the meteorological station installed with the non steady state closed dynamic accumulation chambers. The dataset includes, in order: rain gauge [mm], wind direction [°], wind Speed [m/s], air temperature [°C], air humidity [%] and atmospheric pressure [hPa].The measurements were conducted at an elevation of approximately 2 meters a.s.l.

The data was collected thanks to EU - Next Generation EU Mission 4 "Education and Research - Component 2: "From research to business" - Investment 3.1: "Fund for the realisation of an integrated system of research and innovation infrastructures" - Project IR0000032 - ITINERIS - Italian Integrated Environmental Research Infrastructures System - CUP B53C22002150006.
DOI: 10.5281/zenodo.14679128
title: Critical Zone Observatory in Pianosa Island: meteorological data (01/01/2024-31/12/2024)

description: This dataset presents meteorological data collected, every 15 minutes, by the meteorological station installed with the non steady state closed dynamic accumulation chambers. The dataset includes, in order: rain gauge [mm], wind direction [°], wind Speed [m/s], air temperature [°C], air humidity [%] and atmospheric pressure [hPa].The measurements were conducted at an elevation of approximately 2 meters a.s.l.

The data was collected thanks to EU - Next Generation EU Mission 4 "Education and Research - Component 2: "From research to business" - Investment 3.1: "Fund for the realisation of an integrated system of research and innovation infrastructures" - Project IR0000032 - ITINERIS - Italian Integrated Environmental Research Infrastructures System - CUP B53C22002150006.
DOI: 10.60893/figshare.jcp.30999907
title: Supplementary Information

description: Working equations and further calculations
DOI: 10.60893/figshare.jcp.30999907.v1
title: Supplementary Information

description: Working equations and further calculations
DOI: 10.5061/dryad.br381mg
title: Data from: Analyzing contentious relationships and outlier genes in phylogenomics

description: Recent studies have demonstrated that conflict is common among gene trees
 in phylogenomic studies, and that less than one percent of genes may
 ultimately drive species tree inference in supermatrix analyses. Here, we
 examined two datasets where supermatrix and coalescent-based species trees
 conflict. We identified two highly influential “outlier” genes in each
 dataset. When removed from each dataset, the inferred supermatrix trees
 matched the topologies obtained from coalescent analyses. We also
 demonstrate that, while the outlier genes in the vertebrate dataset have
 been shown in a previous study to be the result of errors in orthology
 detection, the outlier genes from a plant dataset did not exhibit any
 obvious systematic error and therefore may be the result of some
 biological process yet to be determined. While topological comparisons
 among a small set of alternate topologies can be helpful in discovering
 outlier genes, they can be limited in several ways, such as assuming all
 genes share the same topology. Coalescent species tree methods relax this
 assumption but do not explicitly facilitate the examination of specific
 edges. Coalescent methods often also assume that conflict is the result of
 incomplete lineage sorting (ILS). Here we explored a framework that allows
 for quickly examining alternative edges and support for large phylogenomic
 datasets that does not assume a single topology for all genes. For both
 datasets, these analyses provided detailed results confirming the support
 for coalescent-based topologies. This framework suggests that we can
 improve our understanding of the underlying signal in phylogenomic
 datasets by asking more targeted edge-based questions.
description: Analyzing Contentious
 nodesContains data used that
 is not on the github. For most recent code etc...you can go to the github:
 https://github.com/jfwalker/MGWESysBioContentiousNode.tgz
DOI: 10.5281/zenodo.18350649
title: INRIM_Brand1_1F_4_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 1F SC sample 4 INRIM   - EDLC Single - Brand1

Part of the Constant Temperature DataBase
DOI: 10.5061/dryad.k6tp614
title: Data from: Cavity-mediated collective spin-exchange interactions in a strontium superradiant laser

description: Laser-cooled and quantum degenerate atoms are being pursued as quantum
 simulators and form the basis of today’s most precise sensors. A key
 challenge toward these goals is to understand and control coherent
 interactions between the atoms. We observe long-range exchange
 interactions mediated by an optical cavity, which manifest as tunable
 spin-spin interactions on the pseudo spin-½ system composed of the
 millihertz linewidth clock transition in strontium. This leads to one-axis
 twisting dynamics, the emergence of a many-body energy gap, and gap
 protection of the optical coherence against certain sources of
 decoherence. Our observations will aid in the future design of versatile
 quantum simulators and the next generation of atomic clocks that use
 quantum correlations for enhanced metrology.
description: Fig2aFig2bFig3cminus150kHzFig3cplus150kHzFig4aFig4bFig4cFigS1a_expFigS1b_expFigS1c_exp
DOI: 10.5281/zenodo.18350648
title: INRIM_Brand1_1F_4_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 1F SC sample 4 INRIM   - EDLC Single - Brand1

Part of the Constant Temperature DataBase