cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0f454q8
title: Data from: Increased CAIDE dementia risk, cognition, CSF biomarkers and vascular burden in healthy adults

description: Objective: To investigate the cognitive profile of healthy individuals
 with increased CAIDE dementia risk score, and to explore whether this
 association is related to vascular burden and CSF biomarkers of
 amyloidosis and neurodegeneration. Method: Cognitively normal participants
 (mean age = 57.6 years) from the Gipuzkoa Alzheimer Project study were
 classified as having high risk (HR, n = 82) or low risk (LR, n = 293) for
 dementia according to a CAIDE score cut off of 9. Cognitive composites
 were compared between groups. We explored the role of APOE genotype, MRI
 white matter hyperintensities (WMH) and CSF (n = 218) levels of
 amyloid-β1-42 (Aβ1-42), total tau (t-tau) and phosphorylated tau (p-tau)
 in the association between CAIDE and cognition conducting generalized
 linear models. Results: HR participants obtained lower scores on executive
 function (EF) (p = .001) and visual perception and construction (VPC) (p
 &lt; .001) composites. EFc was associated with CAIDEp-tau (p = .001),
 CAIDEt-tau (p = .001) and WMH (p = .003). VPCc was associated with APOE (p
 = .001), Aβ1-42 (p = .004), the interaction APOEAβ1-42 (p = .003), and WMH
 (p = .004). Performance on global memory was associated with Aβ1-42 (p =
 .006), APOE (p = .008), and their interaction (p = .006). Analyses were
 adjusted for age, education, sex, premorbid intelligence and stress.
 Conclusion: Healthy participants at increased dementia risk, based on
 CAIDE scores, show lower performance in executive function and visual
 perception and construction. This difference is related to APOE, WMH and
 Alzheimer’s biomarkers.
description: e-References_Clinical
 and neuropsychological testsThe appendix includes
 the clinical and neuropsychological references list used in the GAP
 project.Supplementary tables
 Ecay-TorresThese supplemetary
 tables contain the results of the intermediate generalized linear models
 needed to select the variables of the finals models shown in the
 manuscript.
DOI: 10.5061/dryad.qk12c
title: Data from: Ecological adaptation and reproductive isolation in sympatry: genetic and phenotypic evidence for native host races of Rhagoletis pomonella

description: Ecological speciation-with-gene-flow may be an important mode of
 diversification for phytophagous insects. The recent shift of Rhagoletis
 pomonella from its native host downy hawthorn (Crataegus mollis) to
 introduced apple (Malus domestica) in the northeastern United States is a
 classic example of sympatric host race formation. Here, we test whether R.
 pomonella has similarly formed host races on four native Crataegus species
 in the southern United States: western mayhaw (C. opaca), blueberry
 hawthorn (C. brachyacantha), southern red hawthorn (C. mollis var.
 texana), and green hawthorn (C. viridis). These four southern hosts differ
 from each other in their fruiting phenology and in the volatile compounds
 emitted from the surface of their fruits. These two traits form the basis
 of ecological reproductive isolation between downy hawthorn and apple
 flies in the North. We report evidence from microsatellite population
 surveys and eclosion studies supporting the existence of genetically
 differentiated and partially reproductively isolated host races of
 southern hawthorn flies. The results provide an example of host shifting
 and ecological divergence involving native plants and imply that
 speciation-with-gene-flow may be commonly initiated in Rhagoletis when
 ecological opportunity presents itself.
description: Table S5 -
 microsatellite allele frequenciesMicrosatellite allele
 frequencies for the 26 loci analyzed in study for 16 field sites,
 including 6 green hawthorn, 4 western mayhaw, 3 blueberry hawthorn, and 3
 southern red hawthorn populations. See Table 1 of text for site
 descriptions. Allele numbers represent the size (in base pairs) of the PCR
 amplified DNA fragment (including the repeat sequence) generated using
 locus specific primers for each microsatellite, as determined by capillary
 electrophoresis on a Beckman-Coulter CEQ8000.Powell_etal_TableS5_for_DRYAD.xlsxmtDNA sequence alignmentClustal alignment of mtDNA sequences used in Figure 3. See Table S1 for accession numbers.Powell_etal_mtDNA_alignment.txtEclosion dataTable of laboratory eclosion data depicted in Figure 6.Powell_etal_eclosion_data.xlsx
DOI: 10.5061/dryad.4sn22
title: Data from: Neutron imaging investigation of fossil woods: non-destructive characterization of microstructure and detection of in situ changes as occurring in museum cabinets

description: This paper discusses the applicability of neutron imaging techniques for
 probing the internal microstructure of several fossil woods upon wetting
 and drying, two phenomena occurring in museum cabinets and endangering the
 fossil woods. Investigations were carried out using lignites (fossil
 woods) from two French localities (Rivecourt, Parisian Basin, Oise –
 Paleogene; Angeac, Aquitanian Basin, Charente – Cretaceous), which present
 different macroscopic behavior upon drying. Thanks to the high sensitivity
 of neutrons to hydrogen content, it was possible to track water diffusion
 through 3 mm thick samples and to follow in situ changes related to either
 supply or withdrawal of water without any special preparation and in a
 relevant time range (from 1 min to a few hours). Classical image analysis
 allows discriminating between the behavior of the two fossil woods with
 regard to their interaction with water. Further analysis based on a
 Fourier transform of projection images provides additional information
 regarding the existence of large pores in one of the samples. Differences
 in pore network and internal structures have important mechanical
 consequences as one of the samples retains its integrity upon drying,
 whereas the other one shatters into pieces. A better understanding of the
 underlying processes will clearly require multi-scale analyses, using
 additional techniques that could probe the materials at a lower scale.
 Such a combination of multi-scale analyses should provide valuable
 information for a better conservation of wood remnants, which is crucial
 for both paleobotanical research and museum exhibits.
description: Rivecourt_water-sorptionThis file corresponds to a sequence of neutron transmission images recorded during humidification of a fossil wood sample coming from Rivecourt (Parisian Basin, France, paleogene)Rivecourt_water-desorptionThis file corresponds to an image sequence of neutron transmission images of a fossil wood during drying. The wood comes from Rivecourt (Parisian Basin, Oise, Paleogene)Angeac_water-sorptionThis file corresponds to a sequence of neutron transmission images recorded during humidification of a fossil wood sample coming from Angeac (Aquitanian Basin, France, cretaceous:paleocene)Angeac_water-desorptionThis file corresponds to a sequence of neutron transmission images recorded on a fossil wood during drying. The wood comes from Angeac (Aquitanian basin, Cretaceous:Paleocene)
DOI: 10.5061/dryad.7nb8q
title: Data from: Detecting rare asymmetrically methylated cytosines and decoding methylation patterns in the honeybee genome

description: Context-dependent gene expression in eukaryotes is controlled by several
 mechanisms including cytosine methylation that primarily occurs in the CG
 dinucleotides (CpGs). However, less frequent non-CpG asymmetric
 methylation has been found in various cell types, such as mammalian
 neurons, and recent results suggest that these sites can repress
 transcription independently of CpG contexts. In addition, an emerging view
 is that CpG hemimethylation may arise not only from deregulation of
 cellular processes but also be a standard feature of the methylome. Here,
 we have applied a novel approach to examine whether asymmetric CpG
 methylation is present in a sparsely methylated genome of the honeybee, a
 social insect with a high level of epigenetically driven phenotypic
 plasticity. By combining strand-specific ultra-deep amplicon sequencing of
 illustrator genes with whole-genome methylomics and bioinformatics, we
 show that rare asymmetrically methylated CpGs can be unambiguously
 detected in the honeybee genome. Additionally, we confirm differential
 methylation between two phenotypically and reproductively distinct castes,
 queens and workers, and offer new insight into the heterogeneity of brain
 methylation patterns. In particular, we challenge the assumption that
 symmetrical methylation levels reflect symmetry in the underlying
 methylation patterns and conclude that hemimethylation may occur more
 frequently than indicated by methylation levels. Finally, we question the
 validity of a prior study in which most of cytosine methylation in this
 species was reported to be asymmetric.
description: Apis_mellifera_amplicon_bisulfite_sequencing_queen_2Amplicon bisulfite sequencing reads from Apis mellifera newly-emerged queen brains (5 pooled brains). Archive contains four Illumina Miseq libraries (paired end).Apis_mellifera_amplicon_bisulfite_sequencing_queen_3Amplicon bisulfite sequencing reads from Apis mellifera newly-emerged queen brains (5 pooled brains). Archive contains four Illumina Miseq libraries (paired end).queen3.tarApis_mellifera_amplicon_bisulfite_sequencing_worker_1Amplicon bisulfite sequencing reads from Apis mellifera newly-emerged worker brains (5 pooled brains). Archive contains four Illumina Miseq libraries (paired end).worker1.tarApis_mellifera_amplicon_bisulfite_sequencing_worker_2Amplicon bisulfite sequencing reads from Apis mellifera newly-emerged worker brains (5 pooled brains). Archive contains four Illumina Miseq libraries (paired end).worker2.tarApis_mellifera_amplicon_bisulfite_sequencing_worker_3Amplicon bisulfite sequencing reads from Apis mellifera newly-emerged worker brains (5 pooled brains). Archive contains four Illumina Miseq libraries (paired end).worker3.tarApis_mellifera_amplicon_bisulfite_sequencing_queen_1Amplicon bisulfite sequencing reads from Apis mellifera newly-emerged queen brains (5 pooled brains). Archive contains four Illumina Miseq libraries (paired end).
DOI: 10.5281/zenodo.18382397
title: Enhanced water-use efficiency mediates the synergistic effects of nitrogen and phosphorus enrichment on grassland productivity

description: By combining a global meta-analysis of nutrient-addition experiments with a five-year field experiment in the Inner Mongolia grassland, we show that combined N and P addition synergistically increases both community aboveground net primary productivity (ANPP) and ecosystem WUE. The synergistic responses of ANPP are primarily driven by enhanced WUE, as indicated by the strong coupling between the N–P interactive effects on ANPP and those on WUE. Shifts in community structure—reflected by an increased grass/forb ratio—serve as a bridge linking nutrient-induced soil environmental changes to improvements in WUE.
DOI: 10.5281/zenodo.15694564
title: Enhanced water-use efficiency mediates the synergistic effects of nitrogen and phosphorus enrichment on grassland productivity

description: By combining a global meta-analysis of nutrient-addition experiments with a five-year field experiment in the Inner Mongolia grassland, we show that combined N and P addition synergistically increases both community aboveground net primary productivity (ANPP) and ecosystem WUE. The synergistic responses of ANPP are primarily driven by enhanced WUE, as indicated by the strong coupling between the N–P interactive effects on ANPP and those on WUE. Shifts in community structure—reflected by an increased grass/forb ratio—serve as a bridge linking nutrient-induced soil environmental changes to improvements in WUE.
DOI: 10.5061/dryad.nt13m
title: Data from: Do mites evolving in alternating host plants adapt to host switch?

description: A fluctuating environment may be perceived as a composition of different
 environments, or as an environment per se, in which it is the fluctuation
 itself that poses a selection pressure. If so, then organisms may adapt to
 this alternation. We tested this using experimental populations of spider
 mites that have been evolving for 45 generations in a homogeneous
 environment (pepper or tomato plants), or in a heterogeneous environment
 composed of an alternation of these two plants approximately at each
 generation. The performance (daily oviposition rate and juvenile survival)
 of individuals from these populations was tested in each of the
 homogeneous environments, and in two alternating environments, one every
 three days and the other between generations. To discriminate between
 potential genetic interactions between alleles conferring adaptation to
 each host plant and environmental effects of evolving in a fluctuating
 environment, we compared the performance of all lines with that of a cross
 between tomato and pepper lines. As a control, two lines within each
 selection regime were also crossed. We found that crosses between
 alternating lines and between pepper and tomato lines performed worse than
 crosses between lines evolving in homogeneous environments when tested in
 that environment. In contrast, alternating lines performed either better
 or similarly to lines evolving in homogeneous environments when tested in
 a fluctuating environment. Our results suggest that fluctuating
 environments are more than the juxtaposition of two environments. Hence,
 tests for adaptation of organisms evolving in such environments should be
 done in fluctuating conditions.
description: datafecaltG1oviposition rate of mites evolving in alternating vs homogeneous environments, when tested in each of these in the first generation of test (ie alternation within a single generation).datafecaltG2oviposition rate of mites evolving in alternating vs homogeneous environments, when tested in each of these in the second generation of test (ie alternation among generations).datafecLA2Goviposition rate of mites evolving in alternating vs homogeneous environments, when tested in either tomato or pepper (test for local adaptation and potential cost of generalism)datasurvaltG1juvenile survival of mites evolving in alternating vs homogeneous environments, when tested in each of these in the first generation of test (ie alternation within a single generation).datasurvaltG2oviposition rate of mites evolving in alternating vs homogeneous environments, when tested in each of these in the second generation of test (ie alternation among generations).datasurvbothGjuvenile survival of mites evolving in alternating vs homogeneous environments, when tested in tomato or pepper
DOI: 10.5061/dryad.55sh1
title: Data from: Interspecific shared collective decision-making in two forensically important species

description: To date, the study of collective behaviour has mainly focused on
 intraspecific situations: the collective decision-making of mixed-species
 groups involving interspecific aggregation-segregation has received little
 attention. Here, we show that, in both conspecific and heterospecific
 groups, the larvae of two species (Lucilia sericata and Calliphora
 vomitoria, calliphorid carrion-feeding flies) were able to make a
 collective choice. In all groups, the choice was made within a few minutes
 and persisted throughout the experiment period. The monitoring of a focal
 individual within a group showed that these aggregations were governed by
 attractive and retentive effects of the group. Furthermore, the similarity
 observed between the conspecific and heterospecific groups suggested the
 existence of shared aggregation signals. The group size was found to have
 a stronger influence than the species of necrophagous larvae. These
 results should be viewed in relation to the well-known correlation between
 group size and heat generation. This study provides the first experimental
 examination of the dynamics of collective decision-making in mixed-species
 groups of invertebrates, contributing to our understanding of the
 cooperation-competition phenomenon in animal social groups.
description: Dataset_Proceed
DOI: 10.5061/dryad.nc763
title: Data from: Mutations of the calcium channel gene cacophony suppress seizures in Drosophila

description: Bang sensitive (BS) Drosophila mutants display characteristic seizure-like
 phenotypes resembling, in some aspects, those of human seizure disorders
 such as epilepsy. The BS mutant parabss1, caused by a gain-of-function
 mutation of the voltage-gated Na+ channel gene, is extremely
 seizure-sensitive with phenotypes that have proven difficult to ameliorate
 by anti-epileptic drug feeding or by seizure-suppressor mutation. It has
 been presented as a model for intractable human epilepsy. Here we show
 that cacophony (cacTS2), a mutation of the Drosophila presynaptic Ca++
 channel α1 subunit gene, is a particularly potent seizure-suppressor
 mutation, reverting seizure-like phenotypes for parabss1 and other BS
 mutants. Seizure-like phenotypes for parabss1 may be suppressed by as much
 as 90% in double mutant combinations with cacTS2. Unexpectedly, we find
 that parabss1 also reciprocally suppresses cacTS2 seizure-like phenotypes.
 The cacTS2 mutant displays these seizure-like behaviors and spontaneous
 high-frequency action potential firing transiently after exposure to high
 temperature. We find that this seizure-like behavior in cacTS2 is
 ameliorated by 85% in double mutant combinations with parabss1.
description: Fig 1. Drosophila cacTS2
 electrophysiology.Fig
 1.xlsFig 2. Suppression of
 bang sensitive behavioral phenotypes by cacTS2.Fig
 2.xlsFig 3. Electrophysiology
 of cacTS2 suppression.Fig
 3.xlsFig 4. Suppression of
 parabss1 and eas behavioral phenotypes by cacRNAi at room
 temperature.Fig
 4.xlsFig 5. Suppression of
 cacTS2 temperature-sensitive seizure-like activity by
 parabss1.Fig
 5.xlsS1 Fig. Giant fiber
 stimulation of cacTS2 and bang sensitive mutants.S1
 Fig.xlsS2 Fig. Suppression of
 eas bang sensitivity by cacRNAi using different GAL4
 drivers.S2
 Fig.xls
DOI: 10.5061/dryad.k06p5
title: Data from: A major range expansion for Platismatia wheeleri

description: Platismatia wheeleri was recently described as a species distinct from the
 highly morphologically variable Platismatia glauca. Previously, P.
 wheeleri was known only from intermountain western North America in
 southern British Columbia, Idaho, Montana, Oregon and Washington. After
 examining collections from the New York Botanical Garden and Arizona State
 University herbaria we discovered that P. wheeleri was collected in
 southern California and the Tatra Mountains of Slovakia. The morphology,
 ecology and biogeography of P. wheeleri are discussed, and the importance
 and utility of historical collections is highlighted. This article is
 intended to alert researchers to the potential presence of P. wheeleri in
 different regions of the world so we can better understand its historical
 and current distribution and abundance.
description: Platismatia_specimens_examined_Allen_et_al_2012This is a list of specimens examined by the authors of this article and includes the following information about each specimen: taxon, collector, collection number, substrate, habitat, locality data, and where each specimen is housed. Most specimens are held by NYBG, but some are from ASU and UBC.
DOI: 10.5281/zenodo.18378437
title: SNAC-DB: Structural NANOBODY® (VHH) and Antibody (VH-VL) Complex Database

description: Welcome to the SNAC-DB — a comprehensive and curated resource of antibody and NANOBODY® VHH structures designed to support computational modeling, machine learning, structural biology research, and available in ML-ready formats. This release includes dataset curated by using the SNAC-DB pipeline (https://github.com/Sanofi-Public/SNAC-DB) on protein structures sourced from the RCSB PDB (https://www.rcsb.org/), as well as a benchmarking dataset for evaluation.

At the moment, we have processed all PDBs released up until 31 December, 2025. 

Paper: https://www.researchgate.net/publication/393900649_SNAC-DB_The_Hitchhiker's_Guide_to_Building_Better_Predictive_Models_of_Antibody_NANOBODY_R_VHH-Antigen_Complexes
DOI: 10.5061/dryad.110nt
title: Data from: Genetic variation in HIF signaling underlies quantitative variation in physiological and life history traits within lowland butterfly populations

description: Oxygen conductance to the tissues determines aerobic metabolic performance
 in most eukaryotes but has cost/benefit tradeoffs. Here we examine in
 lowland populations of a butterfly a genetic polymorphism affecting oxygen
 conductance via the hypoxia inducible factor (HIF) pathway, which senses
 intracellular oxygen and controls the development of oxygen delivery
 networks. Genetically distinct clades of Glanville fritillary (Melitaea
 cinxia) across a continental scale maintain, at intermediate frequencies,
 alleles in a metabolic enzyme (succinate dehydrogenase, SDH) that
 regulates hypoxia inducible factor (HIF-1α). One Sdhd allele was
 associated with reduced SDH activity rate, two-fold greater
 cross-sectional area of tracheoles in flight muscle, and better flight
 performance. Butterflies with less tracheal development had greater
 post-flight hypoxia signaling, swollen, disrupted mitochondria and
 accelerated aging of flight metabolic performance. Allelic associations
 with metabolic and aging phenotypes were replicated in samples from
 different clades. Experimentally elevated succinate in pupae increased the
 abundance of hypoxia inducible factor (HIF-1α) and expression of genes
 responsive to HIF activation, including tracheal morphogenesis genes.
 These results indicate that the hypoxia inducible pathway, even in lowland
 populations, can be an important axis for genetic variation underlying
 intraspecific differences in oxygen delivery, physiological performance
 and life history.
description: enzyme rate and SDHD
 transcript qPCRMitochondrial
 traitsSpain flight
 metabolismFrench males flight
 metabolism etcNrv2 and Phd expression
 in new adultsPhd_Noc_Nrv2_Hif1a in
 pupae