cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1nt11
title: Data from: Fold or hold: experimental evolution in vitro

description: We introduce a system for experimental evolution consisting of populations
 of short oligonucleotides (Oli populations) evolving in a modified
 quantitative polymerase chain reaction (qPCR). It is tractable at the
 genetic, genomic, phenotypic and fitness levels. The Oli system uses DNA
 hairpins designed to form structures that self-prime under defined
 conditions. Selection acts on the phenotype of self-priming, after which
 differences in fitness are amplified and quantified using qPCR. We outline
 the methodological and bioinformatics tools for the Oli system here and
 demonstrate that it can be used as a conventional experimental evolution
 model system by test-driving it in an experiment investigating adaptive
 evolution under different rates of environmental change.
description: Roche SFF sequence files
 for all 16 Oli populationsThese are the SFF files
 from Roche 454 titanium sequencing of the Oli populations. Populations
 were barcode indexed using the Roche MIDs, sequenced on the 454 titanium,
 base-called using the Roche pipeline version 2.53, then split into the 16
 separate populations using the MID index. These sff files have been
 bzip2'ed into one tar archive for easier upload and
 download.sff_files_from_all_16_oli_populations.tar.bz2Perl script to filter reads by start and end primer sequencesA Perl script to filter 454 reads by the start and end primer sequence. Input reads are in fasta format. Outputs several files for reads that match the primers, and reads that are too short or too long, or don't match.filter_by_primers_for_Sinead_Collins.plPerl script to count unique sequencesScript to count unique sequences from fast input file, reverse complementing if necessary so forward primer is at start of the sequence.count_unique_sequences_for_Sinead_Collins.plREADMEThis Readme file gives details about the initial submission of manuscript to arXiv.org, before it subsequently accepted by the Journal of Evolutionary Biology.
DOI: 10.5064/f6vanjl8/8oggsw
title: Silan-Ciruelas_PHL_Opt2_16B_Rozel_10-20_High_Median-High.pdf
DOI: 10.5064/f6vanjl8/4zk5wz
title: Silan-Ciruelas_Opt2_Therapist13.pdf
DOI: 10.5064/f6vanjl8/fy0crl
title: Silan-Ciruelas_BRA_Opt2_13A_10_20_Low_Low-Median.pdf
DOI: 10.5061/dryad.6bp0f
title: Data from: Building a responsive teacher: how temporal contingency of gaze interaction influences word learning with virtual tutors

description: Animated pedagogical agents are lifelike virtual characters designed to
 augment learning. A review of developmental psychology literature led to
 the hypothesis that the temporal contingency of such agents would promote
 human learning. We developed a Pedagogical Agent with Gaze Interaction
 (PAGI), an experimental animated pedagogical agent that engages in gaze
 interaction with students. In this study, university students learned
 words of a foreign language, with temporally contingent PAGI (live group)
 or recorded version of PAGI (recorded group), which played pre-recorded
 sequences from live sessions. The result revealed that students in the
 live group scored considerably better than those in the recorded group.
 The finding indicates that incorporating temporal contingency of gaze
 interaction from a pedagogical agent has positive effect on learning.
description: Raw gaze data as
 tab-separated values file.Raw gazed data taken
 during the experiment. Exported using Tobii studio (Tobii,
 Sweden).GazeData_Export.tsv
DOI: 10.5064/f6vanjl8/aw3jdq
title: Silan-Ciruelas_TUR_Opt2_21A_Anil_LGBTAnyLength_Low_Low-Median.pdf
DOI: 10.5064/f6vanjl8/yo4jba
title: Silan-Ciruelas_BRA_Opt2_10B_MariaPaula_5-10_High_Low-Median.pdf
DOI: 10.5061/dryad.vk048
title: Data from: Genomic prediction accuracies in space and time for height and wood density of Douglas-fir using exome capture as the genotyping platform

description: Background Genomic selection (GS) can offer unprecedented gains, in terms
 of cost efficiency and generation turnover, to forest tree selective
 breeding; especially for late expressing and low heritability traits.
 Here, we used: 1) exome capture as a genotyping platform for 1372
 Douglas-fir trees representing 37 full-sib families growing on three sites
 in British Columbia, Canada and 2) height growth and wood density (EBVs),
 and deregressed estimated breeding values (DEBVs) as phenotypes.
 Representing models with (EBVs) and without (DEBVs) pedigree structure.
 Ridge regression best linear unbiased predictor (RR-BLUP) and generalized
 ridge regression (GRR) were used to assess their predictive accuracies
 over space (within site, cross-sites, multi-site, and multi-site to single
 site) and time (age-age/ trait-trait). Results The RR-BLUP and GRR models
 produced similar predictive accuracies across the studied traits.
 Within-site GS prediction accuracies with models trained on EBVs were high
 (RR-BLUP: 0.79–0.91 and GRR: 0.80–0.91), and were generally similar to the
 multi-site (RR-BLUP: 0.83–0.91, GRR: 0.83–0.91) and multi-site to
 single-site predictive accuracies (RR-BLUP: 0.79–0.92, GRR: 0.79–0.92).
 Cross-site predictions were surprisingly high, with predictive accuracies
 within a similar range (RR-BLUP: 0.79–0.92, GRR: 0.78–0.91). Height at 12
 years was deemed the earliest acceptable age at which accurate predictions
 can be made concerning future height (age-age) and wood density
 (trait-trait). Using DEBVs reduced the accuracies of all cross-validation
 procedures dramatically, indicating that the models were tracking pedigree
 (family means), rather than marker-QTL LD. Conclusions While GS models’
 prediction accuracies were high, the main driving force was the pedigree
 tracking rather than LD. It is likely that many more markers are needed to
 increase the chance of capturing the LD between causal genes and markers.
description: Douglas-fir exomic SNP
 fileExomic genotype file for
 Douglas-fir produced by RAPiD Genomics© , containing 74199 biallelic SNPs
 with less than 40% missing data and minQ=10.FiltStep1_minQ10_Gen.txtDouglas-fir phenotypesPhenotypic measurements from Douglas-fir trial over 3 sites in British Columbia, Canada. Courtesy of Forests, Lands and Natural Resource Operations, BC, Canada.DF_phenotypes_dryad.txt
DOI: 10.5064/f6vanjl8/ctudpb
title: Silan-Ciruelas_USA_Opt2_1B_AnaliliaReglaGutierrez_1_Median_Low-Median.pdf
DOI: 10.5064/f6vanjl8/o4edhw
title: Silan-Ciruelas_PHL_Opt2_15B_Rozel_10-20_Low_Median-High.pdf
DOI: 10.5064/f6vanjl8/rtr9ty
title: Silan-Ciruelas_TUR_Opt2_2A_Sinem_1_High_Low-Median.pdf
DOI: 10.5064/f6vanjl8/rawytc
title: Silan-Ciruelas_FRA_Opt1_24B_LGBT_High_Median-High.pdf
DOI: 10.5061/dryad.83k00
title: Data from: Divergence history of the Carpathian and smooth newts modelled in space and time

description: Information about demographic history is essential for the understanding
 of the processes of divergence and speciation. Patterns of genetic
 variation within and between closely related species provide insights into
 the history of their interactions. Here, we investigated historical
 demography and genetic exchange between the Carpathian (Lissotriton
 montandoni, Lm) and smooth (L. vulgaris, Lv) newts. We combine an
 extensive geographical sampling and multilocus nuclear sequence data with
 the approximate Bayesian computation framework to test alternative
 scenarios of divergence and reconstruct the temporal and spatial pattern
 of gene flow between species. A model of recent (last glacial period)
 interspecific gene flow was favoured over alternative models. Thus,
 despite the relatively old divergence (4–6 mya) and presumably long
 periods of isolation, the species have retained the ability to exchange
 genes. Nevertheless, the low migration rates (ca. 10−6 per gene copy per
 generation) are consistent with strong reproductive isolation between the
 species. Models allowing demographic changes were favoured, suggesting
 that the effective population sizes of both species at least doubled as
 divergence reaching the current ca. 0.2 million in Lm and 1 million in Lv.
 We found asymmetry in rates of interspecific gene flow between Lm and one
 evolutionary lineage of Lv. We suggest that intraspecific polymorphism for
 hybrid incompatibilities segregating within Lv could explain this pattern
 and propose further tests to distinguish between alternative explanations.
 Our study highlights the importance of incorporating intraspecific genetic
 structure into the models investigating the history of divergence.
description: L.montandoni
 VCF'sVariant calling files
 (VCF) for L. montandoni individuals. Archive consists of 2886 VCF files -
 one for each individual (39) times each gene (74)L_montandoni_VCFs.zipL.vulgaris VCF'sVariant calling files (VCF) for L. vulgaris individuals. Archive consists of 3330 VCF files - one for each individual (45) times each gene (74)L_vulgaris_VCFs.zipPoly datasetAlignments of sequenced markers used to calculate polymorphism and differentiation, so called Poly dataset in the publication. Archive consists of 74 fasta files. Sequence names consist of marker name, individual name (correspond to Table S1) and allele.Poly_dataset.zipABC datasetFasta file containing alignment of sequences used to calculate observed summary statistics. So called ABC dataset in the publication.Exons_dataset.fastaCleaned fasta filesABC dataset was obtained from these files by subsampling random gene copy per population. Archive consists of 66 cleaned (no gaps, no alignment columns with missing data, no individuals with more than 10% missing data) fasta files.Fasta files.zip
DOI: 10.5064/f6vanjl8/wdxvvi
title: Silan-Ciruelas_Redaction Protocols.pdf
DOI: 10.5064/f6vanjl8/tcqsya
title: Silan-Ciruelas_TUR_Opt2_11A_Sinem_5-10_Low_Median-High.pdf
DOI: 10.5061/dryad.96p24
title: Data from: Paternal B vitamin intake is a determinant of growth, hepatic lipid metabolism and intestinal tumor volume in female Apc1638N mouse offspring

description: Background The importance of maternal nutrition to offspring health and
 risk of disease is well established. Emerging evidence suggests paternal
 diet may affect offspring health as well. Objective In the current study
 we sought to determine whether modulating pre-conception paternal B
 vitamin intake alters intestinal tumor formation in offspring.
 Additionally, we sought to identify potential mechanisms for the observed
 weight differential among offspring by profiling hepatic gene expression
 and lipid content. Methods Male Apc1638N mice (prone to intestinal tumor
 formation) were fed diets containing replete (control, CTRL), mildly
 deficient (DEF), or supplemental (SUPP) quantities of vitamins B2, B6,
 B12, and folate for 8 weeks before mating with control-fed wild type
 females. Wild type offspring were euthanized at weaning and hepatic gene
 expression profiled. Apc1638N offspring were fed a replete diet and
 euthanized at 28 weeks of age to assess tumor burden. Results No
 differences in intestinal tumor incidence or burden were found between
 male Apc1638N offspring of different paternal diet groups. Although in
 female Apc1638N offspring there were no differences in tumor incidence or
 multiplicity, a stepwise increase in tumor volume with increasing paternal
 B vitamin intake was observed. Interestingly, female offspring of SUPP and
 DEF fathers had a significantly lower body weight than those of CTRL fed
 fathers. Moreover, hepatic trigylcerides and cholesterol were elevated
 3-fold in adult female offspring of SUPP fathers. Weanling offspring of
 the same fathers displayed altered expression of several key
 lipid-metabolism genes. Hundreds of differentially methylated regions were
 identified in the paternal sperm in response to DEF and SUPP diets. Aside
 from a few genes including Igf2, there was a striking lack of overlap
 between these genes differentially methylated in sperm and differentially
 expressed in offspring. Conclusions In this animal model, modulation of
 paternal B vitamin intake prior to mating alters offspring weight gain,
 lipid metabolism and tumor growth in a sex-specific fashion. These results
 highlight the need to better define how paternal nutrition affects the
 health of offspring.
description: Fathers
 dataData file includes blood
 vitamin concentrations and body weight of fathers consuming different
 quantities of B vitaminsFathers Sperm MeDIP raw
 dataRaw data of methyl-DNA
 immunoprecipitation analysis of fathers sperm with Nimblegen arrays.
 Sample number in the top row.Offspring
 dataFile includes offspring
 data on body weight, hepatic endpoints (triglycerides, cytokines, folate),
 blood endpoints (leptin, insulin) and small intestinal
 tumorsOffspring gene
 expression FPKM valuesFile includes raw gene
 expression values as Fragments Per Kilobase of transcript per Million
 mapped reads (FPKM) from Cufflinks v2.2.1
DOI: 10.5064/f6vanjl8/p1nx5o
title: Silan-Ciruelas_Opt2_Therapist17.pdf
DOI: 10.5064/f6vanjl8/syndsr
title: Silan-Ciruelas_TUR_Opt1_12B_Sinem_5-10_High_Median-High.pdf
DOI: 10.5064/f6vanjl8/udzume
title: Silan-Ciruelas_FRA_Opt1_22B_Hector_LGBT_High_Low-Median.pdf
DOI: 10.5281/zenodo.18379983
title: "A Unified Cosmological Framework Reconciling DESI 2025 Observations with Fundamental Principles"
DOI: 10.5061/dryad.8fh42
title: Data from: Floral colour change in the eyes of pollinators: testing possible constraints and correlated evolution

description: 1. Many of the ‘adaptive' traits in angiosperm flowers occur only in
 some species within a clade. One good example of such traits is floral
 colour change, that is the retention of old, nonreproductive, rewardless,
 but fully turgid flowers in an altered colour. This trait has been viewed
 as a plant strategy to enhance distant pollinator attraction while
 minimizing visits to nonreproductive flowers. Considering that the same
 scenario appears true for most visually oriented flower visitors, however,
 it is unclear why this trait does not prevail in nature. 2. To understand
 such evolutionary patterns, we conducted a screening search for floral
 colour change in 219 angiosperm species. We quantified spectral
 alterations in petals or petaloid organs and translated them into colour
 shifts through insect eyes. Using phylogeny-based comparative methods, we
 further explored possibilities accounting for the infrequent occurrences
 of floral colour change: tendency of related species to resemble each
 other more than those randomly drawn from the phylogenetic tree (i.e.
 phylogenetic signal), constraints imposed through pigment coloration and
 their functions and evolutionary correlates of floral colour change. 3.
 Ultraviolet-sensitive insect eyes were estimated to perceive floral colour
 change more often than previously noticed. We detected significant
 phylogenetic signal in the degree of floral colour change. The evolution
 of floral colour change appeared constrained by pigment chemistry, because
 greater changes were more likely to occur in yellow or red floral parts.
 Postchange colours tended to retain distant visual detectability (i.e.
 green-receptor contrast), while reducing attractiveness in a close range
 (i.e. colour contrast), indicating another constraint imposed through the
 functions of pigment coloration. Data also suggest a possible evolutionary
 association between floral colour change and bee pollination. 4. Results
 indicate that floral colour change is scarce in nature because it
 primarily evolved to accommodate bees or comparable pollinators and
 because its occurrence was constrained by phylogenetic relatedness,
 pigment chemistry and ecological functions. An understanding of floral
 evolution thus requires considering different causalities for trait
 diversity in an integrative manner.
description: Floral spectral
 reflectance measured at different stages of flowering for 219 angiosperm
 species in JapanOhashi_etal.zip
DOI: 10.5064/f6vanjl8/hgxvas
title: Silan-Ciruelas_TUR_Opt2_5B_EdaDamla_1-5_Low_Low-Median.pdf
DOI: 10.5064/f6vanjl8/9rznn8
title: Silan-Ciruelas_USA_Opt2_8A_Silky_1-5_High_Median-High.pdf
DOI: 10.5064/f6vanjl8/4aesm2
title: Silan-Ciruelas_USA_Opt2_25B_Marina_Non-Monogamous_Any_Median-High.pdf
DOI: 10.5064/f6vanjl8/mff5t6
title: Silan-Ciruelas_BRA_Opt2_21B_Camilla_LGBT_Low_Low-Median.pdf
DOI: 10.5061/dryad.c5g9s
title: Data from: Small beetle, large-scale drivers: how regional and landscape factors affect outbreaks of the European spruce bark beetle

description: Unprecedented bark beetle outbreaks have been observed for a variety of
 forest ecosystems recently, and damage is expected to further intensify as
 a consequence of climate change. In Central Europe, the response of
 ecosystem management to increasing infestation risk has hitherto focused
 largely on the stand level, while the contingency of outbreak dynamics on
 large-scale drivers remains poorly understood. To investigate how factors
 beyond the local scale contribute to the infestation risk from Ips
 typographus (Col., Scol.), we analysed drivers across seven orders of
 magnitude in scale (from 103 to 1010 m²) over a 23-year period, focusing
 on the Bavarian Forest National Park. Time-discrete hazard modelling was
 used to account for local factors and temporal dependencies. Subsequently,
 beta regression was applied to determine the influence of regional and
 landscape factors, the latter characterized by means of graph theory. We
 found that in addition to stand variables, large-scale drivers also
 strongly influenced bark beetle infestation risk. Outbreak waves were
 closely related to landscape-scale connectedness of both host and beetle
 populations as well as to regional bark beetle infestation levels.
 Furthermore, regional summer drought was identified as an important
 trigger for infestation pulses. Large-scale synchrony and connectivity are
 thus key drivers of the recently observed bark beetle outbreak in the
 area. Synthesis and applications. Our multiscale analysis provides
 evidence that the risk for biotic disturbances is highly dependent on
 drivers beyond the control of traditional stand-scale management. This
 finding highlights the importance of fostering the ability to cope with
 and recover from disturbance. It furthermore suggests that a stronger
 consideration of landscape and regional processes is needed to address
 changing disturbance regimes in ecosystem management.
description: Multiscale bark beetle
 disturbance datadata.txt
DOI: 10.5064/f6vanjl8/sqnqar
title: Silan-Ciruelas_Opt2_Therapist12.pdf
DOI: 10.5064/f6vanjl8/vkbhrd
title: Silan-Ciruelas_USA_Opt1_16B_Jon_10-20_High_Median-High.pdf
DOI: 10.5061/dryad.2h0g7
title: Data from: Characterization of leukemia-inducing genes using a proto-oncogene/homeobox gene retroviral human cDNA library in a mouse in vivo model

description: The purpose of this research is to develop a method to screen a large
 number of potential driver mutations of acute myeloid leukemia (AML) using
 a retroviral cDNA library and murine bone marrow
 transduction-transplantation system. As a proof-of-concept, murine bone
 marrow (BM) cells were transduced with a retroviral cDNA library encoding
 well-characterized oncogenes and homeobox genes, and the virus-transduced
 cells were transplanted into lethally irradiated mice. The proto-oncogenes
 responsible for leukemia initiation were identified by PCR amplification
 of cDNA inserts from genomic DNA isolated from leukemic cells. In an
 initial screen of ten leukemic mice, the MYC proto-oncogene was detected
 in all the leukemic mice. Of ten leukemic mice, 3 (30%) had MYC as the
 only transgene, and seven mice (70%) had additional proto-oncogene
 inserts. We repeated the same experiment after removing MYC-related genes
 from the library to characterize additional leukemia-inducing gene
 combinations. Our second screen using the MYC-deleted proto-oncogene
 library confirmed MEIS1and the HOX family as cooperating oncogenes in
 leukemia pathogenesis. The model system we introduced in this study will
 be valuable in functionally screening novel combinations of genes for
 leukemogenic potential in vivo, and the system will help in the discovery
 of new targets for leukemia therapy.
description: A_1 plasmid retroviral
 cDNA library QCA raw data file of NGS
 anaysis of cDNA frequency of the PCR amplification products of retroviral
 cDNA library of plasmid mixture.A_1.fastqD_1 QC of retroviral vector library with bone marrow genomic DNATo verify the effective ness of the retroviral cDNA library, bone marrow cells from the C57BL6 mouse were transduced withe library, and the cDNAs were amplified from the genomic DNA. The amplified PCR product was subjected to NGS analysis to evaluate equal contribution from different members of the library.D_1.fastq
DOI: 10.5064/f6vanjl8/hhtedi
title: Silan-Ciruelas_InterviewGuide-SamplingScheme.pdf
DOI: 10.5064/f6vanjl8/bae0sm
title: Silan-Ciruelas_USA_Opt2_2A_Silky_1_High_Low-Median.pdf
DOI: 10.5064/f6vanjl8/70srb9
title: Silan-Ciruelas_BRA_Opt2_10A_MariaPaula_5-10_High_Low-Median.pdf
DOI: 10.5064/f6vanjl8/re1coj
title: Silan-Ciruelas_PHL_Opt2-24A-Nica_LGBTAnyLength_High_Median-High.pdf
DOI: 10.5064/f6vanjl8/zhc1yf
title: Silan-Ciruelas_Opt2_Therapist4.pdf
DOI: 10.5061/dryad.f37km
title: Data from: No effect of ambient odor on the affective appraisal of a desktop virtual environment with signs of disorder

description: Background: Desktop virtual environments (VEs) are increasingly deployed
 to study the effects of environmental qualities and interventions on human
 behavior and safety related concerns in built environments. For these
 applications it is essential that users appraise the affective qualities
 of the VE similar to those of its real world counterpart. Previous studies
 have shown that factors like simulated lighting, sound and dynamic
 elements all contribute to the affective appraisal of a desktop VE. Since
 ambient odor is known to affect the affective appraisal of real
 environments, and has been shown to increase the sense of presence in
 immersive VEs, it may also be an effective tool to tune the affective
 appraisal of desktop VEs. This study investigated if exposure to ambient
 odor can modulate the affective appraisal of a desktop VE with signs of
 public disorder. Method: Participants explored a desktop VE representing a
 suburban neighborhood with signs of public disorder (neglect, vandalism
 and crime), while being exposed to either room air or subliminal levels of
 unpleasant (tar) or pleasant (cut grass) ambient odor. Whenever they
 encountered signs of disorder they reported their safety related concerns
 and associated affective feelings. Results: Signs of crime in the desktop
 VE were associated with negative affective feelings and concerns for
 personal safety and personal property. However, there was no significant
 difference between reported safety related concerns and affective
 connotations in the control (no-odor) and in each of the two ambient odor
 conditions. Conclusion: Ambient odor did not affect safety related
 concerns and affective connotations associated with signs of disorder in
 the desktop VE. Thus, semantic congruency between ambient odor and a
 desktop VE may not be sufficient to influence its affective appraisal, and
 a more realistic simulation in which simulated objects appear to emit
 scents may be required to achieve this goal.
description: QuestionnairesFiletype: Microsoft Word 2010 Contents: Questionnaires (in Dutch)Walkthrough_virtual_environmentA WMV movie file showing a walkthrough of the virtual environment used in this study.ReadMeReadMe file describing the contents of this dataset.Results_Main_ExperimentOriginal (anonymized) score sheets, labeled with the numbers of the subject.
DOI: 10.5064/f6vanjl8/vtlgl2
title: Silan-Ciruelas_FRA_Opt1_3B_1_Low-Median-High.pdf
DOI: 10.5064/f6vanjl8/ortvkc
title: Silan-Ciruelas_USA_Opt2_22A_Marina_LGBTQ+AnyLength_High_Low-Median.pdf