cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9g0k0t0
title: Data from: Cover crops in arable lands increase functional complementarity and redundancy of bacterial communities

description: 1. Reducing the deleterious effects of intensive tillage and fertilisation
 on ecosystem integrity and human health is challenging for sustainable
 agriculture. The use of cover crops has been advocated as a suitable
 technique for this purpose, but scientific evidence to support this has
 been scarce. 2. After four years and a complete rotation; including wheat,
 maize and green pea as main crops in a ploughing system, we investigated
 the respective and combined effects of cover crops and nitrogen
 fertilisation on soil chemical and biological properties using a
 controlled experiment combining soil chemical analyses, high-throughput
 sequencing and community level physiological profiles. 3. Cover crops
 impeded the soil carbon and nitrogen depletion induced by intensive
 tillage, not only in the topsoil but also within deeper soil horizons,
 where more specialized bacterial communities established. 4. Cover crops
 induced a significant shift in soil bacterial community diversity and
 composition, which was associated with changes in soil chemical features
 and bacterial metabolic activities along the entire soil profile. 5. Cover
 crops enhanced soil resilience to nitrogen fertilisation by increasing
 functional redundancy and complementarity within soil bacterial
 communities and across soil horizons. 6. Synthesis and applications. In
 the ploughing systems commonly used for intensive agriculture in Western
 Europe, the use of cover crops fosters a high functional diversity among
 soil bacteria and thus can help to achieve a more sustainable agriculture
 by reducing nitrogen fertilization while maintaining yields.
description: Fastq
 filesFastq files performed on
 the 16S rRNAV3-V4 regions.Alahmad et al. Journal of
 Applied Ecology.tar
DOI: 10.5061/dryad.nr2h5
title: Data from: Molecular analysis of carnivore Protoparvovirus detected in white blood cells of naturally infected cats

description: Background: Cats are susceptible to feline panleukopenia virus (FPV) and
 canine parvovirus (CPV) variants 2a, 2b and 2c. Detection of FPV and CPV
 variants in apparently healthy cats and their persistence in white blood
 cells (WBC) and other tissues when neutralising antibodies are
 simultaneously present, suggest that parvovirus may persist long-term in
 the tissues of cats post-infection without causing clinical signs. The aim
 of this study was to screen a population of 54 cats from Sardinia (Italy)
 for the presence of both FPV and CPV DNA within buffy coat samples using
 polymerase chain reaction (PCR). The DNA viral load, genetic diversity,
 phylogeny and antibody titres against parvoviruses were investigated in
 the positive cats. Results: Carnivore protoparvovirus 1 DNA was detected
 in nine cats (16.7%). Viral DNA was reassembled to FPV in four cats and to
 CPV (CPV-2b and 2c) in four cats; one subject showed an unusually high
 genetic complexity with mixed infection involving FPV and CPV-2c.
 Antibodies against parvovirus were detected in all subjects which tested
 positive to DNA parvoviruses. Conclusions: The identification of FPV and
 CPV DNA in the WBC of asymptomatic cats, despite the presence of specific
 antibodies against parvoviruses, and the high genetic heterogeneity
 detected in one sample, confirmed the relevant epidemiological role of
 cats in parvovirus infection.
description: ML
 TreeUnrooted phylogenetic
 tree. The phylogenetic tree was constructed with the nucleotide sequences
 of the partial VP2 gene. Bootstrap values, calculated on 1000 replicates,
 are indicated on the respective branches.S22165
DOI: 10.5061/dryad.m2fr6
title: Data from: The diverse dietary profiles of MIS 3 cave bears from the Romanian Carpathians: insights from stable isotope (δ13C and δ15N) analysis

description: Late Pleistocene European cave bears (Ursus spelaeus) have been considered
 to be largely vegetarian, although stable isotope data (δ13C and δ15N
 values) from the Romanian Carpathians has suggested considerable dietary
 variation. Here we evaluate previous and additional adult cave bear
 isotopic data from four Marine Isotope Stage 3 (MIS 3) sites in the
 Carpathians. Peştera Urşilor (N = 35), Peştera Cioclovina (N = 32),
 Peştera Muierilor (N = 8), and Peştera cu Oase (N = 72) provide both a
 dichotomy between samples suggesting vegetarian diets (from Cioclovina and
 Muierilor) and more omnivorous diets (from Urşilor and Oase), and
 considerable isotopic variation within samples from each site. While an
 inference of a strictly vegetarian diet may apply to groups that lived in
 ecosystems which restricted the available animal protein for these large
 ursids, the within and between sample isotopic variation among the
 Carpathian cave bears indicates considerable flexibility in their sources
 of protein and hence in their dietary regimes. In addition, developmental
 assessment of Cioclovina isotopic profiles (neonates, juveniles,
 sub-adults and adults) provides patterns of transfer of stable isotope
 signatures throughout immature life for both δ13C and δ15N (increase and
 decrease, respectively), whereas those from Urşilor show little
 developmental shift.
description: RO Cave Bear Isotopes
 SITable S1.
 Romanian/Carpathian MIS 3 cave bear and large-bodied mammals carbon (δ13C)
 and nitrogen (δ15N) stable isotope samples and results. Table S2. Sites
 providing comparative European data, all central and western European
 except Sunghir. The number for each species indicates the sample size for
 that species providing stable isotopic data from the site employed in the
 comparisons
DOI: 10.5061/dryad.79q870b
title: Data from: Evolutionary and food supply implications of ongoing maize domestication by Mexican campesinos

description: Maize evolution under domestication is a process that continues today.
 Case studies suggest that Mexican smallholder family farmers, known as
 campesinos, contribute importantly to this, but their significance has not
 been explicitly quantified and analyzed as a whole. Here we examine the
 evolutionary and food security implications of the scale and scope under
 which campesinos produce maize. We gathered official municipal-level data
 on maize production under rainfed conditions and identified campesino
 agriculture as occurring in municipalities with average yields of ≤ 3
 t/ha. Environmental conditions vary widely in those municipalities and are
 associated with a great diversity of maize races, representing 85.3% of
 native maize samples collected in the country. We estimate that in those
 municipalities around 1.38 x 1011 genetically different individual plants
 are subjected to evolution under domestication each season. This implies
 that 5.24x108 mother plants contribute to the next generation with their
 standing genetic diversity and rare alleles. Such a large breeding
 population size also increases the total number of adaptive mutations that
 may appear and be selected for. We also estimate that campesino
 agriculture could potentially feed around 54.7 million people in Mexico.
 These analyses provide insights about the contributions of smallholder
 agriculture around the world.
description: SpatialDataContains Data, scripts and shapefiles needed for the analyses of the section "Environmental conditions of areas planted with maize" of the paper, which produced Figures 2, 3, S2 and S3 and Tables S5, S6 and S7. See README inside for details.contributionMaizeGenDivR script to perform the estimates of the *Campesinos´ contribution to maize genetic diversity* section of the manuscript presented in Table S8.CampesinoMaizeProductionContains data, Excel files and R scripts used to produce the results from the sections "Identifying campesino maize production at the national level" and "Assessing the potential contribution of rainfed production to maize demand". Results of this section produced Table S1, S3 and S4 and Figures 1, 4, S1 and S4 of the paper. See README inside for details.
DOI: 10.5061/dryad.v28f9
title: Data from: The de novo genome assembly and annotation of a female domestic dromedary of North African origin

description: The single-humped dromedary (Camelus dromedarius) is the most numerous and
 widespread of domestic camel species and is a significant source of meat,
 milk, wool, transportation and sport for millions of people. Dromedaries
 are particularly well adapted to hot, desert conditions and harbour a
 variety of biological and physiological characteristics with evolutionary,
 economic and medical importance. To understand the genetic basis of these
 traits, an extensive resource of genomic variation is required. In this
 study, we assembled at 65× coverage, a 2.06 Gb draft genome of a female
 dromedary whose ancestry can be traced to an isolated population from the
 Canary Islands. We annotated 21 167 protein-coding genes and estimated
 ~33.7% of the genome to be repetitive. A comparison with the recently
 published draft genome of an Arabian dromedary resulted in 1.91 Gb of
 aligned sequence with a divergence of 0.095%. An evaluation of our genome
 with the reference revealed that our assembly contains more error-free
 bases (91.2%) and fewer scaffolding errors. We identified ~1.4 million
 single-nucleotide polymorphisms with a mean density of 0.71 × 10−3 per
 base. An analysis of demographic history indicated that changes in
 effective population size corresponded with recent glacial epochs. Our de
 novo assembly provides a useful resource of genomic variation for future
 studies of the camel's adaptations to arid environments and
 economically important traits. Furthermore, these results suggest that
 draft genome assemblies constructed with only two differently sized
 sequencing libraries can be comparable to those sequenced using additional
 library sizes, highlighting that additional resources might be better
 placed in technologies alternative to short-read sequencing to physically
 anchor scaffolds to genome maps.
description: Archive of all
 annotation and alignment dataThis file is an archive
 of all data not publicly archived. Please see the README.txt file for a
 detailed description of all contents. The archive can be uncompressed by
 either double-clicking on the file in most operating systems or using the
 command: "tar -zxvf file.tar.gz" in a UNIX
 terminal.Drom800.tar.gz
DOI: 10.5281/zenodo.18344512
title: Tumor Subtype-Specific Transcriptional Signatures Predict Recurrence Risk in Hepatocellular Carcinoma

description: Hepatocellular carcinoma exhibits substantial molecular heterogeneity that current clinical staging inadequately captures for predicting post-treatment recurrence. To address this limitation, we developed a survival modeling framework using cell-type-specific transcriptional signatures from RNA sequencing to stratify recurrence risk in HCC patients.

Analysis of 1,059 samples across four cohorts demonstrated that tumor immunogenic and proliferative scores satisfied proportional hazards assumptions, enabling construction of a stable multivariable Cox model. The linear predictor showed strong correlation with one-year survival probability, with recurrent patients exhibiting significantly higher risk scores compared to non-recurrent cases. Risk stratification into tertile groups achieved significant survival separation in both training and test datasets.

AUC performance analysis revealed optimal discrimination for early recurrence prediction, with maintained but declining accuracy at later timepoints. This biologically-informed risk stratification tool demonstrates robust performance across institutions and may facilitate personalized surveillance strategies for HCC patients following curative treatment.
DOI: 10.5281/zenodo.18344513
title: Tumor Subtype-Specific Transcriptional Signatures Predict Recurrence Risk in Hepatocellular Carcinoma

description: Hepatocellular carcinoma exhibits substantial molecular heterogeneity that current clinical staging inadequately captures for predicting post-treatment recurrence. To address this limitation, we developed a survival modeling framework using cell-type-specific transcriptional signatures from RNA sequencing to stratify recurrence risk in HCC patients.

Analysis of 1,059 samples across four cohorts demonstrated that tumor immunogenic and proliferative scores satisfied proportional hazards assumptions, enabling construction of a stable multivariable Cox model. The linear predictor showed strong correlation with one-year survival probability, with recurrent patients exhibiting significantly higher risk scores compared to non-recurrent cases. Risk stratification into tertile groups achieved significant survival separation in both training and test datasets.

AUC performance analysis revealed optimal discrimination for early recurrence prediction, with maintained but declining accuracy at later timepoints. This biologically-informed risk stratification tool demonstrates robust performance across institutions and may facilitate personalized surveillance strategies for HCC patients following curative treatment.
DOI: 10.5061/dryad.8rd4v
title: Data from: Visual effects in great bowerbird sexual displays and their implications for signal design

description: It is often assumed that the primary purpose of a male's sexual
 display is to provide information about quality, or to strongly stimulate
 prospective mates, but other functions of courtship displays have been
 relatively neglected. Male great bowerbirds (Ptilonorhynchus nuchalis)
 construct bowers that exploit the female's predictable field of view
 (FOV) during courtship displays by creating forced perspective illusions,
 and the quality of illusion is a good predictor of mating success. Here,
 we present and discuss two additional components of male courtship
 displays that use the female's predetermined viewpoint: (i) the rapid
 and diverse flashing of coloured objects within her FOV and (ii) chromatic
 adaptation of the female's eyes that alters her perception of the
 colour of the displayed objects. Neither is directly related to mating
 success, but both are likely to increase signal efficacy, and may also be
 associated with attracting and holding the female's attention. Signal
 efficacy is constrained by trade-offs between the signal components; there
 are both positive and negative interactions within multicomponent signals.
 Important signal components may have a threshold effect on fitness rather
 than the often assumed linear relationship.
description: Data From
 EndlerGaburroKelleyData and some MATLAB
 files which are the basis of this publication.DataFromEndlerGaburroKelley.zip
DOI: 10.5061/dryad.5h9s7
title: Data from: Host resistance and pathogen aggressiveness are key determinants of coinfection in the wild

description: Coinfection, whereby the same host is infected by more than one pathogen
 strain, may favor faster host exploitation rates as strains compete for
 the same limited resources. Hence, coinfection is expected to have major
 consequences for pathogen evolution, virulence and epidemiology. Theory
 predicts genetic variation in host resistance and pathogen infectivity to
 play a key role in how coinfections are formed. The limited number of
 studies available have demonstrated coinfection to be a common phenomenon,
 but little is known about how coinfection varies in space, and what its
 determinants are. Our aim is to understand how variation in host
 resistance and pathogen infectivity and aggressiveness contribute to how
 coinfections are formed in the interaction between fungal pathogen
 Podosphaera plantaginis and Plantago lanceolata. Our phenotyping study
 reveals that more aggressive strains are more likely to form coinfections
 than less aggressive strains in the natural populations. In the natural
 populations most of the variation in coinfection is found at the
 individual plant level, and results from a common garden study confirm the
 prevalence of coinfection to vary significantly among host genotypes.
 These results show that genetic variation in both the host and pathogen
 populations are key determinants of coinfection in the wild.
description: Determinants of
 coinfectionThe data contains
 prevalence of Posophaera plantaginis coinfections in Populations in Åland
 Islands and in common garden populations and results of an inoculation
 experiment.DRYAD_determinants of
 coinfection.xlsx
DOI: 10.5281/zenodo.17196590
title: [ICLR 2026 submission] SpoilDICE Experiment Dataset (2/2)

description: This content is shared anonymously for reviews and will include author and publication details if accepted.

The dataset is organized into the following directory structure for SafetyHumanoidVelocity-v1:



The 'replay' directory contains replay data designed to replicate a realistic data collection environment.It consists of three subsets: safe, performance, and shuffled. A detailed description of each dataset is provided in the Appendix of the paper.

The 'controlled' directory includes datasets collected using four distinct types of policies: safe-high, safe-medium, unsafe-high, and unsafe-medium. These datasets capture different safety and performance trade-offs. For further explanations of each dataset, please refer to the Appendix of the paper.

The 'stats' directory contains statistical information files summarizing all datasets within both the 'replay' and 'controlled' directories. These files report key statistics such as the mean return, mean cost, mean feasible return, and the number of trajectories, offering essential insights into the properties of each dataset.
DOI: 10.5281/zenodo.17196589
title: [ICLR 2026 submission] SpoilDICE Experiment Dataset (2/2)

description: This content is shared anonymously for reviews and will include author and publication details if accepted.

The dataset is organized into the following directory structure for SafetyHumanoidVelocity-v1:



The 'replay' directory contains replay data designed to replicate a realistic data collection environment.It consists of three subsets: safe, performance, and shuffled. A detailed description of each dataset is provided in the Appendix of the paper.

The 'controlled' directory includes datasets collected using four distinct types of policies: safe-high, safe-medium, unsafe-high, and unsafe-medium. These datasets capture different safety and performance trade-offs. For further explanations of each dataset, please refer to the Appendix of the paper.

The 'stats' directory contains statistical information files summarizing all datasets within both the 'replay' and 'controlled' directories. These files report key statistics such as the mean return, mean cost, mean feasible return, and the number of trajectories, offering essential insights into the properties of each dataset.
DOI: 10.5061/dryad.1s7v5
title: Data from: Evaluation of redundancy analysis to identify signatures of local adaptation

description: Ordination is a common tool in ecology that aims at representing complex
 biological information in a reduced space. In landscape genetics,
 ordination methods such as principal component analysis (PCA) have been
 used to detect adaptive variation based on genomic data. Taking advantage
 of environmental data in addition to genotype data, redundancy analysis
 (RDA) is another ordination approach that is useful to detect adaptive
 variation. This paper aims at proposing a test statistic based on RDA to
 search for loci under selection. We compare redundancy analysis to
 pcadapt, which is a nonconstrained ordination method, and to a latent
 factor mixed model (LFMM), which is a univariate genotype-environment
 association method. Individual-based simulations identify evolutionary
 scenarios where RDA genome scans have a greater statistical power than
 genome scans based on PCA. By constraining the analysis with environmental
 variables, RDA performs better than PCA in identifying adaptive variation
 when selection gradients are weakly correlated with population structure.
 Additionally, we show that if RDA and LFMM have a similar power to
 identify genetic markers associated with environmental variables, the
 RDA-based procedure has the advantage to identify the main selective
 gradients as a combination of environmental variables. To give a concrete
 illustration of RDA in population genomics, we apply this method to the
 detection of outliers and selective gradients on an SNP data set of
 Populus trichocarpa (Geraldes et al., 2013). The RDA-based approach
 identifies the main selective gradient contrasting southern and coastal
 populations to northern and continental populations in the northwestern
 American coast.
description: SimulationsThe 100 simulations used to test the RDA-based genome scan method and compare it to pcadapt method.
DOI: 10.5281/zenodo.17257883
title: Lung-associated_vOTU
DOI: 10.5281/zenodo.18359452
title: Lung-associated_vOTU
DOI: 10.5061/dryad.df2463b
title: Data from: The evolution of chemical defenses along invasion routes: Harmonia axyridis Pallas (Coccinellidae: Coleoptera) as a case study

description: The Evolution of Increased Competitive Ability (EICA) hypothesis (Blossey
 & Nötzold, 1995) postulates that escaping from coevolved enemies
 increases invaders fitness by energy reallocation from defenses and
 immunity to growth and reproduction. In this context, we evaluated the
 evidence of evolutionary change in invasive populations of Harmonia
 axyridis Pallas (Coccinellidae: Coleoptera). We measured egg defenses –
 cocktail of hydrocarbons on the egg’s surface flagging egg toxicity, and
 the concentration of the main alkaloid harmonine - in individuals from
 three populations along the invasion route (Japan: native, USA: introduced
 more than 30 years ago, South Africa: introduced in the early 2000s) in a
 common garden experiment. Our results support the EICA hypothesis: we
 found changes along the invasion route in the profiles of the hydrocarbons
 coating the eggs’ surface, and a decrease in the concentration of
 harmonine in eggs from the most recent invasive South African population
 compared to the long established in the USA and the native Japanese ones.
description: Table Harmonine &
 Egg mass 3 Pops HarmoniaHarmonine content in
 eggs (µg/mg egg) and egg masses for the 3 populations of Harmonia
 axyridisTable Hydrocarbons 3
 Pops HarmoniaQuantity of hydrocarbons
 present on the coating of eggs (μg per egg) from the 3 populations of
 Harmonia axyridis (three trials per population)Table HCs 3 Pops
 Harmonia.xls