cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.55p667b
title: Data from: Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects

description: Background: Transposable elements (TEs) are a major component of metazoan
 genomes and are associated with a variety of mechanisms that shape genome
 architecture and evolution. Despite the ever-growing number of insect
 genomes sequenced to date, our understanding of the diversity and
 evolution of insect TEs remains poor. Results: Here, we present a
 standardized characterization and an order-level comparison of arthropod
 TE repertoires, encompassing 62 insect and 11 outgroup species. The insect
 TE repertoire contains TEs of almost every class previously described, and
 in some cases even TEs previously reported only from vertebrates and
 plants. Additionally, we identified a large fraction of unclassifiable
 TEs. We found high variation in TE content, ranging from less than 6 % in
 the antarctic midge (Diptera), the honey bee and the turnip sawfly
 (Hymenoptera) to more than 58 % in the malaria mosquito (Diptera) and the
 migratory locust (Orthoptera), and a possible relationship between the
 content and diversity of TEs and the genome size. Conclusion: While most
 insect orders exhibit a characteristic TE composition, we also observed
 intraordinal differences, e.g., in Diptera, Hymenoptera, and Hemiptera.
 Our findings shed light on common patterns and reveal lineage-specific
 differences in content and evolution of TEs in insects. We anticipate our
 study to provide the basis for future comparative research on the insect
 TE repertoire.
description: Petersen_Insect_Mobilome_Repeat_Libraries.tarRepeat libraries including filter patterns and list of elements to be excluded.
DOI: 10.5061/dryad.n14p52b
title: Data from: Antibody responses to Plasmodium vivax Duffy binding and erythrocyte binding proteins predict risk of infection and are associated with protection from clinical malaria

description: Background. The Plasmodium vivax Duffy Binding Protein (PvDBP) is a key
 target of naturally acquired immunity. However, the functional
 receptor-binding region II of PvDBP (PvDBPII) is highly polymorphic. The
 natural acquisition of antibodies to different variants of PvDBPII,
 including AH, O, P and Sal1 alleles, the central region III-V, and P.
 vivax Erythrocyte Binding Protein region II (PvEBPII) and their
 associations with risk of clinical P. vivax malaria are not well
 understood. Methodology. Total IgG and IgG subclasses 1, 2, and 3 that
 recognize four alleles of PvDBPII (AH, O, P, and Sal1), PvDBPIII-V and
 region II of PvEBP (PvEBPII) were measured in samples collected from a
 cohort of Papua New Guinean (PNG) children of aged 1-3 years living in a
 highly endemic area of PNG. The levels of binding inhibitory antibodies
 (BIAbs) to PvDBPII (AH, O, and Sal1) were also tested in a subset of
 children. The association of presence of IgG with age, cumulative exposure
 (measured as the product of age and malaria infections during follow-up,
 i.e. molFOB) and prospective risk of clinical malaria were evaluated.
 Results. Increase in antigen-specific total IgG, IgG1, and IgG3 with age
 and cumulative exposure was only observed for PvDBPII AH and PvEBPII. High
 total IgG responders and IgG3 specific responses to the predominant
 PvDBPII AH allele, were associated with decreased incidence of clinical P.
 vivax episodes (aIRR=0.56-0.68, P=&lt;0.001-0.021 ). High total IgG
 and IgG1 to PvEBPII correlated more strongly with protection against
 clinical vivax malaria compared with those of all PvDBPII variants
 (aIRR=0.38, P&lt;0.001). Antibodies to PvDBPII AH and PvEBPII showed
 evidence of an additive effect, with a joint protective association of
 70%. The six children with high levels of Binding Inhibitory Antibodies
 (BIAbs) to PvDBPII and high strain-transcending blocking ability (i.e.
 &gt;80%) tended to have less clinical diseases (IRR=0.45, P=0.083).
 Conclusion. Antibodies to the key parasite invasion ligands PvDBPII and
 PvEBPII are good correlates of protection against P. vivax malaria in PNG.
 This further strengthens the rationale for inclusion of PvDBPII in a
 recombinant subunit vaccine for P. vivax malaria and highlights the need
 for further functional studies to determine the potential of PvEBPII as a
 component of a subunit vaccine for P. vivax malaria.
description: PNG young children
 cohort study datasetThe explanation of the
 variables are included in the README.DBP_data_fid.xlsx
DOI: 10.5061/dryad.482h6h2
title: Data from: Nutrition in extreme food specialists: an illustration using termites

description: 1. Recent nutritional ecology theories predict that an organism feeding on
 a single, highly predictable food should lack the typical active
 regulation of nutrient balance observed in all other organisms studied so
 far. It could instead limit itself to controlling the amount of food eaten
 alone. Such an animal would however be strongly affected by nutrient
 imbalances. 2. Termites are an ideal model animal to test those
 predictions. 3. We investigated how the nutritional content of food
 affected termites’ intake and performance by constraining groups of
 Nasutitermes exitiosus to artificial diets varying in their macronutrient
 ratios. 4. We showed that (1) termites, contrary to other insects, did not
 compensate for nutrient imbalance by adjusting food collection (2)
 longevity in workers was strongly influenced by carbohydrate intake, while
 in soldiers it depended almost entirely on the number of workers remaining
 to feed them (3) tunnelling activity increased with the quantity of food
 collected and (4) intake had very little influence on lipid and protein
 termite body contents. 5. We provide evidence that extreme food
 specialists might have lost the ability to regulate macronutrient intake.
description: BodyContentSoldiersBody content in protein and lipid of soldier that died during the experiment.BodyContentWorkersBody content in protein and lipid of workers that died during the experiment.FoodCollectionFood collection of each nest measured every 3 days.LifespanLifespan of workers and soldiers for each nest (until all the individuals in the artificial diet treatment are dead)TunnellingTunnelling activity for each nest, measured every 6 days.
DOI: 10.5061/dryad.r3f10b5
title: Data from: Environmental extremes drive population structure at the northern range limit of Atlantic salmon in North America

description: Conservation of exploited species requires an understanding of both
 genetic diversity and the dominant structuring forces, particularly near
 range limits, where climatic variation can drive rapid expansions or
 contractions of geographic range. Here, we examine population structure
 and landscape associations in Atlantic salmon (Salmo salar) across a
 heterogeneous landscape near the northern range limit in Labrador, Canada.
 Analysis of two amplicon-based data sets containing 101 microsatellites
 and 376 single nucleotide polymorphisms (SNPs) from 35 locations revealed
 clear differentiation between populations spawning in rivers flowing into
 a large marine embayment (Lake Melville) compared to coastal populations.
 The mechanisms influencing the differentiation of embayment populations
 were investigated using both multivariate and machine-learning landscape
 genetic approaches. We identified temperature as the strongest correlate
 with genetic structure, particularly warm temperature extremes and wider
 annual temperature ranges. The genomic basis of this divergence was
 further explored using a subset of locations (n=17) and a 220K SNP array.
 SNPs associated with spatial structuring and temperature mapped to a
 diverse set of genes and molecular pathways, including regulation of gene
 expression, immune response, and cell development and differentiation. The
 results spanning molecular marker types and both novel and established
 methods clearly show climate-associated, fine-scale population structure
 across an environmental gradient in Atlantic salmon near its range limit
 in North America, highlighting valuable approaches for predicting
 population responses to climate change and managing species
 sustainability.
description: Labrador Atlantic Salmon
 Sequenced SNP DataGenepop file of SNP
 genotype data for 1389 individuals across 35 salmon populations in
 Labrador Canada.SNPs_Labrador376_genepop.txt
DOI: 10.5061/dryad.35vr46g
title: Data from: Structural and compositional dynamics of strictly protected woodland communities with silvicultural implications, using Białowieża Forest as an example

description: • Key message: Long-term strict protection of woodland communities may
 lead to their compositional simplification and homogenisation. • Context:
 In the past, it has often been postulated that structures and processes
 typical for natural forests should be mimicked by silvicultural activities
 in the case of managed tree stands. • Aims: To determine which features
 and traits of natural woodland communities (alongside typical old-growth
 attributes) should be imitated in managed forests, as well as which should
 not (and for what reasons). • Methods: Tree data from five permanent study
 plots (of a total area of 15.44 ha) established in 1936 in the core area
 of the Białowieża National Park (NE Poland) are used to calculate several
 quantitative indices describing the temporal dynamics (in terms of stand
 structure and composition) of eight major woodland community types. •
 Results: Most structural attributes revealed rather high stability over
 time. In contrast to these, during the observation period, noticeable
 changes in the composition of particular Białowieża woodland communities
 have been taking place, related to declining occurrence and reduced roles
 characteristic for a large number of tree species. • Conclusion: In many
 ways, natural forests can serve as an important model for managed forest
 stands. However, in certain circumstances, silvicultural treatments
 counteracting natural developmental trends may appear to be indispensable,
 especially when more diverse and stable tree species composition (at a
 given spatial and temporal scale) is indicated or desirable.
description: Supplementary
 dataThis data file contains
 tree quantities and basal area sums in 50mm-wide classes of diameter at
 breast height (dbh), given separately for (a) all live, ingrowth and
 outgrowth trees, (b) 8 major woodland community types, (c) 5 research
 plots, (d) 57 separate community patches, (e) 7 subsequent measurement
 censuses, and (f) 11 tree species. Additionally, community patch areas are
 given.DATA.xls
DOI: 10.5061/dryad.3f31m01
title: Data from: Free vibration analysis of transmission lines based on the dynamic stiffness method

description: An improved mathematical model used to study coupling characteristic of
 the multi-span transmission lines is developed. Based on the solution
 method for single-span cable, an expression for the dynamic stiffness of
 two-span transmission lines with an arbitrary inclination angle is
 formulated. The continuity of displacements and forces at a suspension
 point is used to derive the dynamic stiffness. Interactions between
 insulator strings and adjacent spans are accommodated. Considering the
 infinite dynamic stiffness corresponds to the natural frequencies of the
 transmission lines, the finite element method(FEM) is employed to assess
 the validity of the dynamic stiffness. In the numerical investigation,
 attention is focused on the effect of the inclination angles, Irvine
 parameter, insulator string length and damping parameter. In addition,
 modal function corresponding to the natural frequencies are derived. Then,
 the results of comprehensive parametric studies are presented and
 discussed. Special attention is paid to the effect of Irvine parameter and
 damping parameter on the in-plane modal shapes. Finally, according to the
 theoretical model of two-span transmission lines, the generalized dynamic
 stiffness of transmission lines with arbitrary number of spans and
 inclination angles is derived. The method can be used as the basis of the
 vibration analysis on a wide variety of multi-span transmission lines.
description: data of Free vibration
 analysis of transmission lines based on the dynamic stiffness
 methodThe data file is
 calculated by the formula in the manuscript and ABAQUS.date.zip
DOI: 10.5061/dryad.b3d257g
title: Data from: Identifying the morphologic basis for radiomic features in distinguishing different Gleason grades of prostate cancer on MRI: preliminary findings

description: Translation of radiomics into the clinic may require a more comprehensive
 understanding of the underlying morphologic tissue characteristics they
 reflect. In the context of prostate cancer (PCa), some studies have
 correlated gross histological measurements of gland lumen, epithelium, and
 nuclei with disease appearance on MRI. Quantitative histomorphometry (QH),
 like radiomics for radiologic images, is the computer based extraction of
 features for describing tumor morphology on digitized tissue images. In
 this work, we attempt to establish the histomorphometric basis for
 radiomic features for prostate cancer by (1) identifying the radiomic
 features from T2w MRI most discriminating of low vs. intermediate/high
 Gleason score, (2) identifying QH features correlated with the most
 discriminating radiomic features previously identified, and (3) evaluating
 the discriminative ability of QH features found to be correlated with
 spatially co-localized radiomic features. On a cohort of 36 patients (23
 for training, 13 for validation), Gabor texture features were identified
 as being most predictive of Gleason grade on MRI (AUC of 0.69) and gland
 lumen shape features were identified as the most predictive QH features
 (AUC=0.75). Our results suggest that the PCa grade discriminability of
 Gabor features is a consequence of variations in gland shape and
 morphology at the tissue level.
description: Region-wise radiomic
 & histomorphometric features from 2 sitesRadPath.zip
DOI: 10.5061/dryad.f53j0dk
title: Data from: Tangled banks: a landscape genomic evaluation of wallace's riverine barrier hypothesis for three amazon plant species

description: Wallace’s Riverine Barrier hypotheses is one of the earliest biogeographic
 explanations for Amazon speciation, but it has rarely been tested in
 plants. In this study, we used three woody Amazonian plant species to
 evaluate Wallace’s Hypothesis using tools of landscape genomics. We
 generated unlinked single-nucleotide polymorphism (SNP) data from the
 nuclear genomes of 234 individuals (78 for each plant species) across 13
 sampling sites along the Rio Branco, Brazil, for Amphirrhox longifolia
 (8,075 SNPs), Psychotria lupulina, (9,501 SNPs) and Passiflora spinosa
 (14,536 SNPs). Although significantly different migration rates were
 estimated between species, the population structure data do not support
 the hypothesis that the Rio Branco – an allopatric barrier for primates
 and birds – is a significant genetic barrier for Amphirrhox longifolia,
 Passiflora spinosa, or Psychotria lupulina. Overall, we demonstrated that
 medium-sized rivers in the Amazon Basin, such as the Rio Branco, are
 permeable barriers to gene flow for animal dispersed and animal pollinated
 plant species.
description: raw
 dataSNPs data for A.
 longifolia, P. spinosa and P. lupulina
DOI: 10.5061/dryad.fr88s7f
title: Data from: Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental adaptation and acclimation

description: Domestication and selective breeding has resulted in over 1000 extant
 cattle breeds. Many of these breeds do not excel in important traits but
 are adapted to local environments. These adaptations are a valuable source
 of genetic material for efforts to improve commercial breeds. As a step
 toward this goal we identified candidate regions to be under selection in
 genomes of nine Russian native cattle breeds adapted to survive in harsh
 climates. After comparing our data to other breeds of European and Asian
 origins we found known and novel candidate genes that could potentially be
 related to domestication, economically important traits and environmental
 adaptations in cattle. The Russian cattle breed genomes contained regions
 under putative selection with genes that may be related to adaptations to
 harsh environments (e.g., AQP5, RAD50, and RETREG1). We found genomic
 signatures of selective sweeps near key genes related to economically
 important traits, such as the milk production (e.g., DGAT1, ABCG2), growth
 (e.g., XKR4), and reproduction (e.g., CSF2). Our data point to candidate
 genes which should be included in future studies attempting to identify
 genes to improve the extant breeds and facilitate generation of commercial
 breeds that fit better into the environments of Russia and other countries
 with similar climates.
description: Raw GGP HD150K SNP data
 for 9 Russian cattle breedsThis set includes 9
 Russian cattle breeds genotyped on the GeneSeek HD150K SNP array. The
 breeds included are: Kalmyk, Buryat, Yakut, Kazakh Whiteheaded, Kostroma,
 Kholmogory, Bestuzhev, Yaroslavl, and Black Pied.Russian_cattle_150K_Dryad_9_breeds.zipGGP HD150K SNP data for 5 breeds of Asian originThis set includes autosomal genotypes for 3 Russian breeds of Asian origin on the GeneSeek HD150K SNP array (MAF&lt;0.05): Kalmyk, Yakut, and Buryat combined with the sequence-based genotypes of Hanwoo and Illumina HD based genotypes of Japanese Black breeds.ASIA_Group_Dryad.zipGGP HD150K SNP data for 10 breeds of European originThis set includes autosomal genotyping data for 6 Russian breeds of European origin genotyped on the GeneSeeek HD150K SNP array (MAF&lt;0.05): Bestuzhev, Black Pied, Kazakh Whiteheaded, Kholmogory, Kostroma, and Yaroslavl combined with sequence-based genotypes of Angus, Holstein, Jersey, and Fleckvieh from the 1000 bull genome project.EUR_Groups_1_2_Angus_Dryad.zip
DOI: 10.5281/zenodo.17763476
title: INRIM_Brand1_10F_3_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 10F SC sample 3 INRIM   - EDLC Single - Brand1

Part of the Constant Temperature DataBase
DOI: 10.5281/zenodo.17763477
title: INRIM_Brand1_10F_3_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 10F SC sample 3 INRIM   - EDLC Single - Brand1

Part of the Constant Temperature DataBase
DOI: 10.5061/dryad.kf6q10b
title: Data from: Spatial phylogenetics reveals evolutionary constraints on the assembly of a large regional flora

description: Premise of the study: We use spatial phylogenetics to analyze the assembly
 of the Wisconsin flora, linking processes of dispersal and niche evolution
 to spatial patterns in floristic and phylogenetic diversity, and testing
 whether phylogenetic niche conservatism can account for these patterns.
 Methods: We use digitized records and a new molecular phylogeny for all
 vascular plants in Wisconsin to estimate spatial variation in species
 richness and phylogenetic  and  diversity in a native flora shaped
 mainly by post-glacial dispersal and response to environmental gradients.
 We develop distribution models for all species and use these to infer
 fine-scale variation in potential diversity, phylogenetic distance, and
 interspecific range overlaps. We identify 11 bioregions based on floristic
 composition, map areas of neo- and paleo-endemism to establish new
 conservation priorities, and predict how community-assembly patterns
 should shift with climatic change. Key results: Spatial phylogenetic
 turnover most strongly reflects differences in temperature and spatial
 distance. For all vascular plants, assemblages shift from phylogenetically
 clustered to over-dispersed northward, contrary to most other studies.
 This pattern is lost for angiosperms alone, illustrating the importance of
 phylogenetic scale.Conclusions: Species ranges and assemblage composition
 appear driven primarily by phylogenetic niche conservatism. Closely
 related species are ecologically similar and occupy similar territories.
 The average level and geographic structure of plant phylogenetic diversity
 within Wisconsin will greatly decline over the next half-century, while
 potential species richness will increase throughout the state. Our methods
 can be applied to allochthonous communities throughout the world.
description: thresholdingExample script to transform MAXENT models to binary presence-absence matrices.DNA sequence alignmentsDNA sequence alignments in FASTA format. These alignments were used to construct the phylogeny of the flora of Northeastern North America and adjacent Canada.fasta.zipConstrained RAXML phylogenyPhylogeny constructed using RAXML based on a 7-gene alignment (see associated FASTA files). Most genera were constrained to be monophyletic (see associated constraint file).june_2_7gene_contrained_genera.treConstraint treeTopological constraint used in RAXML to constrain most genera as monophyletic.constrain_genera.treUltrametric treeChronogram developed with treePL using the RAXML phylogeny and associated config file.GC.ultrametric_genera_constrained.tretreePL configuration fileConfiguration file with age offsets used to develop the associated chronogram.june2.configGenbank_accession_numbersGenbank accession numbers for samples used in phylogenetic analysis.
DOI: 10.5061/dryad.5337hv7
title: Data from: Out of sight of wind turbines – reindeer response to wind farms in operation

description: To meet the expanding land use required for wind energy development a
 better understanding of the effects on terrestrial animals’ responses to
 such development is required. Using GPS-data from 50 freely ranging female
 reindeer (Rangifer tarandus) in the Malå reindeer herding community,
 Sweden, we determined reindeer calving sites and estimated reindeer
 habitat selection using resource selection functions (RSF). RSFs were
 estimated at both second- (selection of home range) and third-order
 (selection within home range) scale in relation to environmental
 variables, wind farm (WF) development phase (before construction,
 construction, and operation), distance to the WFs and at the second-order
 scale whether the wind turbines were in or out of sight of the reindeer.
 We found that the distance between reindeer calving site and wind farms
 increased during the operation phase, compared to before construction. At
 both scales of selection we found a significant decrease in habitat
 selection of areas in proximity of the WFs, in the same comparison. The
 results also revealed a shift in home range selection away from habitats
 where wind turbines became visible towards habitats where the wind
 turbines were obscured by topography (increase in use by 79% at 5 km). We
 interpret the reindeer shift in home range selection as an effect of the
 wind turbines per se. Using topography and land cover information together
 with the positions of wind turbines could therefore help identify
 sensitive habitats for reindeer and improve the planning and placement of
 WFs. In addition, we found that operation phase of these WFs had a
 stronger adverse impact on reindeer habitat selection than the
 construction phase. Thus, the continuous running of the wind turbines
 making a sound both day and night seemed to have disturbed the reindeer
 more than the sudden sounds and increased human activity during
 construction work.
description: rsfdata_2nd_and_3rd_order_scaledata used for estimation of resource selection functions at the second- and third-order scale of selection (Table 3 and 4)gpsdatagps-positions used to identify the calving sites using the ResidenceTime-function in adehabitatLT in R