cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m27qq
title: Data from: Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

description: The evolutionary importance of hybridization and introgression has long
 been debated. Hybrids are usually rare and unfit, but even infrequent
 hybridization can aid adaptation by transferring beneficial traits between
 species. Here we use genomic tools to investigate introgression in
 Heliconius, a rapidly radiating genus of neotropical butterflies widely
 used in studies of ecology, behaviour, mimicry and speciation. We
 sequenced the genome of Heliconius melpomene and compared it with other
 taxa to investigate chromosomal evolution in Lepidoptera and gene flow
 among multiple Heliconius species and races. Among 12,669 predicted genes,
 biologically important expansions of families of chemosensory and Hox
 genes are particularly noteworthy. Chromosomal organization has remained
 broadly conserved since the Cretaceous period, when butterflies split from
 the Bombyx (silkmoth) lineage. Using genomic resequencing, we show hybrid
 exchange of genes between three co-mimics, Heliconius melpomene,
 Heliconius timareta and Heliconius elevatus, especially at two genomic
 regions that control mimicry pattern. We infer that closely related
 Heliconius species exchange protective colour-pattern genes promiscuously,
 implying that hybridization has an important role in adaptive radiation.
description: heliconius_genome_scaffolding_scripts.tarPredicted chemosensory proteins, odorant binding proteins and olfactory receptors in the H. melpomene reference genomeThe data file contains putative coding and amino acid sequences for the chemosensory protein (CSP), odorant binding protein (OBP) and olfactory receptor (Or) gene families identified in the version 1.1 Heliconius melpomene melpomene reference genome. These gene predictions were based on manual curation of automated gene predictions (Maker, Augustus) or in silico gene predictions based on reciprocal blast searches of the monarch Danaus plexippus and silkmoth Bombyx mori genomes. Future refinements of these gene models will be greatly improved by the availability of RNA-seq data.HGC_Nature_2012_CSP_OBP_OR_Gene_Predictions.xls
DOI: 10.5061/dryad.vc7ss
title: Data from: Intra-ejaculate sperm selection in female zebra finches

description: Among internal fertilizers, typically fewer than 1% sperm survive the
 journey through the oviduct. Several studies suggest that the sperm
 reaching the ovum—the ‘fertilizing set’—comprise a non-random
 sub-population, but the characteristics of this group remain unclear. We
 tested whether oviductal selection in birds results in a morphologically
 distinct subset of sperm, by exploiting the fact that the fertilizing set
 are trapped by the perivitelline layer of the ovum. We show that these
 sperm have remarkably low morphological variation, as well as smaller head
 size and greater tail length, compared with those inseminated. Our study
 shows that the morphological composition of sperm—rather than length
 alone—influences success in reaching the ovum.
description: Morphology data for
 faecal sample sperm and egg PVL spermHead length, midpiece
 length, tail length, and total length of sperm from faecal (unselected)
 samples and egg PVL (selected) samples from the same male, across 27 male
 zebra finches.faecal and pvl sperm morphology
 data2.csvSperm morphology data
 for faecal and seminal glomerus samplesHead length, midpiece
 length, tail length, and total length of sperm from faecal samples (i.e.
 obtained non-invasively) and seminal glomerus samples (obtained by
 dissection) from 13 male zebra finches. These were used to validate the
 assumption that faecal sample sperm are representative of the population
 of sperm that are stored in the male tract prior to
 ejaculation.faecal and seminal glomerus
 sperm morphology data.csv
DOI: 10.5061/dryad.pd670
title: Data from: How innovative are new drugs launched in the UK? A retrospective study of new drugs listed in the British National Formulary (BNF) 2001-2012

description: Objectives: Innovative new drugs offer potential benefits to patients,
 healthcare systems, governments and the pharmaceutical industry. Recent
 data suggest annual numbers of new drugs launched in the UK have increased
 in recent years, and we sought to understand whether this represents
 increasing numbers of highly innovative drugs being made available or the
 introduction of increasing numbers of drugs with limited additional
 therapeutic value. Design and setting: Retrospective observational study
 of new drug entries in the British National Formulary (BNF). Primary and
 secondary outcome measures: Number of new drugs launched in the UK each
 year (based on first appearance in the BNF) from 2001 to 2012, including
 new chemical entities and new biological drugs, categorised by degree of
 innovativeness according to published criteria that incorporate both
 clinical usefulness and the nature of the innovation. Results: Highly
 innovative, moderately innovative and slightly innovative drugs made up
 26%, 18% and 56% of all newly launched drugs, respectively, for the study
 period (n=290). There was an upward trend in annual numbers of slightly
 innovative drugs from 2004 onwards (R2=0.44), which aligned closely with
 the recovery in total numbers of new drugs launched each year since that
 time. There were no discernible time trends in the highly or moderately
 innovative categories. New drugs for malignancy and skin disease were most
 likely to be characterised as highly innovative (44% and 57%,
 respectively). Conclusions: Highly innovative new drugs comprise only
 around a quarter of all new drug launches in the UK. In contrast, drugs
 categorised as only slightly innovative comprised well over half of all
 new drugs and annual numbers in this category are increasing. Current
 policy initiatives that seek to increase the supply of innovative new
 drugs have long-lead times to impact, and will need careful assessment to
 ensure they deliver their aims without unintended consequences.
description: New drugs in the UK by
 year and innovation level 2001-2012New drugs listed in the
 British National Formulary (BNF) from 2001 to 2012 (inclusive) categorised
 as slightly innovative (1), moderately innovative (2), and highly
 innovative (3).Supplementary data - new drugs
 by year and innovation level 2001-2012 -
 revised.docx
DOI: 10.5061/dryad.0sn4046
title: Data from: The impact of income, land, and wealth inequality on agricultural expansion in Latin America

description: Agricultural expansion remains the most prominent proximate cause of
 tropical deforestation in Latin America, a region characterized by
 deforestation rates substantially above the world average and extremely
 high inequality. This paper deploys several multivariate statistical
 models to test whether different aspects of inequality, within a context
 of increasing agricultural productivity, promote agricultural expansion
 (Jevons paradox) or contraction (land-sparing) in 10 Latin American
 countries over 1990–2010. Here I show the existence of distinct patterns
 between the instantaneous and the overall (i.e., accounting for temporal
 lags) effect of increasing agricultural productivity, conditional on the
 degree of income, land, and wealth inequality. In a context of perfect
 equality, the instantaneous effect of increases in agricultural
 productivity is to promote agricultural expansion (Jevons paradox). When
 temporal lags are accounted for, agricultural productivity appears to be
 mainly land-sparing. Increases in the level of inequality, in all its
 forms, promote agricultural expansion, thus eroding the land-sparing
 effects of increasing productivity. The results also suggest that the
 instantaneous impact of inequality is larger than the overall effect
 (accounting for temporal lags) and that the effects of income inequality
 are stronger than those of land and wealth inequality, respectively.
 Reaping the benefits of increasing agricultural productivity, and
 achieving sustainable agricultural intensification in Latin America,
 requires policy interventions that specifically address inequality.
description: PNAS_DataData for the PNAS publication "The impact of income, land and wealth inequality on agricultural expansion in Latin America" by M.G. Ceddia
DOI: 10.25824/redu/ex1mqd
title: Controlled imaging dataset of sugarcane stems for varietal classification studies

description: This repository contains a dataset of high-quality images of sugarcane stems from two varieties—Vertix 03 and Vertix 12—collected at approximately ten months of growth. The images were produced under controlled laboratory conditions following a dedicated acquisition protocol specifically developed to ensure high image quality and consistency. The dataset was originally created for Lemos’ doctoral research, in which it served as the foundation for training and evaluating artificial intelligence models aimed at varietal classification of sugarcane. To the best of our knowledge, all samples were obtained from healthy plants. Each image depicts a single sugarcane stem photographed against a neutral black background under standardized lighting conditions. The images are stored in JPEG format, with a resolution of approximately 24 megapixels (6000 × 4000 pixels) and an average file size of about 5 megabytes. No post-processing was applied. The dataset is organized as follows: • 1 PDF file (this document): Description and metadata of the repository • 4 JPEG files: Random image samples illustrating the dataset contents • 1 ZIP file: Images of the empty background • 1 ZIP file: Images of the studio and the image acquisition setup • 2 ZIP files: Images of Vertix 03 (parts 1 and 2), for focal distances of 35 mm • 2 ZIP files: Images of Vertix 03 (parts 1 and 2), for focal distances of 50 mm • 1 ZIP file: References for Vertix 03 * • 2 ZIP files: Images of Vertix 12 (parts 1 and 2), for focal distances of 35 mm • 2 ZIP files: Images of Vertix 12 (parts 1 and 2), for focal distances of 50 mm • 1 ZIP file: References for Vertix 12 * * Reference images, such as sugarcane stems photographed alongside rulers or pens for scale calibration. This dataset is intended primarily for research in varietal classification and related fields such as computer vision, plant phenotyping, and machine learning applied to agricultural analysis. Details about the photographic setup and acquisition parameters are provided in the following sections of this document.
DOI: 10.6084/m9.figshare.31160746
title: Supplementary Material for: Effect of changing NAVA levels on tidal ventilation in extremely preterm infants supported with NIV-NAVA

description: Introduction
Non-invasive neurally adjusted ventilatory assist (NIV-NAVA) is used in preterm infants as a synchronized and proportional mode of non-invasive ventilation. Finding the ideal NAVA level to support preterm infants remains challenging.
Methods
A single-center prospective interventional study was conducted to study the effect of increasing NAVA levels on tidal ventilation measured with electrical impedance tomography (EIT). Preterm infants supported with NIV-NAVA were included. After a baseline registration and following a predefined titration protocol, NAVA levels were progressively increased by 0.5 cmH2O/µV up to a NAVA level of 3 cmH2O/µV. Before and during the titration procedure the evolution of (EIT) parameters (end-expiratory lung impedance (EELI), end-inspiratory lung impedance (EILI), silent spaces (SS) and center of ventilation (CoV)) and respiratory parameters (electrical diaphragm activity (Edi) peak and minimum (Edimin) and peak inspiratory pressure (PIP)) were measured.
Results
16 patients with a mean (standard deviation (SD)) gestational age (GA) at birth 26.7 (1.2) weeks and birth weight (BW) of 838 (205) grams were included for analysis. EIT parameters did not change significantly with titration of NAVA levels. PIP increased significantly with each increase in NAVA level and Edi peak decreased significantly from NAVA level 1 tot 1.5 cmH2O/µV. Edi min and transcutaneous CO2 (TcCO2) remained constant during the titration procedure. 
Conclusion
There was no effect of increasing NAVA levels on regional ventilation parameters. PIP increased with each increase in NAVA level, whereas Edi peak largely remained stable.
DOI: 10.6084/m9.figshare.31160746.v1
title: Supplementary Material for: Effect of changing NAVA levels on tidal ventilation in extremely preterm infants supported with NIV-NAVA

description: Introduction
Non-invasive neurally adjusted ventilatory assist (NIV-NAVA) is used in preterm infants as a synchronized and proportional mode of non-invasive ventilation. Finding the ideal NAVA level to support preterm infants remains challenging.
Methods
A single-center prospective interventional study was conducted to study the effect of increasing NAVA levels on tidal ventilation measured with electrical impedance tomography (EIT). Preterm infants supported with NIV-NAVA were included. After a baseline registration and following a predefined titration protocol, NAVA levels were progressively increased by 0.5 cmH2O/µV up to a NAVA level of 3 cmH2O/µV. Before and during the titration procedure the evolution of (EIT) parameters (end-expiratory lung impedance (EELI), end-inspiratory lung impedance (EILI), silent spaces (SS) and center of ventilation (CoV)) and respiratory parameters (electrical diaphragm activity (Edi) peak and minimum (Edimin) and peak inspiratory pressure (PIP)) were measured.
Results
16 patients with a mean (standard deviation (SD)) gestational age (GA) at birth 26.7 (1.2) weeks and birth weight (BW) of 838 (205) grams were included for analysis. EIT parameters did not change significantly with titration of NAVA levels. PIP increased significantly with each increase in NAVA level and Edi peak decreased significantly from NAVA level 1 tot 1.5 cmH2O/µV. Edi min and transcutaneous CO2 (TcCO2) remained constant during the titration procedure. 
Conclusion
There was no effect of increasing NAVA levels on regional ventilation parameters. PIP increased with each increase in NAVA level, whereas Edi peak largely remained stable.
DOI: 10.5061/dryad.m0584
title: Data from: CLIP test: a new fast, simple and powerful method to distinguish between linked or pleiotropic quantitative trait loci in linkage disequilibria analysis

description: An important question arises when mapping quantitative trait loci (QTLs)
 for genetically correlated traits: is the correlation due to pleiotropy (a
 single QTL affecting more than one trait) and/or close linkage (different
 QTLs that are physically close to each other and influence the traits)? In
 this article, we propose the Close Linkage versus Pleiotropism (CLIP)
 test, a fast, simple and powerful method to distinguish between these two
 situations. The CLIP test is based on the comparison of the square of the
 observed correlation between a combination of apparent effects at the
 marker level to the minimal value it can take under the pleiotropic
 assumption. A simulation study was performed to estimate the power and
 alpha risk of the CLIP test and compare it to a test that evaluated
 whether the confidence intervals of the two QTLs overlapped or not (CI
 test). On average, the CLIP test showed a higher power (68%) to detect
 close-linked QTLs than the CI test (43%) and a same alpha risk (4%).
description: simulation
 programscript, fortran and R
 programs to perform the simulationsPROG_SIMULATION.7zCLIP testfortran program to perform the CLIP testCLIP_corrected.f90
DOI: 10.5061/dryad.sf937
title: Data from: Symbiont-mediated RNA interference in insects

description: RNA interference (RNAi) methods for insects are often limited by problems
 with double-stranded (ds) RNA delivery, which restricts reverse genetics
 studies and the development of RNAi-based biocides. We therefore delegated
 to insect symbiotic bacteria the task of: (i) constitutive dsRNA synthesis
 and (ii) trauma-free delivery. RNaseIII-deficient, dsRNA-expressing
 bacterial strains were created from the symbionts of two very diverse pest
 species: a long-lived blood-sucking bug, Rhodnius prolixus, and a
 short-lived globally invasive polyphagous agricultural pest, Western
 Flower Thrips (Frankliniella occidentalis). When ingested, the manipulated
 bacteria colonized the insects, successfully competed with the wildtype
 microflora, and sustainably mediated systemic knockdown phenotypes that
 were horizontally transmissible. This represents a significant advance in
 the ability to deliver RNAi, potentially to a large range of non-model
 insects.
description: Thrips
 QRTPCRRaw cq values for thrips
 QRTPCRPRS raw data
 23Feb
DOI: 10.5061/dryad.754c6
title: Data from: Quantifying hummingbird preference for floral trait combinations: the role of selection on trait interactions in the evolution of pollination syndromes

description: Darwin recognized the flower's importance for the study of adaptation
 and emphasized that the flower's functionality reflects the
 coordinated action of multiple traits. Here we use a multi-trait
 manipulative approach to quantify the potential role of selection acting
 on floral trait combinations underlying the divergence and maintenance of
 three related North American species of Silene (Caryophyllaceae). We
 artificially generated 48 plant phenotypes corresponding to all
 combinations of key attractive traits differing among the three Silene
 species (color, height, inflorescence architecture, flower orientation,
 and corolla-tube width). We quantified main and interaction effects of
 trait manipulation on hummingbird visitation preference using experimental
 arrays. The main effects of floral display height and floral orientation
 strongly influenced hummingbird visitation, with hummingbirds preferring
 flowers held high above the ground and vertically to the sky. Hummingbirds
 also prefer traits in a non-additive manner as multiple two-way and
 higher-order interaction effects were important predictors of hummingbird
 visitation. Contemporary trait combinations found in hummingbird
 pollinated S. virginica are mostly preferred. Our study demonstrates the
 likelihood of pollination syndromes evolving due to selection on trait
 combinations and highlights the importance of trait interactions in
 understanding the evolution of complex adaptations.
description: All visits to the 48
 combinations, each replicated 28 timesThis is an excel spread
 sheet of the visitation data for each of the 48 combinations, summed
 across the 28 replicatesFor
 Dryad.xlsR Code for
 DryadThis is the R code used
 to determine the importance of different models for explaining hummingbird
 visitation followed by the R code for best subsets
 regression
DOI: 10.48656/sa8e-n775
title: Everyday Dialogues
title: Alltagsdialoge
DOI: 10.48656/830w-qy48
title: Everyday Dialogues
title: Alltagsdialoge
DOI: 10.5061/dryad.b0551
title: Data from: Early Pennsylvanian (Langsettian) fish assemblages from the Joggins Formation, Canada, and their implications for palaeoecology and palaeogeography

description: A review of all available specimens of fossil fishes from the classic
 Pennsylvanian Joggins locality of Nova Scotia, Canada, reveals the
 existence of a diverse community of chondrichthyans (xenacanthids,
 ctenacanthids and the enigmatic Ageleodus), acanthodians (gyracanthids),
 sarcopterygians (rhizodontids, megalichthyids, rhizodopsids and dipnoans)
 and actinopterygians (haplolepids). Reassessment of supposed endemic
 species (Ctenoptychius cristatus, Sagenodus plicatus, Gyracanthus
 duplicatus) indicates they are invalid, and overall, the assemblage
 comprises cosmopolitan taxa that were widespread around the coasts of
 tropical Pangaea. Strontium isotope analysis of fish remains and a
 critical study of their facies context suggest that these fish communities
 occupied bodies of water with salinities across the marine–freshwater
 spectrum. This preponderance of euryhaline forms implies a community
 structure quite distinct from that of today and might represent a
 transitory phase prior to the establishment of fully freshwater fish
 communities. Interpretation of fish ecology provides further evidence that
 the Joggins Formation was deposited in a paralic setting, and the
 recognition of one previously undetected brackish incursion strengthens
 the link between sedimentary cycles at Joggins and Milankovitch-induced
 glacio-eustatic change. Furthermore, interregional correlation of these
 marine transgressions supports palynostratigraphical arguments for an
 early Langsettian age for the Joggins Formation. This places tighter
 constraints on the age of the earliest known crown amniote, Hylonomus
 lyelli, an important calibration point used in phylogenomic studies.
description: Appendix
 S1Excel file containing a
 complete list of all known fossil fish specimens from Joggins accessioned
 in museum collections, with revised identification where appropriate.
 Abbreviations in 'specimen examined?' column: Y = yes; N = no; P
 = only photograph(s) of specimen examined.
DOI: 10.5061/dryad.1n1p0b5
title: Data from: The putative lissamphibian stem-group: phylogeny and evolution of the dissorophoid temnospondyls

description: Dissorophoid temnospondyls are widely considered to have given rise to
 some or all modern amphibians (Lissamphibia), but their ingroup
 relationships still bear major unresolved questions. An inclusive
 phylogenetic analysis of dissorophoids gives new insights into the
 large-scale topology of relationships. Based on a TNT 1.5 analysis (33
 taxa, 108 characters), the enigmatic taxon Perryella is found to nest just
 outside Dissorophoidea (phylogenetic defintion) but shares a range of
 synapomorphies with this clade. The dissorophoids proper are found to
 encompass a first dichotomy between the largely paedomorphic
 Micromelerpetidae and all other taxa (Xerodromes). Within the latter,
 there is a basal dichotomy between the large, heavily ossified
 Olsoniformes (Dissorophidae + Trematopidae) and the small salamander-like
 Amphibamiformes (new taxon), which include four clades: (1) Micropholidae
 (Tersomius, Pasawioops, Micropholis), (2) Amphibamidae sensu stricto
 (Doleserpeton, Amphibamus), Branchiosauridae (Branchiosaurus, Apateon,
 Leptorophus, Schoenfelderpeton) and (4) Lissamphibia. The genera
 Platyrhinops and Eoscopus are here found to nest at the base of
 Amphibamiformes. Represented by their basalmost stem-taxa
 (Triadobatrachus, Karaurus, Eocaecilia), lissamphibians nest with
 Gerobatrachus rather than Amphibamidae as repeatedly found by former
 analyses.
description: Schoch_Dis_Appendix
 1List
 of morphological characters for phylogenetic analysisSchoch_Dis_Appendix
 2Appendix 2:
 Character-taxon matrix.