cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1v074
title: Data from: Expression and function of ATP-dependent potassium channels in zebrafish islet β-cells

description: ATP-sensitive potassium channels (KATP channels) are critical nutrient
 sensors in many mammalian tissues. In the pancreas, KATP channels are
 essential for coupling glucose metabolism to insulin secretion. While
 orthologous genes for many components of metabolism–secretion coupling in
 mammals are present in lower vertebrates, their expression, functionality
 and ultimate impact on body glucose homeostasis are unclear. In this
 paper, we demonstrate that zebrafish islet β-cells express functional KATP
 channels of similar subunit composition, structure and metabolic
 sensitivity to their mammalian counterparts. We further show that
 pharmacological activation of native zebrafish KATP using diazoxide, a
 specific KATP channel opener, is sufficient to disturb glucose tolerance
 in adult zebrafish. That β-cell KATP channel expression and function are
 conserved between zebrafish and mammals illustrates the evolutionary
 conservation of islet metabolic sensing from fish to humans, and lends
 relevance to the use of zebrafish to model islet glucose sensing and
 diseases of membrane excitability such as neonatal diabetes.
description: Zebrafish_KATP_Emfinger_et_al_RSOS_DataThis is the data for the paper: Expression and function of ATP-dependent potassium channels in zebrafish islet β-cells Christopher H. Emfinger, Alecia Welscher, Zihan Yan, Yixi Wang, Hannah Conway, Jennifer B. Moss, Larry G. Moss, Maria S. Remedi, and Colin G. Nichols These data are organized into sub-folders which include PCRs for the sorted cells (cf Figure 3), the whole islets (cf Figure 3), the electrophysiological records (cf Figures 2 and 4; raw and data-reduced, with subfolders for the ATP sensitivity, ADP activation, and pharmacology (Diazoxide and Pinacidil activation and glibenclamide and tolbutamide inhibition), as well as the injection studies (cf figure 1). These are uploaded as a single zip file for download. The raw electrophysiological traces are in pClamp-compatible file formats. The PCR gels are in PDFs. The data for injections are in an excel file with processing in a GraphPad prism.
DOI: 10.5061/dryad.31f77
title: Data from: The red coral (Corallium rubrum) transcriptome: a new resource for population genetics and local adaptation studies

description: The question of species survival and evolution in heterogeneous
 environments has long been a subject for study. Indeed, it is often
 difficult to identify the molecular basis of adaptation to contrasted
 environments, and nongenetic effects increase the difficulty to
 disentangle fixed effects, such as genetic adaptation, from variable
 effects, such as individual phenotypic plasticity, in adaptation.
 Nevertheless, this question is also of great importance for understanding
 the evolution of species in a context of climate change. The red coral
 (Corallium rubrum) lives in the Mediterranean Sea, where at depths ranging
 from 5 to 600 m, it meets very contrasted thermal conditions. The
 shallowest populations of this species suffered from mortality events
 linked with thermal anomalies that have highlighted thermotolerance
 differences between individuals. We provide here a new transcriptomic
 resource, as well as candidate markers for the study of local adaptation.
 We sequenced the transcriptome of six individuals from 5 m and six
 individuals from 40 m depth at the same site of the Marseilles bay, after
 a period of common garden acclimatization. We found differential
 expression maintained between the two depths even after common garden
 acclimatization, and we analysed the polymorphism pattern of these
 samples. We highlighted contigs potentially implicated in the response to
 thermal stress, which could be good candidates for the study of thermal
 adaptation for the red coral. Some of these genes are also involved in the
 response to thermal stress in other corals. Our method enables the
 identification of candidate loci of local adaptation useful for other
 nonmodel organisms.
description: CoralliumRubrum_ContigsCoralliumRubrum_SNPCoralliumRubrum_AnnotationFile
DOI: 10.5061/dryad.82h58
title: Data from: Excavation and aggregation as organizing factors in de novo construction by mound-building termites

description: Termites construct complex mounds that are orders of magnitude larger than
 any individual and fulfil a variety of functional roles. Yet the processes
 through which these mounds are built, and by which the insects organize
 their efforts, remain poorly understood. The traditional understanding
 focuses on stigmergy, a form of indirect communication in which actions
 that change the environment provide cues that influence future work.
 Termite construction has long been thought to be organized via a putative
 ‘cement pheromone’: a chemical added to deposited soil that stimulates
 further deposition in the same area, thus creating a positive feedback
 loop whereby coherent structures are built up. To investigate the detailed
 mechanisms and behaviours through which termites self-organize the early
 stages of mound construction, we tracked the motion and behaviour of major
 workers from two Macrotermes species in experimental arenas. Rather than a
 construction process focused on accumulation of depositions, as models
 based on cement pheromone would suggest, our results indicated that the
 primary organizing mechanisms were based on excavation. Digging activity
 was focused on a small number of excavation sites, which in turn provided
 templates for soil deposition. This behaviour was mediated by a mechanism
 of aggregation, with termites being more likely to join in the work at an
 excavation site as the number of termites presently working at that site
 increased. Statistical analyses showed that this aggregation mechanism was
 a response to active digging, distinct from and unrelated to putative
 chemical cues that stimulate deposition. Agent-based simulations
 quantitatively supported the interpretation that the early stage of de
 novo construction is primarily organized by excavation and aggregation
 activity rather than by stigmergic deposition.
description: BehaviorThis file contains data about the termite behaviors observed in our trials. The file contains the following four sheets: 1) Initiations: information about every termite and the number of excavation sites it initiated. 2) Joining: information about every time a termite encountered an excavation site, and whether or not it joined in excavating there. 3) Duration: information about the length of time for every excavation event. 4) Metadata: descriptions of the column headers included in sheets 1–3.behavior.xlsxVideo S1. Sample clip from one of our experiments.Video S1.movVideo S2. Sample clips of the two building behaviors classified.Video S2.mp4Video S3. Timelapse video of termites working over approximately ten hours.Video S3.mp4Video S4. Timelapse and building process from simulations.Video S4.mp4
DOI: 10.5061/dryad.7v1f8
title: Data from: Shifts in diversification rates linked to biogeographic movement into new areas: an example of a recent radiation in the Andes

description: PREMISE OF THE STUDY: Clade-specific bursts in diversification are often
 associated with the evolution of key innovations. However, in groups with
 no obvious morphological innovations, observed upticks in diversification
 rates have also been attributed to the colonization of a new geographic
 environment. In this study, we explore the systematics, diversification
 dynamics, and historical biogeography of the plant clade Rhinantheae in
 the Orobanchaceae, with a special focus on the Andean clade of the genus
 Bartsia. METHODS: We sampled taxa from across Rhinantheae, including a
 representative sample of Andean Bartsia species. Using standard
 phylogenetic methods, we reconstructed evolutionary relationships,
 inferred divergence times among the clades of Rhinantheae, elucidated
 their biogeographic history, and investigated diversification dynamics.
 KEY RESULTS: We confirmed that the South American Bartsia species form a
 highly supported monophyletic group. The median crown age of Rhinantheae
 was determined to be ca. 30 Myr, and Europe played an important role in
 the biogeographic history of the lineages. South America was first
 reconstructed in the biogeographic analyses around 9 Myr ago, and with a
 median age of 2.59 Myr, this clade shows a significant uptick in
 diversification. CONCLUSIONS: Increased net diversification of the South
 American clade corresponds to biogeographic movement into the New World.
 This movement happened at a time when the Andes were reaching the
 necessary elevation to host an alpine environment. Although a specific
 route could not be identified with certainty, we provide plausible
 hypotheses to how the group colonized the New World.
description: Uribe-Convers_and_Tank_AJB_2015The data included in this directory was used for every analysis in the publication "Shifts in diversification rates linked to biogeographic movement into new areas, an example of disparate continental distributions and a recent radiation in the Andes" by Simon Uribe-Convers and David C. Tank (University of Idaho), as part of Uribe-Convers' dissertation.
DOI: 10.5061/dryad.2727k
title: Data from: Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution

description: The evolution of the ratite birds has been widely attributed to vicariant
 speciation, driven by the Cretaceous breakup of the supercontinent
 Gondwana. The early isolation of Africa and Madagascar implies that the
 ostrich and extinct Madagascan elephant birds (Aepyornithidae) should be
 the oldest ratite lineages. We sequenced the mitochondrial genomes of two
 elephant birds and performed phylogenetic analyses, which revealed that
 these birds are the closest relatives of the New Zealand kiwi and are
 distant from the basal ratite lineage of ostriches. This unexpected result
 strongly contradicts continental vicariance and instead supports flighted
 dispersal in all major ratite lineages. We suggest that convergence toward
 gigantism and flightlessness was facilitated by early Tertiary expansion
 into the diurnal herbivory niche after the extinction of the dinosaurs.
description: Phylogenetic
 AnalysesInput-files (data) and
 resulting phylogenetic tree(s) for all RAxML, MrBayes, PAUP* and BEAST
 analyses.DataFiles+Trees.zipAepyornis hildebrandti Sequence DataFASTQ file containing filtered and de-mulitplexed Ion Torrent PGM (Life Technologies) sequencing reads corresponding to the Aepyornis hildebrandti (MNZ S38301) enriched genomic library. See main publication for full details on data processing.Aepyornis.fastq.gzMullerornis agilis Sequence DataFASTQ file containing filtered and de-mulitplexed Ion Torrent PGM (Life Technologies) sequencing reads corresponding to the Mullerornis agilis (MNZ S38300) enriched genomic library. See main publication for full details on data processing.Mullerornis.fastq.gz
DOI: 10.5064/f6vanjl8/k3opdw
title: Silan-Ciruelas_Opt2_Therapist3.pdf
DOI: 10.5061/dryad.0bk52
title: Data from: De novo and reference transcriptome assembly of transcripts expressed during flowering provide insight into seed setting in tetraploid red clover

description: Red clover (Trifolium pratense L.) is one of the most important legume
 forage species in temperate livestock agriculture. Tetraploid red clover
 cultivars are generally producing less seed than diploid cultivars.
 Improving the seed setting potential of tetraploid cultivars is necessary
 to utilize the high forage quality and environmentally sustainable
 nitrogen fixation ability of red clover. In the current study, our aim was
 to identify candidate genes involved in seed setting. Two genotypes,
 ‘Tripo’ with weak seed setting and ‘Lasang’ with strong seed setting were
 selected for transcriptome analysis. De novo and reference based analyses
 of transcriptome assemblies were conducted to study the global
 transcriptome changes from early to late developmental stages of flower
 development of the two contrasting red clover genotypes. Transcript
 profiles, gene ontology enrichment and KEGG pathway analysis indicate that
 genes related to flower development, pollen pistil interactions,
 photosynthesis and embryo development are differentially expressed between
 these two genotypes. A significant number of genes related to pollination
 were overrepresented in ‘Lasang’, which might be a reason for its good
 seed setting ability. The candidate genes detected in this study might be
 used to develop molecular tools for breeding tetraploid red clover
 varieties with improved seed yield potentials.
description: Tripo42_redclover_denovoassembly.TrinityDe novo assembly for genotype "Tripo" generated by Trinity programTripo55_redclover_denovoassembly.TrinityDe novo assembly for genotype "Tripo55" derived from Trinity programLork77_redclvoer_denovoassembly.TrinityLork108_redclover_denovovassembly.TrinityDe novo assembly for genotype "Lork108" derived from Trinity programTripo_redclover_GFF3Annotation file (GFF3) for genotype Tripo generated by GFF3 python script (script can be found at the end)Tripo_redclover_sorted.gff3Lork_redclover_GFF3Annotation file (GFF3) for genotype "Lork" generated by GFF3 python script (script can be found at the end)Lork_redclover_sorted.gff3Make_GFF3_Python scriptPython script to generate Annotation files (GFF3) for genotypes Tripo (Tripo_redclover_sorted.gff3) and Lork (Lork_redclover_sorted.gff3).Make_GFF3_KMR.py
DOI: 10.5064/f6vanjl8/uippxi
title: Silan-Ciruelas_TUR_Opt2_15B_NejlaNaz_10-20_Low_Median-High.pdf
DOI: 10.5064/f6vanjl8/myzwau
title: Silan-Ciruelas_TUR_Opt2_16B_Kerem_10-20_High_Median-High.pdf
DOI: 10.5061/dryad.11b0f
title: Data from: Range-dependent flexibility in the acoustic field of view of echolocating porpoises (Phocoena phocoena)

description: Toothed whales use sonar to detect, locate, and track prey. They adjust
 emitted sound intensity, auditory sensitivity and click rate to target
 range, and terminate prey pursuits with high-repetition-rate,
 low-intensity buzzes. However, their narrow acoustic field of view (FOV)
 is considered stable throughout target approach, which could facilitate
 prey escape at close-range. Here, we show that, like some bats, harbour
 porpoises can broaden their biosonar beam during the terminal phase of
 attack but, unlike bats, maintain the ability to change beamwidth within
 this phase. Based on video, MRI, and acoustic-tag recordings, we propose
 this flexibility is modulated by the melon and implemented to accommodate
 dynamic spatial relationships with prey and acoustic complexity of
 surroundings. Despite independent evolution and different means of sound
 generation and transmission, whales and bats adaptively change their FOV,
 suggesting that beamwidth flexibility has been an important driver in the
 evolution of echolocation for prey tracking.
description: frame_hydro31102012a schematic showing the arrangement of individual hydrophones on the arrayframe more31102012an excel sheet linking the hydrophones id numbers to the channels in the recording systemdtag audio filedtag audio file for the 12th trial of the afternoon session on 31/10/2012, as well as matlab structures with outputs of click detectors, an echogram and an inter-click interval scatter plot (color-coded with relative apparent output level of the clicks)dtag.ziphydrophone relative calibration valuescalibration values (linear scale) of hydrophones relative to the hydrophone in the located in the centre of the array. each day a calibration was conducted to account for small differences int the array orientation or hydrophone placement between recording days. a short sweep was played from across the porpoise pool and recorded on all hydrophones. raw data available upon requestcalibrationValues.matfreja31102012_af12(ADpeak5.0V)_31-10-2012_14_01_52the folder contains recordings from 48 hydrophones, and manually verified detector data (matlab structures) from 21 of the hydrophones as well as combined click detector data (in sound_20121031_af12_50.mat)
DOI: 10.5064/f6vanjl8/q7wj4x
title: Silan-Ciruelas_Opt2_Therapist15.pdf
DOI: 10.5064/f6vanjl8/xtrcgv
title: Silan-Ciruelas_PHL_Opt1_8A_Nica_1-5_High_Med-High.pdf
DOI: 10.5064/f6vanjl8/xhkekp
title: Silan-Ciruelas_USA_Opt2_2B_Silky_1_High_Low-Median.pdf
DOI: 10.5064/f6vanjl8/rth0is
title: Silan-Ciruelas_PHL_Opt2_15A_Rozel_10-20_Low_Median-High.pdf
DOI: 10.5061/dryad.4s4b3nf
title: Data from: Anisotropic growth is achieved through the additive mechanical effect of material anisotropy and elastic asymmetry

description: Fast directional growth is a necessity for the young seedling; after
 germination, it needs to quickly penetrate the soil to begin its
 autotrophic life. In most dicot plants, this rapid escape is due to the
 anisotropic elongation of the hypocotyl, the columnar organ between the
 root and the shoot meristems. Anisotropic growth is common in plant organs
 and is canonically attributed to cell wall anisotropy produced by oriented
 cellulose fibers. Recently, a mechanism based on asymmetric pectin-based
 cell wall elasticity has been proposed. Here we present a harmonizing
 model for anisotropic growth control in the dark-grown Arabidopsis
 thaliana hypocotyl: basic anisotropic information is provided by cellulose
 orientation) and additive anisotropic information is provided by
 pectin-based elastic asymmetry in the epidermis. We quantitatively show
 that hypocotyl elongation is anisotropic starting at germination. We
 present experimental evidence for pectin biochemical differences and wall
 mechanics providing important growth regulation in the hypocotyl. Lastly,
 our in silico modelling experiments indicate an additive collaboration
 between pectin biochemistry and cellulose orientation in promoting
 anisotropic growth.
description: Data for Bou Daher at
 al. 2018This .zip file contains
 all raw experimental data associated with the publication of record
 (produced by Bou Daher, Chen and Braybrook). Data organization is by
 Figure, then by data type. Details in the README file.DATA-2018-BOUDAHER-BRAYBROOK.zip
DOI: 10.5064/f6vanjl8/0d7nmt
title: Silan-Ciruelas_PHL_Opt1_8B_-Nica_1-5_High_Med-High.pdf
DOI: 10.5064/f6vanjl8/hyu4ka
title: Silan-Ciruelas_PHL_Opt1_2B_Nica_1_High_Low-Median.pdf
DOI: 10.5064/f6vanjl8/xb2rfu
title: Silan-Ciruelas_FRA_Opt1_8B_1_5_High_Median-High.pdf
DOI: 10.5061/dryad.768vg4f
title: Data from: Phenotypic plasticity in the mandibular morphology of Japanese macaques: captive–wild comparison

description: Despite the accumulating evidence suggesting the importance of phenotypic
 plasticity in diversification and adaptation, little is known about
 plastic variation in primate skulls. The present study evaluated the
 plastic variation of the mandible in Japanese macaques by comparing wild
 and captive specimens. The results showed that captive individuals are
 square-jawed with relatively longer tooth rows than wild individuals. We
 also found that this shape change resembles the sexual dimorphism,
 indicating that the mandibles of captive individuals are to some extent
 masculinized. In contrast, the mandible morphology was not clearly
 explained by ecogeographical factors. These findings suggest the
 possibility that perturbations in the social environment in captivity and
 resulting changes of androgenic hormones may have influenced the
 development of mandible shape. As the high plasticity of social properties
 is well known in wild primates, social environment may cause the inter-
 and intra-population diversity of skull morphology, even in the wild. The
 captive–wild morphological difference detected in this study, however, can
 also be possibly formed by other untested sources of variation (e.g.,
 inter-population genetic variation), and therefore this hypothesis should
 be validated further.
description: READMEmain_TI_RSOS_2018main R codefunctions_TI_RSOS_2018supplemental R codedata_TI_RSOS_2018the data including ID, sex, population, prefecture, environment, generation, age (age class), latitude, longitude, island, captivity, age_y (age in years), generationcoordinates_of_landmarksthe raw data of coordinates of landmarks in csv formatreference_shapethe reference mesh and landmarks data (PRI_2584) used for visualizationresultsthe implementation results
DOI: 10.5064/f6vanjl8/is6jmr
title: Silan-Ciruelas_TUR_Opt2_7A_NejlaNaz_1-5_Low_Median-High.pdf
DOI: 10.5064/f6vanjl8/83xjcb
title: Silan-Ciruelas_PHL_Opt1_9A_Rozel_5-10_Low_Low-Median.pdf
DOI: 10.5281/zenodo.18352288
title: Map of the architectural design process

description: This dataset presents a map of the architectural design process, from Strategic Definition to Spatial Coordination, highlighting the flow, maturity, and granularity of information across project stages. Grounded in grey literature, technical manuals, and international standards, the map explicates how information evolves and becomes traceable, demonstrating how its structure can condition decision-making throughout the design process.

An interactive version of the map can be accessed via the provided link (click here to access the interactive map), allowing users to explore the sequence of activities and the articulation between inputs, analyses, and outputs. In the interactive map, references and figure captions can be consulted through the lower tabs, and each information element is accompanied by a descriptive note.

The levels of information granularity associated with each stage are documented in annexes available for download.
DOI: 10.5064/f6vanjl8/mx8csw
title: Silan-Ciruelas_FRA_Opt1_16A_10-20_High_Median-High.pdf
DOI: 10.5281/zenodo.18352287
title: Map of the architectural design process

description: This dataset presents a map of the architectural design process, from Strategic Definition to Spatial Coordination, highlighting the flow, maturity, and granularity of information across project stages. Grounded in grey literature, technical manuals, and international standards, the map explicates how information evolves and becomes traceable, demonstrating how its structure can condition decision-making throughout the design process.

An interactive version of the map can be accessed via the provided link (click here to access the interactive map), allowing users to explore the sequence of activities and the articulation between inputs, analyses, and outputs. In the interactive map, references and figure captions can be consulted through the lower tabs, and each information element is accompanied by a descriptive note.

The levels of information granularity associated with each stage are documented in annexes available for download.