cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s853qg7
title: Data from: A unified rheological model for cells and cellularised materials

description: The mechanical response of single cells and tissues exhibits a broad
 distribution of time scales that gives often rise to a distinctive
 power-law rheology. Such complex behaviour cannot be easily captured by
 traditional rheological approaches, making material characterisation and
 predictive modelling very challenging. Here, we present a novel model
 combining conventional viscoelastic elements with fractional calculus that
 successfully captures the macroscopic relaxation response of epithelial
 monolayers. The parameters extracted from the fitting of the relaxation
 modulus allow prediction of the response of the same material to slow
 stretch and creep, indicating that the model captured intrinsic material
 properties. Two characteristic times, derived from the model parameters,
 delimit different regimes in the materials response. We compared the
 response of tissues with the behaviour of single cells as well as intra
 and extra-cellular components, and linked the power-law behaviour of the
 epithelium to the dynamics of the cell cortex. Such a unified model for
 the mechanical response of biological materials provides a novel and
 robust mathematical approach to consistently analyze experimental data and
 uncover similarities and differences in reported behaviour across
 experimental methods and research groups. It also sets the foundations for
 more accurate computational models of tissues mechanics.
description: Slow_StretchTime - Stress - Strain data of the slow stretch experiments.Ramp_stretch.xlsxCreepFile containing the creep response of epithelial monolayers for two different applied stresses.
DOI: 10.5061/dryad.8b876q6
title: Data from: Migratory passage structures at hydropower plants as potential physiological and behavioural selective agents

description: Anthropogenic activities affect fish populations worldwide. River dams
 have profound impacts on ecosystems by changing habitats and hindering
 migration. In an effort to counteract such effects a diversity of
 mitigation measures has been installed at hydroelectric power plants.
 Still, not all individuals in a population use these measures, creating
 potentially strong selection processes at hydroelectric power plants.
 Especially, during migration, when fish can get heavily delayed or pass
 through a hydropower turbine, facing increased mortality compared to those
 using a safe bypass route. In this study, we quantify migration route
 choices of descending wild PIT-tagged Atlantic salmon smolts released
 upstream from a hydroelectric plant. We demonstrate how only a few meters’
 displacement of bypass canals can have a large impact on the fish guidance
 efficiency. The proportion of fish using the bypasses increased when water
 was released in surface gates closer to the turbine intake. During a
 period of low fish guidance efficiency, we observed two different smolt
 migratory strategies. While some individuals spent little time in the
 forebay before migrating through the turbine tunnel, others remained in
 the forebay. We suggest that these groups represent different behavioural
 types, and that sub-optimal mitigation measures at hydropower intakes may
 therefore induce strong selection on salmon behavioural traits. The
 ultimate outcome of these selection mechanisms is discussed in light of
 potential trade-offs between turbine-migration mortality costs and optimal
 sea-entrance timing survival benefits.
description: R
 scriptumerk.rstCatches of Atlantic salmon in River RST-trapsall.pit.dataMark recapture data. PIT-tagged Atlantic salmon smoltsFGEdistFish guidance efficiency vs. distance to turbinetime2event.dataData for time-to-event analysis
DOI: 10.5281/zenodo.18393087
title: weecology/EvergladesWadingBird: 3.2.0

description: v3.2.0
DOI: 10.5061/dryad.mb004d1
title: Data from: High fat diet induces microbiota-dependent silencing of enteroendocrine cells

description: Enteroendocrine cells (EECs) are specialized
 sensory cells in the intestinal epithelium that sense
 and transduce nutrient information. Consumption of
 dietary fat contributes to metabolic disorders, but EEC
 adaptations to high fat feeding were unknown.
 Here, we established a new experimental system to directly investigate EEC
 activity in vivo using a zebrafish reporter of EEC calcium signaling. Our
 results reveal that high fat feeding alters EEC
 morphology and converts them into a nutrient insensitive state that is
 coupled to endoplasmic reticulum (ER) stress. We called this novel
 adaptation 'EEC silencing'. Gnotobiotic studies
 revealed that germ-free zebrafish are resistant
 to high fat diet induced
 EEC silencing. High fat feeding
 altered gut microbiota composition including enrichment
 of Acinetobacter species, and we identified
 an Acinetobacter strain sufficient to induce
 EEC silencing. These results establish a new mechanism by which
 dietary fat and
 gut microbiota modulate EEC nutrient sensing and
 signaling.
description: Source data for
 "High fat diet induces microbiota-dependent silencing of
 enteroendocrine cells" Source data for
 Fig1-9 and Fig2-figure supplement 1 Source data.zip
DOI: 10.5061/dryad.1t61c80
title: Auditory cortex shapes sounds responses in the inferior colliculus

description: The extensive feedback from the auditory cortex (AC) to the inferior
 colliculus (IC) supports critical aspects of auditory behavior, but has
 not been extensively characterized. Previous studies demonstrated that
 activity in IC is altered by focal electrical stimulation and
 pharmacological inactivation of AC, but these methods lack the ability to
 selectively manipulate projection neurons. We measured the effects of
 selective optogenetic modulation of cortico-collicular feedback
 projections on IC sound responses in mice. Activation of feedback
 increased spontaneous activity and decreased stimulus selectivity in IC,
 whereas suppression had no effect. To further understand how microcircuits
 in AC may control collicular activity, we optogenetically modulated
 different cortical neuronal subtypes, specifically parvalbumin-positive
 (PV) and somatostatin-positive (SOM) inhibitory interneurons. We found
 that modulating either type of interneuron did not affect IC sound-evoked
 activity. Combined, our results identify that activation of excitatory
 projections, but not inhibition-driven increases in cortical activity,
 affects collicular sound responses.
description: Blackwell2019The file contains the spike time data and the code to create the figures in the manuscript.
DOI: 10.5061/dryad.978406n
title: Data from: Nanometer-scale structure differences in the myofilament lattice spacing of two cockroach leg muscles correspond to their different functions

description: Muscle is highly organized across multiple length scales. Consequently,
 small changes in the arrangement of myofilaments can influence macroscopic
 mechanical function. Two leg muscles of a cockroach, have identical
 innervation, mass, twitch responses, length-tension curves, and
 force-velocity relationships. However, during running, one muscle is
 dissipative (a "brake"), while the other dissipates and produces
 significant positive mechanical work (bifunctional). Using time resolved
 x-ray diffraction in intact, contracting muscle, we simultaneously
 measured the myofilament lattice spacing, packing structure, and
 macroscopic force production of these muscle to test if structural
 differences in the myofilament lattice might correspond to the
 muscles' different mechanical functions. While the packing patterns
 are the same, one muscle has 1 nm smaller lattice spacing at rest. Under
 isometric activation, the difference in lattice spacing disappeared
 consistent with the two muscles' identical steady state behavior.
 During periodic contractions, one muscle undergoes a 1 nm greater change
 in lattice spacing, which correlates with force. This is the first
 identified structural feature in the myofilament lattice of these two
 muscles that shares their whole muscle dynamic differences and steady
 state similarities.
description: X-ray diffraction data during work loops and isometric twitches
 of Blaberus discoidalis X-ray diffraction can be used
 to measure the myofilament lattice spacing of muscle. We measured the
 lattice spacing of two leg muscles from Blaberus discoidalis (cockroach)
 under sinusoidally driven, periodically activated strain trajectories
 (work loop) and isometric twitches. X-ray diffraction images have been
 analysed and compiled into two Matlab structures, along with force and
 length. d10_blaberus_discoidalis.mat
DOI: 10.5061/dryad.8v6j202
title: Phylogeny and floral character evolution of Mentzelia section Bicuspidaria (Loasaceae)

description: Mentzelia section Bicuspidaria (Loasaceae) is a monophyletic group of
 desert ephemerals that inhabit the complex, heterogeneous landscapes of
 the southwestern United States and northwestern Mexico. To investigate
 species circumscriptions and evolutionary relationships in Bicuspidaria,
 we employed phylogeny reconstructions based on DNA sequences from the
 plastid trnL-trnF, trnS-trnfM, ndhF-rpl32, and rpl32-trnL regions and the
 nuclear ribosomal ITS and ETS regions. Due to evidence of discordant
 relationships reconstructed from the plastid and nuclear partitions, we
 used coalescent-based methods in addition to concatenated data sets to
 estimate the species tree. Maximum likelihood reconstructions based on the
 combined plastid and nuclear data and coalescent-based reconstructions
 inferred congruent, fully-resolved species-level phylogenies of section
 Bicuspidaria. A monophyletic section Bicuspidaria was composed of two main
 clades, which corresponded to a clade of species endemic to the United
 States composed of M. reflexa, M. tricuspis, and M. tridentata that was
 sister to a clade of species at least partially distributed in Mexico,
 composed of M. hirsutissima and M. involucrata. Despite the unusual floral
 morphology of M. reflexa, molecular reconstructions placed M. reflexa
 sister to M. tridentata. All species of Bicuspidaria were monophyletic,
 except for M. hirsutissima, which was composed of two distinct lineages
 and paraphyletic with respect to M. involucrata. The northern clade of M.
 hirsutissima from California and Baja California was sister to M.
 involucrata, and both, in turn, were sister to a geographically disjunct
 southern clade of M. hirsutissima from Baja California Sur and Cedros
 Island. These phylogeny reconstructions provide evidence for the inclusion
 of five species in section Bicuspidaria and have uncovered cryptic
 diversity that has been largely unrecognized. Character state
 reconstructions based on the phylogeny of section Bicuspidaria suggest
 innovative and, at times, homoplasious floral evolution.
description: DNA Sequence
 AlignmentsDNA sequence alignments
 used in all phylogeny reconstructions in this article.Supplement
 FiguresFigures S1-S4 cited in
 the article.ML
 TreesML Trees reconstructed
 in this article.NJ
 TreesNJ trees reconstructed
 in this article.*BEAST-Run1Trees generated during the 1st *Beast run.BicuspStarBEASTRun1.zip*BEAST-Run2Trees generated in the 2nd run of *BeastBicuspStarBEASTRun2.zip*BEAST .xml fileBicuspStarBEAST.xml
DOI: 10.5061/dryad.307cm0h
title: Data from: Genome-wide association mapping of resistance to Septoria nodorum leaf blotch in a Nordic spring wheat collection

description: Parastagonospora nodorum is the causal agent of septoria nodorum blotch
 (SNB) in wheat. It is the most important leaf blotch pathogen in Norwegian
 spring wheat. Several quantitative trait loci (QTL) for SNB susceptibility
 have been identified. Some of these QTL are the result of underlying
 gene-for-gene interactions involving necrotrophic effectors (NEs) and
 corresponding sensitivity (Snn) genes. A collection of diverse spring
 wheat lines was evaluated for SNB resistance/susceptibility over seven
 growing seasons in the field. In addition, wheat seedlings were inoculated
 and infiltrated with culture filtrates (CFs) from four single spore
 isolates and infiltrated with semi-purified NEs (SnToxA, SnTox1 and
 SnTox3) under greenhouse conditions. In adult plants, the most stable SNB
 resistance QTL were located on 2B, 2D, 4A, 4B, 5A, 6B, 7A and 7B. The QTL
 on 2D was effective most years in the field. At the seedling stage, the
 most significant QTL after inoculation were located on 1A, 1B, 3A, 4B, 5B,
 6B, 7A and 7B. The QTL on 3A and 6B were significant both after
 inoculation and CF infiltration, indicating the presence of novel NE-Snn
 interactions. The QTL on 4B and 7A were significant in both seedlings and
 adult plants. Correlations between SnToxA sensitivity and disease severity
 in the field were significant. To our knowledge, this is the first genome
 wide association mapping study (GWAS) to investigate SNB resistance at the
 adult plant stage under field conditions.
description: Genotype data and
 population structure used for GWASIllumina iSelect 90K SNP
 marker data on the MASBASIS spring wheat collection as well as the
 population structure used for GWAS.Ruud et al GWAS - Genotype
 data.xlsxPhenotype data for
 GWASAll the phenotypic data
 on the MASBASIS spring wheat collection used for the GWAS. Including field
 data, necrotrophic effector (NE) infiltrations, culture filtrate
 infiltrations and seedling inoculations.Ruud et al GWAS - Phenotype
 data.xlsx
DOI: 10.7272/q6z60kzd
title: SIVD (Subcortical Ischemic Vascular Dementia)

description: The overall goal of this project was to determine the extent to which
 subcortical ischemia and infaraction, and Alzheimer's disease,
 contribute to dementia. This project aimed to provide a greater
 understanding of the pathogenesis of dementia in patients with SIVD and
 AD.
description: Data were acquired at several sites: ABS = Aging Brain San
 Francisco (SFVAMC), ABD = Aging Brain UC Davis, and ABL = Aging Brain Los
 Angeles (USC).
DOI: 10.5061/dryad.t9d744k
title: Data from: Knowing when to stick: touch receptors found in the remora adhesive disc

description: Remoras are fishes that piggyback onto larger marine fauna via an adhesive
 disc to increase locomotor efficiency, likelihood of finding mates, and
 access to prey. Attaching rapidly to a large, fast moving host is no easy
 task, and while research to date has focused on how the disc supports
 adhesion, no attention has been paid to how or if remoras are able to
 sense attachment. We identified push-rod-like mechanoreceptor complexes
 embedded in the soft lip of the remora adhesive disc that are known in
 other organisms to respond to touch and shear forces. This is the first
 time such mechanoreceptor complexes are described in fishes as they were
 only known previously in monotremes. Presence of push-rod-like
 mechanoreceptor complexes suggests not only that fishes may be able to
 sense their environment in ways not heretofore described, but that
 specialized tactile mechanoreceptor complexes may be a more basal
 vertebrate feature than previously thought.
description: Knowing when to stick:
 touch receptors found in the remora adhesive disc microCT scan of
 PTA-stained remora lip   RSOS lip
 data_DCM.zip
DOI: 10.5061/dryad.m88gq46
title: Data from: Fear effects associated with predator presence and habitat structure interact to alter herbivory on coral reefs

description: Non-consumptive fear effects are an important determinant of foraging
 decisions by consumers across a range of ecosystems. However, how fear
 effects associated with the presence of predators interact with those
 associated with habitat structure remains unclear. Here, we used predator
 fish models (Plectropomus leopardus) and experimental patches of the
 macroalga Sargassum ilicifolium of varying densities to investigate how
 predator- and habitat-associated fear effects influence herbivory on coral
 reefs. We found the removal of macroalgal biomass (i.e., herbivory) was
 shaped by the interaction between predator- and habitat-associated fear
 effects. Rates of macroalgal removal declined with increasing macroalgal
 density likely due to increased visual occlusion by denser macroalgae
 patches and reduced ability of herbivorous fishes to detect the predators.
 The presence of the predator model reduced herbivory within low macroalgal
 density plots, but not within medium and high density macroalgal plots.
 Our results suggest that fear effects due to predator presence were
 greatest at low macroalgal density, yet these effects were lost at higher
 densities possibly due to greater predation risk associated with habitat
 structure and/or the inability of herbivorous fishes to detect the
 predator model.
description: Final removal data of
 Sargassum assays from Singapore coral reefsSummary of removal data
 of Sargassum ilicifolium assays in high, medium and low densities in the
 presence of predator models and object controls. Data file was created in
 Microsoft Excel and the column headings are as follows: i.weight is
 initial weight, f.weight is final weight, diff is difference between
 initial and final weight, diff.con is difference minus the controls, and
 per.diff is percent difference.final_removal_data.csvFinal fish bite count data of Sargassum assays from Singapore coral reefsSummary of fish bite count data from Sargassum ilicifolium assays in high, medium and low densities in the presence of predator models and object controls. Data file was created in Microsoft Excel and the column headings are as follows: sum.mass.std is sum of mass-standarized bites and meanbites is mean number of bites.final_bitecount_data.csvFinal herbivorous fish species bitecount data of Sargassum assays on Singapore coral reefsSummary of individual herbivorous fish species bite count data from Sargassum ilicifolium assays in high, medium and low densities in the presence of predator models and object controls. Data file was created in Microsoft Excel and the column headings are as follows: tl.bites is total bites and mass.std is mass-standarized bites.final_species_bitecount_data.csvFinal R scriptFinal R script for Sargassum ilicifolium assays removal, total fish bite counts, and individual herbivorous fish species in presence of predator models and object controls. Data file was created in R version 3.4.3.final r script.R
DOI: 10.5061/dryad.6fq3qv7
title: Data from: Competition and specialization in an African forest carnivore community

description: Globally, human activities have led to the impoverishment of species
 assemblages and the disruption of ecosystem function. Determining whether
 this poses a threat to future ecosystem stability necessitates a thorough
 understanding of mechanisms underpinning community assembly and niche
 selection. Here, we tested for niche segregation within an African small
 carnivore community in Kibale National Park, Uganda. We used occupancy
 modelling based on systematic camera trap surveys and fine-scale habitat
 measures, to identify opposing preferences between closely related species
 (cats, genets and mongooses). We modelled diel activity patterns using
 kernel density functions, and calculated the overlap of activity periods
 between related species. We also used co-occupancy modelling and activity
 overlap analyses to test whether African golden cats Caracal aurata
 influenced the smaller carnivores along the spatial and/or temporal axes.
 There was some evidence that related species segregated habitat and
 activity patterns. Specialisation was particularly strong among forest
 species. The cats and genets partitioned habitat, while the mongooses
 partitioned both habitat and activity period. We found little evidence for
 interference competition between African golden cats and other small
 carnivores, although weak interference competition was suggested by lower
 detection probabilities of some species at stations where African golden
 cats were present. This suggests that community assemblage and
 co-existence in this ecosystem are primarily driven by more complex
 processes. The studied carnivore community contains several forest
 specialists, which are typically more prone to localised extinction.
 Preserving the observed community assembly will therefore require the
 maintenance of a large variety of habitats, with a particular focus on
 those required by the more specialised carnivores.
description: Mills_UG_2010–2014_camera_trap_detectionsAll detections of all carnivores and three golden cat prey species during 9 camera trap surveys in Kibale National Park and Maramagambo Forest, Uganda in 2010–2014.Mills_UG_2010–2014_camera station placement dataCamera placement information for 9 camera trap surveys in Kibale National Park and Maramagambo Forest, Uganda in 2010–2014.Mills_UG_2010–2014_camera station trapfunctionFunction of all camera stations during 9 camera trap surveys in Kibale National Park and Maramagambo Forest, Uganda in 2010–2014.Mills_UG_2010–2014_camera station vegetation dataVegetation measures collected in 30 m X 30 m plots established around camera stations during 9 camera trap surveys in Kibale National Park and Maramagambo Forest, Uganda in 2010–2014. The camera was at the centre and the corners of the plot faced the cardinal compass directions.
DOI: 10.5061/dryad.6552r2b
title: Data from: Imaging markers of small vessel disease and ‘brain frailty’ and outcomes in acute stroke

description: Objective: We assessed the association of baseline imaging markers of
 cerebral small vessel disease (SVD) and ‘brain frailty’ with clinical
 outcome after acute stroke in the Efficacy of Nitric Oxide in Stroke
 (ENOS) trial. Methods: ENOS randomised 4011 patients with acute stroke
 (&lt;48 hours of onset) to transdermal glyceryl trinitrate (GTN) or no
 GTN for 7 days. The primary outcome was functional outcome (modified
 Rankin Scale, mRS) at day 90. Cognition was assessed via telephone at day
 90. Stroke syndrome was classified using the Oxfordshire Community Stroke
 Project classification. Brain imaging was adjudicated masked to clinical
 information and treatment, and assessed SVD (leukoaraiosis, old lacunar
 infarcts/lacunes, atrophy) and ‘brain frailty’ (leukoaraiosis, atrophy,
 old vascular lesions/infarcts). Analyses used ordinal logistic regression
 adjusted for prognostic variables. Results: In all participants and those
 with lacunar syndromes (LACS, 1397, 34.8%), baseline CT imaging features
 of SVD and ‘brain frailty’ were common and independently associated with
 unfavourable shifts in mRS at day 90: all participants (SVD score OR 1.15,
 95% CI 1.07-1.24; ‘brain frailty’ score OR 1.25, 95% CI 1.17-1.34); those
 with LACS (SVD score OR 1.30, 95% CI 1.15-1.47; ‘brain frailty’ score OR
 1.28, 95% CI 1.14-1.44). ‘Brain frailty’ was associated with worse
 cognitive scores at 90 days in all and in LACS participants. Conclusions:
 Baseline imaging features of SVD and ‘brain frailty’ were common in
 lacunar stroke and all stroke, predicted worse prognosis after all acute
 stroke with a stronger effect in lacunar stroke, and may aid future
 clinical decision-making. Registration: ISRCTN99414122.
description: Imaging markers of small
 vessel disease and ‘brain frailty’ and outcomes in acute stroke
 supplementary material 20190603Imaging markers of small
 vessel disease and ‘brain frailty’ and outcomes in acute stroke
 supplementary material including additional tables and
 figures.ENOS LACS SVD supplementary
 material 20190603.pdf