cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gtht76hhb
title: Pectoral fin kinematics and motor patterns are shaped by fin ray mechanosensation during steady swimming in Scarus quoyi

description: For many species of fish, rhythmic movement of the pectoral fins, or
 forelimbs, drives locomotion. In terrestrial vertebrates, normal limb-
 based rhythmic gaits require ongoing modulation with limb mechanosensors.
 Given the complexity of the fluid environment and dexterity of fish
 swimming through it, we hypothesize that mechanosensory modulation is also
 critical to normal fin-based swimming. Here, we examined the role of
 sensory feedback from the pectoral fin rays and membrane on the
 neuromuscular control and kinematics of pectoral fin-based locomotion.
 Pectoral fin kinematics and electromyograms of the six major fin muscles
 of the parrotfish, Scarus quoyi, a high-performance pectoral fin swimmer,
 were recorded during steady swimming before and after bilateral
 transection of the sensory nerves extending into the rays and surrounding
 membrane. Alternating activity of antagonistic muscles was observed and
 drove the fin in a figure-of-eight fin stroke trajectory before and after
 nerve transection. After bilateral transections, pectoral fin rhythmicity
 remained the same or increased. Differences in fin kinematics with the
 loss of sensory feedback also included fin kinematics with a significantly
 more inclined stroke plane angle, an increased angular velocity and fin
 beat frequency, and a transition to the body-caudal fin gait at lower
 speeds. After transection, muscles were active over a larger proportion of
 the fin stroke, with overlapping activation of antagonistic muscles rarely
 observed in the trials of intact fish. The increased overlap of
 antagonistic muscle activity might stiffen the fin system in order to
 enhance control and stability in the absence of sensory feedback from the
 fin rays. These results indicate that fin ray sensation is not necessary
 to generate the underlying rhythm of fin movement, but contributes to the
 specification of pectoral fin motor pattern and movement during rhythmic
 swimming.  
description: EMG electrodes were inserted into each muscle and the fish were
 swam in a flow tank at a speed of 2 body lengths per second.
 All other relevant information on data collection can be found in
 the materials and methods section of the manuscript.
description: All code neccessary to analyze 3D kinemtics data is included in
 the "R functions.R" file. The raw data to
 begin this process and re-generate all subsequent files in this data set
 is file: Raw motion data.csv. All other kinematic data
 files can be reproduced using the R code file and this raw motion data
 file, but are also included in the data set for easy reference.
DOI: 10.5061/dryad.wm37pvmhz
title: A non-vector herbivore indirectly increases the transmission of a vector-borne virus by reducing plant chemical defenses

description: Vectors and viruses exist in communities consisting of many interacting
 species. Although the cascading effects of predators or parasitoids on
 disease spread via direct effects on vectors have been investigated,
 little is known about the effects of other free-living species in
 communities on the transmission of vector-borne viruses via indirect
 (host-plant mediated) effects on vectors. In the present study, we used a
 food web consisting of tomato plants (Solanum lycopersicum), two tomato
 herbivores (the vector whitefly, Bemisia tabaci, and the non-vector
 two-spotted spider mite, Tetranychus urticae), and a whitefly-vectored
 plant virus (Tomato yellow leaf curl virus, TYLCV) to study how T. urticae
 may affect TYLCV transmission by B. tabaci via host-plant mediated effects
 on B. tabaci. We found that T. urticae infestation promoted B. tabaci
 feeding and thereby increased TYLCV transmission to tomato plants. These
 increases were associated with T. urticae-induced reductions in two
 flavonoids (rutin and quercetin trisaccharide) of tomato plants. Elevation
 of rutin and quercetin trisaccharide levels in T. urticae-infested plants
 via exogenous stem applications reduced B. tabaci feeding and TYLCV
 transmission. Therefore, suppression of these flavonoids by T. urticae
 infestation was the most likely explanation for the observed changes in B.
 tabaci feeding behavior and TYLCV transmission. Our results show that by
 reducing flavonoids in tomato plants, a non-vector herbivore can
 indirectly increase the transmission of a vector-borne plant virus. These
 findings indicate that species that are far removed from the direct
 vector–virus interactions can indirectly affect vector–borne virus
 transmission by altering the chemical defenses of the shared host plant.
description: Spreadsheet contains tabs with data for Figures 1-3 and S1-S4
 from the article https://doi.org/10.1111/1365-2435.13535
DOI: 10.5061/dryad.kwh70rz0k
title: Mind the gap: natural cleft palates reduce biting performance in bats

description: Novel morphological traits pose interesting evolutionary paradoxes when
 they become widespread in a lineage while being deleterious in others.
 Cleft palate is a rare congenital condition in mammals in which the
 incisor-bearing premaxilla bones of the upper jaw develop abnormally.
 However, ∼50% of bat species have natural, nonpathological cleft palates.
 We used the family Vespertilionidae as a model and linear and geometric
 morphometrics within a phylogenetic framework to (1) explore evolutionary
 patterns in cleft morphology, and (2) test whether cleft morphological
 variation is correlated with skull shape in bats. We also used finite
 element (FE) analyses to experimentally test how presence of a cleft
 palate impacts skull performance during biting in a species with extreme
 cleft morphology (hoary bat, Lasiurus cinereus). We constructed and
 compared the performance of two FE models: one based on the hoary bat’s
 natural skull morphology, and another with a digitally filled cleft
 simulating a complete premaxilla. Results showed that cleft length and
 width are correlated with skull shape in Vespertilionidae, with narrower,
 shallower clefts seen in more gracile skulls and broader, deeper clefts in
 more robust skulls. FE analysis showed that the model with a natural cleft
 produced lower bite forces, and had higher stress and strain than the
 model with a filled cleft. In the rostrum, safety factors were 1.59–2.20
 times higher in the model with a filled cleft than in the natural model.
 Our results demonstrate that cleft palates in bats reduce biting
 performance, and evolution of skull robusticity may compensate for this
 reduction in performance.
DOI: 10.5061/dryad.rn8pk0p5z
title: Data for: Evaluating the impact of physical frailty during ageing in wild chimpanzees (Pan troglodytes schweinfurthii)

description: While declining physical performance is an expected consequence of aging,
 human clinical research has placed increasing emphasis on physical frailty
 as a predictor of death and disability in the elderly. We examined
 non-invasive measures approximating frailty in a richly-sampled
 longitudinal dataset on wild chimpanzees. Using urinary creatinine to
 assess lean body mass, we demonstrated moderate but significant declines
 in physical condition with age in both sexes. While older chimpanzees
 spent less of their day in the trees and feeding, they did not alter
 activity budgets with respect to travel or resting. There was little
 evidence that declining lean body mass had negative consequences
 independent of age. Old chimpanzees with poor lean body mass rested more
 often but did not otherwise differ in activity. Males, but not females, in
 poor condition were more likely to exhibit respiratory illness. Poor
 muscle mass was associated acutely with death in males, but it did not
 predict future mortality in either sex. While there may be some reasons to
 suspect biological differences in the susceptibility to frailty in
 chimpanzees versus humans, our data are consistent with recent reports
 from humans that lean, physically active individuals can successfully
 combat frailty.
DOI: 10.5061/dryad.x95x69pdt
title: Data from: Large-scale metabarcoding analysis of epipelagic and mesopelagic copepods in the Pacific

description: A clear insight into large-scale community structure of planktonic
 copepods is critical to understanding mechanisms controlling diversity and
 biogeography of marine taxa, owing to their high abundance, ubiquity, and
 sensitivity to environmental changes. Here, we applied a 28S metabarcoding
 approach to large-scale communities of epipelagic and mesopelagic copepods
 at 70 stations across the Pacific Ocean and three stations in the Arctic
 Ocean. Major patterns of community structure and diversity, influenced by
 water mass structures, agreed with results from previous morphology-based
 studies. However, large-scale metabarcoding approach could detected
 community changes even under stable environmental conditions, including
 changes in the north/south subtropical gyres and east/west areas within
 each subtropical gyre. There were strong effects of epipelagic environment
 on mesopelagic communities, and community subdivisions were observed in
 the environmentally-stable mesopelagic layer. In each sampling station,
 higher operational taxonomic unit (OTU) numbers and lower phylogenetic
 diversity were observed in the mesopelagic layer than in the epipelagic
 layer, indicating a recent rapid increase of species numbers in the
 mesopelagic layer. The phylogenetic analysis utilizing representative
 sequences of OTUs revealed trends of recent emergence of cold-water OTUs
 mainly distributed at high latitudes with low water temperatures.
 Conversely, high diversity of copepods at low latitudes was suggested to
 have been formed through long evolutionary history under high water
 temperature. The metabarcoding results suggest that evolutionary processes
 have strong impacts on current patterns of copepod diversity, and support
 the “out of the tropics” theory explaining latitudinal diversity gradients
 of copepods. Both diversity patterns in epipelagic and mesopelagic showed
 high correlations to sea surface temperature; thus, predicted global
 warming may have a significant impact on copepod diversity in both
 layers.
DOI: 10.5061/dryad.0vt4b8gvj
title: Interaction of diet and habitat predicts Toxoplasma gondii infection rates in wild birds at a global scale

description: Aim: Free-ranging wildlife are valuable sentinels for zoonotic, multi-host
 pathogens, and novel insight on parasite transmission patterns is possible
 through a macroecological approach. Toxoplasma gondii is a protozoan
 capable of infecting all warm-blooded animals, including humans, primarily
 through a free-living oocyst and/or tissue cyst life-stage. Anthropogenic
 disturbance is facilitating the spread of T. gondii, making it critical to
 understand the general ecological and life history drivers of T. gondii
 infections in wild birds, which are important intermediate hosts. Our goal
 was to determine how habitat (terrestrial vs. aquatic), dietary trophic
 level and scavenging behaviour influence T. gondii infection prevalence in
 wild birds on a global scale. Location: Global Time period: 1952-2017
 Major taxa studied: Birds Methods: Our analysis used the serological,
 bioassay and molecular prevalence data of T. gondii in avian species
 compiled from 81 studies conducted worldwide and encompassing 24,344
 individuals from 393 avian species from 84 families. Results: We show that
 at a global scale, trophic level and habitat significantly interact to
 influence T. gondii prevalence in avian intermediate hosts. In the
 terrestrial environment, T. gondii prevalence increases with trophic
 level, consistent with predominant tissue cyst transmission. The highest
 prevalence was in terrestrial omnivores, which may reflect their
 synanthropic foraging behaviour. In aquatic species, prevalence was more
 consistent across trophic levels, but high prevalence in aquatic
 herbivores and insectivores reflects significant waterborne exposure to
 oocysts. Contrary to our predictions, generalized scavenging per se was
 not associated with increased prevalence. Main conclusions: This study
 highlights the value of comparing pathogen prevalence among multiple
 ecological guilds and ecosystem types for a comprehensive understanding of
 the epidemiology of generalist pathogens, such as T. gondii. Increased
 effort is needed to reduce T. gondii spillover from the domestic cat cycle
 into wildlife populations.
description: The dataset was collected through systematic review
DOI: 10.5061/dryad.7sqv9s4pj
title: Macroalgal blooms caused by marine nutrient changes resulting from human activities

description: 1. Macroalgal blooms (green tides) are occurring more frequently in many
 regions of the world, leading to significant impacts on marine ecology and
 economies. Although many studies and hypotheses have been proposed, the
 exact mechanism of green tide formation remains unclear. 2. The world’s
 largest green tides recur in the Yellow Sea and this area is
 representative for studying the origin and mechanism of green tide
 formation. We conducted a meta-analysis of studies related to green tides
 and associated hypotheses for their formation. 3. Rapid
 industrialization/urbanization and environmental protection actions in
 coastal zones have led to an increase in nitrate (nitrite) and decline in
 ammonium (ammonia), and this has resulted in increasing levels of
 dissolved inorganic nitrogen in seawater. 4. We found that presence of
 appropriate attachment substrates for Ulva including laver culture rafts
 and certain hydrological conditions are supplementary factors to green
 tide formation in the Yellow Sea. 5. Changes in marine nutrient levels
 promote the production of nitric oxide, which is essential for Ulva
 sporulation. Consequently, numerous spores are created and attach to
 substrates including laver culture rafts and parent Ulva thalli. These
 spores then develop into new thalli that are capable of producing further
 spores. As a result, Ulva thalli rapidly occupy vast areas of the sea and
 develop into green tides. 6. Synthesis and applications. Our synthesis
 identifies that escalating marine nitric oxide generation caused by
 various factors and its essential role in Ulva sporulation are underlying
 and significant components in the mechanism of green tide formation. We
 provide solutions such as the improvement of comprehensive management of
 aquaculture and strict restriction of marine nitrate pollution, to prevent
 green tides. Furthermore, we propose an innovative wastewater treatment
 programme combined with Ulva application to fulfil the standard of
 sustainable development and circular economy.
description: All data we collected are open-acess via internet.
DOI: 10.5061/dryad.8sf7m0chx
title: A new method to reconstruct quantitative food webs and nutrient flows from isotope tracer addition experiments

description: Understanding how nutrients flow through food webs is central in ecosystem
 ecology. Tracer addition experiments are powerful tools to reconstruct
 nutrient flows by adding an isotopically enriched element into an
 ecosystem, and tracking its fate through time. Historically, the design
 and analysis of tracer studies have varied widely, ranging from
 descriptive studies to modeling approaches of varying complexity.
 Increasingly, isotope tracer data is being used being used to compare
 ecosystems and analyze experimental manipulations. Currently, a formal
 statistical framework for analyzing such experiments is lacking, making it
 impossible to calculate the estimation errors associated with the model
 fit, the interdependence of compartments, or the uncertainty in the diet
 of consumers. In this paper we develop a method based on Bayesian Hidden
 Markov Models, and apply it to the analysis of $^{15}$N-NH$_4^+$ tracer
 additions in two Trinidadian streams in which light was experimentally
 manipulated. Through this case study, we illustrate how to estimate N
 fluxes between ecosystem compartments, turnover rates of N within those
 compartments and the associated uncertainty. We also show how the method
 can be used to compare alternative models of food web structure, calculate
 the error arround derived parameters, and make statistical comparisons
 between sites or treatments.
DOI: 10.5061/dryad.w3r2280m8
title: Stepwise construction of dynamic microscale concentration gradients around hydrogel-encapsulated cells in a microfluidic perfusion culture device

description: Inside living organisms, concentration gradients dynamically change as
 biological processes progress. Therefore, methods to construct dynamic
 microscale concentration gradients in a spatially controlled manner are
 needed to provide more realistic research environments. Here, we report a
 novel method for the construction of dynamic microscale concentration
 gradients in a stepwise manner around cells in micropatterned hydrogel. In
 our method, cells are encapsulated in a photodegradable hydrogel formed
 inside a microfluidic perfusion culture device, and perfusion
 microchannels are then fabricated in the hydrogel by micropatterned
 photodegradation. The cells in the micropatterned hydrogel can then be
 cultured by perfusing culture medium through the fabricated microchannels.
 By using this method, we demonstrate the simultaneous construction of two
 dynamic concentration gradients, which allowed us to expose the cells
 encapsulated in the hydrogel to a dynamic microenvironment.
DOI: 10.15468/dl.n8wxvj
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (c2ecae57-6701-485e-9ebd-5f87b2945cb2, f9b67ad0-9c9b-11d9-b9db-b8a03c50a862, 6ea87510-0561-11d8-b851-b8a03c50a862)",
 "TaxonKey is Melanoplus chiricahuae",
 "Year 1900-2026"
 ]
}

 The dataset includes 15 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002158-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dbrv15dxg
title: Pedigree-free quantitative genetic approach provides evidence for heritability of movement tactics in wild roe deer

description: Assessing the evolutionary potential of animal populations in the wild is
 crucial to understanding how they may respond to selection mediated by
 rapid environmental change (e.g. habitat loss and fragmentation). A
 growing number of studies have investigated the adaptive role of
 behaviour, but assessments of its genetic basis in a natural setting
 remain scarce. We combined intensive biologging technology with
 genome-wide data and a pedigree-free quantitative genetic approach to
 quantify repeatability, heritability and evolvability for a suite of
 behaviours related to the risk avoidance-resource acquisition trade-off in
 a wild roe deer (Capreolus capreolus) population inhabiting a
 heterogeneous, human-dominated landscape. These traits, linked to the
 stress response, movement and space-use behaviour, were all moderately to
 highly repeatable. Furthermore, the repeatable among-individual component
 of variation in these traits was partly due to additive genetic variance,
 with heritability estimates ranging from 0.19±0.07 to 0.71±0.11 and
 evolvability ranging from 1.1 to 4.3%. Changes in the trait mean can
 therefore occur under hypothetical directional selection over just a few
 generations. To the best of our knowledge, this is the first empirical
 demonstration of additive genetic variation in space-use behaviour in a
 free-ranging population based on genomic relatedness data. We conclude
 that wild animal populations may have the potential to adjust their
 spatial behaviour to human-driven environmental modifications through
 micro-evolutionary change.
DOI: 10.15139/s3/codh7f
title: Data Management and Sharing Plan for: Gut Microbial Enzymes and Human Disease

description: The Data Management and Sharing Plan describes the scientific data to be generated and/or used in the research and outlines a strategy for managing and sharing project data.
description: Data Management and Sharing Plan
DOI: 10.5061/dryad.cnp5hqc1x
title: Divalent cations bind to phosphoinositides to induce ion and isomer specific propensities for nano-cluster initiation in bilayer membranes

description: We report all-atom molecular dynamics simulations of physiologically
 composed asymmetric bilayers containing phosphoinositides in the presence
 of monovalent and divalent cations. We have characterized the molecular
 mechanism by which these divalent cations interact with phosphoinositides.
 Calcium desolvates more readily, consistent with single-molecule
 calculations, and forms a network of ionic-like bonds that serve as a
 "molecular glue'' that allows a single ion to coordinate
 with up to three phosphatidylinositol-(4,5)-bisphosphate lipids. The
 phosphatidylinositol-(3,5)-bisphosphate isomer shows no such effect and
 neither does PI(4,5)P2 in the presence of Mg. The resulting network of
 Ca-mediated lipid-lipid bonds grows to span the entire simulation space
 and therefore has implications for the lateral distribution of
 phosophoinositides in the bilayer. We observe context-specific differences
 in lipid diffusion rates, lipid surface densities, and bilayer structure.
 The molecular-scale delineation of ion-lipid arrangements reported here
 provides insight into similar nanocluster formation induced by peripheral
 proteins to regulate the formation of functional signaling complexes on
 the membrane.
description: GROMACS: we included the setup files
description: We are including a readme file, gromacs files for the
 simulation, two movies, and supplementary figures
DOI: 10.5061/dryad.15dv41nt8
title: Disease modifying therapy reduces the risk of disability in relapsing-remitting multiple sclerosis over 15 years

description: Objective: To test the hypothesis that immunotherapy prevents long-term
 disability in relapsing-remitting multiple sclerosis, we modelled
 disability outcomes in 14,717 patients. Methods: We studied patients from
 MSBase followed for ≥1 year, with ≥3 visits, ≥1 visit per year and exposed
 to a multiple sclerosis therapy, and a subset of patients with ≥15-year
 follow-up. Marginal structural models were used to compare the hazard of
 12-month confirmed increase and decrease in disability, EDSS step 6 and
 the incidence of relapses between treated and untreated periods. Marginal
 structural models were continuously re-adjusted for patient age, sex,
 pregnancy, date, disease course, time from first symptom, prior relapse
 history, disability and MRI activity. Results: 14,717 patients were
 studied. During the treated periods, patients were less likely to
 experience relapses (hazard ratio 0.60, 95% confidence interval 0.43-0.82,
 p=0.0016), worsening of disability (0.56, 0.38-0.82, p=0.0026) and
 progress to EDSS step 6 (0.33, 0.19-0.59, p=0.00019). Among 1085 patients
 with ≥15-year follow-up, the treated patients were less likely to
 experience relapses (0.59, 0.50-0.70, p=10-9) and worsening of disability
 (0.81, 0.67-0.99, p=0.043). Conclusions: Continued treatment with multiple
 sclerosis immunotherapies reduces disability accrual by 19-44% (95%CI
 1-62%), the risk of need of a walking aid by 67% (95%CI 41-81%) and the
 frequency of relapses by 40-41% (95%CI 18-57%) over 15 years. This study
 provides the evidence that disease modifying therapies are effective in
 improving disability outcomes in relapsing-remitting multiple sclerosis
 over the long-term. Classification of Evidence: This study provides class
 IV evidence that for patients with relapsing-remitting multiple sclerosis,
 long-term exposure to immunotherapy prevents neurological disability.