cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8931zcrmz
title: Data from: Shade trees preserve avian insectivore biodiversity on coffee farms in a warming climate

description: Includes a dataset of avian insectivore occurance data from 77 avian
 insectivores from 1970 to 2018 used in "Shade trees preserve avian
 insectivore biodiversity on coffee farms in a warming climate"
 downloaded from GBIF. Also included are full Maxent models and raster
 projections for the best selected model for each species for all climate
 scenarios, as well as a file on which threshold was selected for each
 species. Also included is all R code used to generate the
 results, coffee farm locations where bird richness was estimated, and
 iButton temperature files.
description: Code is uncommented.
DOI: 10.5061/dryad.gtht76hhz
title: Weed seedling images of species common to Manitoba, Canada

description: This dataset contains 34666 RGB-images taken from different angles and
 distances of weeds common in Manitoba. The imaged species common name,
 scientific name, and number of their images are: Echinochloa crus-galli
 Large Barnyard Grass 8621 Cirsium arvense Canada Thistle 4706 Brassica
 napus Volunteer Canola 6723 Taraxacum officinale Dandelion 4797 Persicaria
 spp. Smartweed 870 Fallopia convolvulus Wild Buckwheat 4165 Avena fatua
 Wild Oat 1218 Setaria pumila Yellow Foxtail 3566 Furthermore, this dataset
 contains a trained ResNet50 convolutional neural network model. It is
 trained to distinguish between monocots and dicots. A small collection of
 test datasets is included that can be used to measure the generalization
 capabilities of trained models. The single-plant dataset and all
 test-datasets are accompanied by a csv-file containing filenames with
 respective labels.
description: The data was collected by the EAGL-I system, an autonomous
 robotic platform that takes images and labels them. The
 plants are being placed in a volume that can be traversed by a camera on a
 robotic arm. Using the knowledge of the plant's position, the
 camera's position, and the label of the plant, the position of the
 plant in the image (in terms of pixels) can be calculated and thus a
 labeled bounding box created. This bounding box is cropped out to generate
 the single-plant images. The above dataset is the
 "minimal" dataset used to train the ML model included.<br>
 The original uncropped images and additional metadata on the images (such
 as camera-position and -orientation) are being planned to be made
 accessible. For details, please contact the creators listed above and/or
 follow updates on this dataset.
description: Citation: Cite the following article, when
 using this dataset or parts of it:
 @article{10.1371/journal.pone.0243923,<br>     doi =
 {10.1371/journal.pone.0243923},<br>     author = {Beck, Michael A.
 AND Liu, Chen-Yi AND Bidinosti, Christopher P. AND Henry, Christopher J.
 AND Godee, Cara M. AND Ajmani, Manisha},<br>     journal = {PLOS
 ONE},<br>     publisher = {Public Library of Science},<br>    
 title = {An embedded system for the automated generation of labeled plant
 images to enable machine learning applications in agriculture},<br>
     year = {2020},<br>     month = {12},<br>     volume =
 {15},<br>     url =
 {https://doi.org/10.1371/journal.pone.0243923},<br>     pages =
 {1-23}<br> }   Bugs:
 In some folders the first master-image was incorrectly captured
 (the camera did not pan into position). Thus, not showing the plants that
 are suppossed to be showing. This only affected the first image taken in
 that folder. All other images in that folders are still correctly labeled.
 The folders containing that bug are: 20200312, 20200316, 20200318,
 20200401, 20200406, 20200407.
DOI: 10.5061/dryad.tht76hdwp
title: Sarcomere length non-uniformities dictate force production along the descending limb of the force-length relation

description: The force-length relation is one of the most defining features of the
 sliding filament theory of muscle contraction, and yet a topic of debate
 in the literature. The force-length relation predicts that the force
 produced by muscle fibers is directly proportional to the degree of
 overlap between myosin and actin filaments, but several studies have shown
 forces that are larger than predicted, especially at long sarcomere
 lengths. The reason for such discrepancies may be due to technical
 difficulties – studies have been conducted with muscle fibers, a
 preparation containing thousands of sarcomeres that makes accurate length
 measurements challanging. The aim of this study was to directly evaluate
 force production and sarcomere dynamics in isolated myofibrils and single
 sarcomeres to enhance our understanding about mechanisms governing
 deviations from the theoretically predicted force-length relation.
 Contractions at varying sarcomere lengths (SLs) along the plateau
 (SL=2.25m-2.39m) and the descending limb (SL&gt;2.39m) of the
 force-length relation were induced by solution switching, and different
 modes of force measurements were used. Our results show that single
 sarcomeres and extrapolated forces resemble the theoretical force-length
 relation closely, while myofibrils with sarcomere length dispersions show
 an extension of the plateau region and forces elevated above predicted
 levels. We also found an increase in sarcomere length non-uniformity and
 slowed rate of force production at long lengths in myofibrils with
 sarcomeres in series but not in single sarcomere preparations. We conclude
 that the deviation of the descending limb of the force-length relation
 obtained from plateau forces is correlated with the degree of sarcomere
 length non-uniformity and slowed force development.
description: Two needles were tracked during experiments and their
 displacement was measured using Fiji software. The needle tracks (.xls) of
 the video analysis are provided as well as sheets for further analysis
 (macro and R code file). The needle stiffness was measured by the
 cross-bending method as described in the manuscript. 
  
description: In each xls file a single track of displacement of one needle is
 found for further calculation of total displacement of two
 needles. Given displacement, force can be calculated as
 follows: F = delta(displacement) * stiffness
DOI: 10.5061/dryad.63xsj3v0m
title: Vertebral pneumaticity is correlated with serial variation in vertebral shape in storks

description: Birds and their ornithodiran ancestors are unique among vertebrates in
 exhibiting air-filled sinuses in their postcranial bones, a phenomenon
 called postcranial skeletal pneumaticity. The factors that account for
 serial and interspecific variation in postcranial skeletal pneumaticity
 are poorly understood, although body size, ecology, and bone biomechanics
 have all been implicated as influencing the extent to which pneumatizing
 epithelia invade the skeleton and induce bone resorption. Here, I use
 high-resolution computed-tomography to holistically quantify vertebral
 pneumaticity in members of the neognath family Ciconiidae (storks), with
 pneumaticity measured as the relative volume of internal air space. These
 data are used to describe serial variation in extent of pneumaticity and
 to assess whether and how pneumaticity varies with the size and shape of a
 vertebra. Pneumaticity increases dramatically from the middle of the neck
 onwards, contrary to previous predictions that cervical pneumaticity
 should decrease towards the thorax to maintain structural integrity as the
 mass and bending moments of the neck increase. Although the largest
 vertebrae sampled are also the most pneumatic, vertebral size cannot on
 its own account for serial or interspecific variation in extent of
 pneumaticity. Vertebral shape, as quantified by three-dimensional
 geometric morphometrics, is found to be significantly correlated with
 extent of pneumaticity, with elongate vertebrae being less pneumatic than
 craniocaudally short and dorsoventrally tall vertebrae. Considered
 together, the results of this study are consistent with the hypothesis
 that shape- and position-specific biomechanics influence the amount of
 bone loss that can be safely tolerated. These results have potentially
 important implications for the evolution of vertebral morphology in birds
 and their extinct relatives.
description: Code and explanatory text for all analyses are included in the
 file, <em>Stork_Pneumaticity_and_Shape,FINAL.Rmd</em>.
DOI: 10.5061/dryad.crjdfn320
title: Variation in the strength of allometry drives rates of evolution in primate brain shape - Supplementary Material

description: Large brains are a defining feature of primates, as is a clear allometric
 trend between body mass and brain size. However, important questions on
 the macroevolution of brain shape in primates remain unanswered. Here we
 address two: (i), does the relationship between the brain size and its
 shape follow allometric trends and (ii), is this relationship consistent
 over evolutionary time? We employ three-dimensional geometric
 morphometrics and phylogenetic comparative methods to answer these
 questions, based on a large sample representing 151 species and most
 primate families. We found two distinct trends regarding the relationship
 between brain shape and brain size. Hominoidea and Cercopithecinae showed
 significant evolutionary allometry, whereas no allometric trends were
 discernible for Strepsirrhini, Colobinae or Platyrrhini. Furthermore,we
 found that in the taxa characterized by significant allometry, brain shape
 evolution accelerated, whereas for taxa in which such allometrywas absent,
 the evolution of brain shape decelerated.We conclude that although
 primates in general are typically described as largebrained, strong
 allometric effects on brain shape are largely confined to the order’s
 representatives that display more complex behavioural repertoires.
DOI: 10.5061/dryad.rjdfn2z7p
title: Data from: Landscape does matter: disentangling founder effects from natural and human-aided post-introduction dispersal during an ongoing biological invasion

description: Environmental features impacting the spread of invasive species after
 introduction can be assessed using population genetic structure as a
 quantitative estimation of effective dispersal at the landscape scale.
 However, in the case of an ongoing biological invasion, deciphering
 whether genetic structure represents landscape connectivity or founder
 effects is particularly challenging. We examined the modes of dispersal
 (natural and human-aided) and the factors (landscape or founders history)
 shaping genetic structure in range edge invasive populations of the Asian
 tiger mosquito, Aedes albopictus, in the region of Grenoble (Southeast
 France). Based on detailed occupancy-detection data and
 environmental variables (climatic, topographic, land-cover), we modelled
 A. albopictus potential suitable area and its expansion history since
 first introduction. The relative role of dispersal modes was estimated
 using biological dispersal capabilities and landscape genetics approaches
 using genome-wide SNP dataset. We demonstrate that both natural
 and human-aided dispersal have promoted the expansion of populations.
 Populations in diffuse urban areas, representing highly suitable habitat
 for A. albopictus, tend to disperse less, while roads facilitate
 long-distance dispersal. Yet demographic bottlenecks during introduction
 played a major role in shaping the genetic variability of these range edge
 populations. The present study is one of the few investigating
 the role of founder effects and ongoing expansion processes in shaping
 spatial patterns of genetic variation in an invasive species at the
 landscape scale. The combination of several dispersal modes and large
 proportions of continuous suitable habitats for A. albopictus promoted
 range filling of almost its entire potential distribution in the region of
 Grenoble only few years after introduction.
description: The data comprise two SNP datasets obtained from double digest
 restriction associated DNA sequencing (ddRADseq): -
 Dataset 1 (1,112 SNPs; 411 individuals) used for inferring the origin of
 <em>Aedes albopictus</em> invasive populations in the region
 of Grenoble, France (ABC reconstruction of colonization routes)
 - Dataset 2 (1,960 SNPs; 269 individuals) used for
 identiyfing the geographical and landscape features impacting population
 connectivity The datasets are in VCF format. The
 position (CHROM), loci (LOCI ID), position (POS), reference allele (REF)
 and alternative allele (ALT) are given for each SNP (one SNP per ddRAD
 locus). The genotypes are encoded as "0|0": homozygote REF;
 "0|1": heterozygote; "1|1": homozygote ALT;
 ".|.": missing. The raw sequences analyzed in the study are
 available in the European Nucleotide Archive repository
 (http://www.ebi.ac.uk/ena).
DOI: 10.5061/dryad.63xsj3v0n
title: One-year sustained efficacy of erenumab in episodic migraine: Results of the STRIVE study - supplementary data

description: Objective: To assess efficacy and tolerability of 1-year erenumab
 treatment in patients with episodic migraine. Methods: Patients were
 randomized (n=955; 1:1:1) during the 24-week double-blind treatment phase
 (DBTP) to monthly subcutaneous placebo, erenumab 70 or 140mg. At Week 24,
 845 patients were re-randomized (1:1) to erenumab 70 or 140mg during the
 28-week dose-blinded active-treatment phase (ATP). Monthly migraine days
 (MMD), achieving ≥50%, ≥75% and 100% reduction in MMD, and
 safety/tolerability were assessed. Results: Mean MMD at DBTP baseline was
 8.3. At Week 52, mean changes (SE) from pre-DBTP baseline/Week 24 (pre-ATP
 baseline) in MMD were −4.2 (0.2)/−1.1 (0.2) (70mg) and −4.6 (0.2)/−1.8
 (0.2) (140mg) irrespective of treatment during the DBTP. For patients
 reducing dose from 140 (DBTP) to 70mg (ATP), change in MMD from Week 24 to
 52 was −0.1 (0.3), and for those increasing from 70 (DBTP) to 140mg (ATP)
 was −1.8 (0.3). At Week 52, 61.0%, 38.5% and 19.8% of patients on erenumab
 70mg, and 64.9%, 40.8% and 21.2% on erenumab 140mg, achieved ≥50%, ≥75%
 and 100% reduction in MMD from DBTP baseline, respectively. Among
 erenumab-treated patients in DBTP who showed ≥50% reduction in MMD during
 the last 3 months of DBTP and completed ATP, 86% showed sustained
 responses at ≥50% during the last 3 months of ATP. Safety of erenumab in
 the ATP was similar to the DBTP; exposure-adjusted incidence rates of
 adverse events were similar for either dose. Conclusion: Over 52 weeks,
 erenumab provided sustained efficacy in episodic migraine; the safety
 profiles were similar between erenumab dose groups in the presence of dose
 blinding.
DOI: 10.5061/dryad.m63xsj3zk
title: Data from: The latitudinal diversity gradient of tetrapods across the Permo-Triassic mass extinction and recovery interval

description: The decline in species richness from the equator to the poles is referred
 to as the latitudinal diversity gradient (LDG). Higher equatorial
 diversity has been recognised for over 200 years, but the consistency of
 this pattern in deep time remains uncertain. Examination of spatial
 biodiversity patterns in the past across different global climate regimes
 and continental configurations can reveal how LDGs have varied over Earth
 history and potentially differentiate between suggested causal mechanisms.
 The Late Permian–Middle Triassic represents an ideal time interval for
 study, because it is characterised by large-scale volcanic episodes,
 extreme greenhouse temperatures, and the most severe mass extinction event
 in Earth history. We examined terrestrial and marine tetrapod spatial
 biodiversity patterns using a database of global tetrapod occurrences.
 Terrestrial tetrapods exhibit a bimodal richness distribution throughout
 the Late Permian–Middle Triassic, with peaks in the northern low latitudes
 and southern mid latitudes around 20-40°N and 60°S, respectively. Marine
 reptile fossils are known almost exclusively from the Northern Hemisphere
 in the Early and Middle Triassic, with highest diversity around 20°N.
 Reconstructed terrestrial LDGs contrast strongly with the generally
 unimodal gradients of today, potentially reflecting high global
 temperatures and prevailing Pangaean super-monsoonal climate system during
 the Permo-Triassic.
DOI: 10.5061/dryad.jdfn2z380
title: Data from: A closer examination of the 'abundant center' hypothesis for reef fishes

description: Aim: The ‘abundant center’ hypothesis states that species are more
 abundant at the center of their range. However, several recent large-scale
 studies have failed to find evidence for such a pattern. Here we use
 extensive global data of reef fishes to test the strength of the
 'abundant center' pattern, and to examine variation in the
 patterns across species using life history and ecological traits.
 Location: Marine habitat at a global extent: from Indo-Pacific to Atlantic
 reefs. Methods: We used underwater visual estimates of fish abundance,
 containing 22,963 transects and 1,215 species. For each species we
 calculated the slope between abundance and distance to the range center,
 with the range center estimated using four different methods. We tested
 whether abundance patterns differ between the range core and margins using
 segmented regression. Meta-analytic methods were used to synthesize
 results across species, and to test whether species traits can explain
 variation in the fit to the pattern among species. Results: The method
 used to define the range center had a large effect on the results.
 Nevertheless, in all cases we found large variation between species.
 Results of the segmented regression revealed that changes in abundance
 across the range core are very small and that steep declines in abundance
 happen only toward the range margins. Body size and mean abundance were
 the main traits affecting the fit to the pattern across species. Main
 conclusions: We find large variation across species in the fit to the
 abundance center pattern. Nevertheless, we do find support for a general
 pattern of a range core with high, but variable, abundance and steep
 decline in abundance toward the range periphery. Thus, species do tend to
 be rare at the range margins, making then sensitive to extirpation due to
 both natural and anthropogenic impacts.
description: Underwater visual fish census surveys data collected by several
 researchers around the world. Data columns are very
 informative.
DOI: 10.5061/dryad.m37pvmczv
title: Effects of embryo energy, egg size and larval food supply on the development of asteroid echinoderms

description: Organisms have limited resources available to invest in reproduction,
 causing a tradeoff between the number and size of offspring. One
 consequence of this tradeoff is the evolution of disparate egg sizes and,
 by extension, developmental modes. In particular, echinoid echinoderms
 (sea urchins and sand dollars) have been widely used to experimentally
 manipulate how changes in egg size affect development. Here we test the
 generality of the echinoid results by 1) using laser ablations of
 blastomeres to experimentally reduce embryo energy in the asteroid
 echinoderms (sea stars), Pisaster ochraceus and Asterias forbesi and 2)
 comparing naturally produced, variably-sized eggs (1.7 fold volume
 difference between large and small eggs) in A. forbesi. In P. ochraceus
 and A. forbesi there were no significant differences between juveniles
 from both experimentally reduced embryos and naturally produced eggs of
 variable size. However, in both embryo reduction and egg size variation
 experiments, simultaneous reductions in larval food had a significant and
 large effect on larval and juvenile development. These results indicate
 that 1) food levels are more important than embryo energy or egg size in
 determining larval and juvenile quality in sea stars and 2) the relative
 importance of embryo energy or egg size to fundamental life history
 parameters (time-to and size-at metamorphosis), does not appear to be
 consistent within echinoderms.
DOI: 10.5061/dryad.msbcc2fvr
title: Data from: Thyroid hormone receptor beta mutations alter photoreceptor development and function in Danio rerio (zebrafish)

description: We investigate mutations in trβ2, a splice variant of thrb, identifying
 changes in function, structure, and behavior in larval and adult zebrafish
 retinas. Two N-terminus CRISPR mutants were identified. The first is a
 6BP+1 insertion deletion frameshift resulting in a truncated protein. The
 second is a 3BP in frame deletion with intact binding domains. ERG
 recordings of isolated cone signals showed that the 6BP+1 mutants did not
 respond to red wavelengths of light while the 3BP mutants did respond.
 6BP+1 mutants lacked optomotor and optokinetic responses to red/black and
 green/black contrasts. Both larval and adult 6BP+1 mutants exhibit a loss
 of red-cone contribution to the ERG and an increase in UV-cone
 contribution. Transgenic reporters show loss of cone trβ2 activation in
 the 6BP+1 mutant but increase in the density of cones with active blue,
 green, and UV opsin genes.  Antibody reactivity for red-cone LWS1
 and LWS2 opsin was absent in the 6BP+1 mutant, as was reactivity for
 arrestin3a. Our results confirm a critical role for trβ2 in
 long-wavelength cone development.
description: ERG Recording Raw Data Isolated amplitudes
 from cone photoreceptors were collected through ERG electrode recordings.
 These datasets include the information for the stimulus flash including
 irradiance and wavelength. Responses are shown as the raw cone PIII
 amplitude response and the normalized response. Isolated zebrafish eyes
 were stimulated with each wavelength at varied irradiance levels.
 This stimulus information is then listed along with the corresponding
 response on the same line of the spreadsheet. The protocol runs through 70
 stimuli per fish eye. Recordings are separated into datasets by genotype
 (6BP+1/3BP/WT) and developmental stage (larval/adult). There are only
 6BP+1 and WT adults as 3BP mutants did not survive to adulthood.
description: These datasets provide the irradiance, wavelength, and respective
 amplitude response for 70 stimulus points per fish eye. There are 9
 wavelengths: 650, 610, 570, 530, 490, 450, 410, 370, and 330. Repetition
 of wavelength stimuli allows for log step increases in irradiance level
 within each wavelength. Amplitude responses and their corresponding
 stimulus wavelength and irradiance level can be used for modeling the
 physiological properties of the cones. We used Origin Lab for analysis,
 but other programs can use this data easily. Normalized amplitudes are
 provided to control for non-biological variation between recordings. There
 are no missing values.