cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.br5h13d
title: Data from: New endoscopic finding of esophageal achalasia with ST Hood short type: corona appearance

description: Background and Study Aims: Detecting esophageal achalasia remains a
 challenge. We describe the diagnostic utility of corona appearance, a
 novel endoscopic finding specific to esophageal achalasia. Patients and
 Methods: Corona appearance and seven conventional endoscopic findings were
 compared for sensitivity and consistency (-value) among 53 untreated
 esophageal achalasia patients who underwent endoscopy at our hospital. The
 following criteria had to be met during lower esophageal sphincter
 examination using the attached ST Hood short-type for positive corona
 appearance: A) congestion inside the hood, B) ischemic change around the
 hood, and C) palisade vessels outside the hood. Results: Corona appearance
 had the highest sensitivity (91%; -value, 0.71). Other findings in
 descending order of sensitivity included 1) functional stenosis of the
 esophagogastric junction (EGJ; 86%; -value, 0.58), 2) mucosal thickening
 and whitish change (71%; -value, 0.27), 3) abnormal contraction of the
 esophageal body (59%; -value, 0.32), 4) dilation of the esophageal lumen
 (58%; -value, 0.53), 5) liquid remnant (57%; -value, 0.51), 6) Wrapping
 around EGJ (49%; -value, 0.14), and 7) food remnant (30%; -value, 0.88).
 Even in 22 patients with poor (grade 1) intraluminal expansion, corona
 appearance had highest sensitivity (88%) compared to other endoscopic
 findings (-value, 0.63). Conclusions: Among endoscopic findings using a
 ST Hood short-type to diagnose esophageal achalasia, corona appearance had
 the highest sensitivity and its consistency (-value) among endoscopists
 was substantial compared to other endoscopic findings. Similar results
 were obtained for esophageal achalasia cases with poor expansion.
 Endoscopic diagnosis of esophageal achalasia with hood attached is useful.
description: Video
 Supporting_file_01[1]Video for CA was defined
 as positive when all of the following three criteria were met upon
 observation of the LES performed with the attached ST Hood short-type: a)
 Congestion inside the hood, b) ischemic change around the hood, and c)
 palisade vessels outside the hood.Supporting_file_01[1].wmv
DOI: 10.5061/dryad.5d8k268
title: Data from: Flower signal variability overwhelms receptor-noise and requires plastic color learning in bees

description: Color discrimination thresholds proposed by receptor-noise type models are
 frequently used in animal vision studies to predict a precise limit on the
 capacity of an animal to discriminate between stimuli. Honeybees and
 bumblebees are two closely related hymenopteran species for which precise
 data on photoreceptor sensitivities and receptor noise exist, enabling
 accurate testing on how their vision conforms to model predictions. Color
 vision has been proven in these species, and they are known to
 predominantly visit flowers using visual signals to collect nutrition.
 Surprisingly, however, the natural variability of flower signals has been
 rarely considered, and recent work also suggests bees may tune color
 vision through experience. We initially measured the spectral variability
 of flowers from two species: Goodenia ovata and Rosemarinus officinalis
 where free-flying honeybees were observed constantly foraging from
 conspecific flowers. We empirically determined honeybee color
 discrimination thresholds for color stimuli considering either absolute-
 or differential-conditioning discrimination functions. Secondly, we
 analyzed greenhouse grown wild type Antirrhinum majus flower petal spectra
 as well as spectra from mixta and nivea strains of this species, and
 empirically determined bumblebee color discrimination considering
 conditioning experience. In all measured cases within-flower type spectral
 variability exceeded a 1.0 Receptor Noise threshold, often by several
 units. Observed behavioral color discrimination functions considering the
 respective conditioning procedures closely matched the range of signal
 variability for both honeybees and bumblebees, showing that color vision
 in bees cannot be described by a single fixed value, and plasticity is a
 key component of bee foraging behavior in natural environments.
description: Reflectance data from
 flower species and strains used for the paper "Flower signal
 variability overwhelms receptor-noise and requires plastic color learning
 in bees" by Garcia et al. 2018Zip file containing the
 reflectance spectra measured from Rosemarinus officinalis, Goodenia ovata
 and three strains of Antirrhinum majus used for the analyses. Data are
 stored as .csv files for each species/strain. Please refer to the README
 and the associated manuscript for details.Garciaetal_2018_reflectance_datasets.zip
DOI: 10.5061/dryad.3h70d78
title: Data from: Modularity speeds up motor learning by overcoming mechanical bias in musculoskeletal geometry

description: We can easily learn and perform a variety of movements that fundamentally
 require complex neuromuscular control. Many empirical findings have
 demonstrated that a wide range of complex muscle activation patterns could
 be well captured by the combination of a few functional modules, the
 so-called muscle synergies. Modularity represented by muscle synergies
 would simplify the control of a redundant neuromuscular system. However,
 how the reduction of neuromuscular redundancy through a modular controller
 contributes to sensorimotor learning remains unclear. To clarify such
 roles, we constructed a simple neural network model of the motor control
 system that included three intermediate layers representing neurons in the
 primary motor cortex, spinal interneurons organized into modules and
 motoneurons controlling upper-arm muscles. After a model learning period
 to generate the desired shoulder and/or elbow joint torques, we compared
 the adaptation to a novel rotational perturbation between modular and
 non-modular models. A series of simulations demonstrated that the modules
 reduced the effect of the bias in the distribution of muscle pulling
 directions, as well as in the distribution of torques associated with
 individual cortical neurons, which led to a more rapid adaptation to
 multi-directional force generation. These results suggest that modularity
 is crucial not only for reducing musculoskeletal redundancy but also for
 overcoming mechanical bias due to the musculoskeletal geometry allowing
 for faster adaptation to certain external environments.
description: SimulationScriptsScripts needed for simulation are included in this Zip folder.
DOI: 10.18112/openneuro.ds007058.v1.0.0
title: Silent Visual Reading EEG
DOI: 10.5061/dryad.g0j11kf
title: Data from: Adaptive periodicity in the infectivity of malaria gametocytes to mosquitoes

description: Daily rhythms in behaviour, physiology, and molecular processes are
 expected to enable organisms to appropriately schedule activities
 according to consequences of the daily rotation of the Earth. For
 parasites, this includes capitalizing on periodicity in transmission
 opportunities and for hosts/vectors, this may select for rhythms in immune
 defence. We examine rhythms in the density and infectivity of transmission
 forms (gametocytes) of rodent malaria parasites in the host’s blood,
 parasite development inside mosquito vectors, and potential for onwards
 transmission. Furthermore, we simultaneously test whether mosquitoes
 exhibit rhythms in susceptibility. We reveal that at night, gametocytes
 are twice as infective, despite being less numerous in the blood. Enhanced
 infectiousness at night interacts with mosquito rhythms to increase
 sporozoite burdens four-fold when mosquitoes feed during their rest phase.
 Thus, changes in mosquito biting time (due to bed nets) may render
 gametocytes less infective, but this is compensated for by the greater
 mosquito susceptibility.
description: malaria infection data
 from mice and mosquitoesMalaria parasite
 prevalences and densities (gametocytes, oocysts and sporozoites) for
 mosquito infections of 4 treatment groups, comprising mosquitoes feeding
 on mice at “mosquito daytime” or “mosquito night time” and ingesting
 either rodent malaria parasites at “parasite daytime” or “parasite night
 time”malariaHawking2018.csvMosquito actiogram raw data (trikinetics monitor file) used to generate average activity profile in figure S2.Locomotor Activity Monitor units (LAM 25) (TriKinetics, Waltham, MA, USA) record individual female mosquito locomotor flight activity. Data were processed using ClockLab software (Actimetrics, Wilmette IL) to generate figure S2, showing the 24-hr activity profile averaged over 3 days of activity for 32 females.mosquito_actiogram_Hawking2018.txt
DOI: 10.5061/dryad.d6d5011
title: Data from: Niche theory and its relation to morphology and phenotype in geographic space: a case study in woodpeckers (Picidae)

description: Ecogeographic analyses have recovered common environmental trends with
 respect to morphology; however discrepancies among trends exist.
 Hypothesized reasons for these divergences vary, but most relate a taxon’s
 morphology to its ecological niche. Morphology is known to diverge when
 species co-occur with competitors or predators and when species occur
 across different habitats and environments. A less understood divergence
 from ecogeographic trends is niche fixation, wherein species become locked
 into particular niches due to their community interactions or foraging
 ecology. A form of niche fixation has been hypothesized in the theory of
 Interspecies Social Dominance Mimicry (ISDM), in which mimics maintain
 relatively constant size ratios with models to perpetuate their mimicry.
 If true, mimics should display variation and trends in tandem with their
 models. Here, I use mass as a proxy for body size and examine
 ecogeographic trends in two sets of woodpeckers (Picidae): a Nearctic
 group which has been reported to interact via ISDM, and a Neotropical
 group which, based on similar appearances and overlapping distributions,
 is a potential ISDM system. I found ecogeographic trends suggestive of
 differential evolutionary responses, and I found evidence against niche
 fixation in the Nearctic clade. The Neotropic clade showed limited
 evidence for tandem size evolution between models and mimics, but
 inconsistencies in the size ratios between mimic and model populations.
 Here, I discuss the implications of observing divergent ecogeographic
 trends within mimicry systems, with specific emphasis on how environment,
 ecology, and community interactions guide evolution.
description: Code and data for
 Cooper, JC: Niche morphology through geographic spaceR code for reproducing
 the results found in the following paper:
 doi:10.1111/jav.01771.JAV_CooperJC.zip
DOI: 10.5281/zenodo.17762912
title: INRIM_Brand1_25F_3_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 25F SC sample 3 INRIM   - EDLC Single - Brand1

Part of the Constant Temperature DataBase
DOI: 10.5281/zenodo.17762913
title: INRIM_Brand1_25F_3_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 25F SC sample 3 INRIM   - EDLC Single - Brand1

Part of the Constant Temperature DataBase
DOI: 10.5061/dryad.rf3664q
title: Data from: More partners, more ranges: generalist legumes spread more easily around the globe

description: How does mutualism affect range expansion? On one hand, mutualists might
 thrive in new habitats thanks to the resources, stress tolerance, or
 defense provided by their partners. On the other, specialized mutualists
 might fail to find compatible partners beyond their range margins,
 limiting further spread. A recent global analysis of legume ranges found
 that non-symbiotic legumes have been successfully introduced to more
 ranges than legumes that form symbioses with rhizobia, but there is still
 abundant unexplained variation in introduction success within symbiotic
 legumes. We test the hypothesis that generalist legumes have spread to
 more ranges than specialist legumes. We used published data and rhizobial
 16S rRNA sequences from GenBank to quantify the number of rhizobia
 partners that associate with 159 legume species, spanning the legume
 phylogeny and the globe. We found that generalist legumes occur in more
 introduced ranges than specialist legumes, suggesting that among
 mutualists, specialization hinders range expansions.
description: Accession numbers for
 16S rhizobia sequencesAll sequences were
 collected from GenBank. Accession numbers are listed as well as the plant
 host each sequence was collected from in addition to the rhizobia
 genus/species name and country of location.Accession_numbers.csvRhizobia genera datasetAll plant hosts that had information on number of rhizobia genera are listed as well as information on number of introduced ranges, latitude of native range, annual, number of human uses, and area of native range.Genus_dataset.csvRhizobia OTU datasetAll hosts with information on number of rhizobia OTUs are included along with number of introduced ranges, latitude of native range, annual, number of human uses, number of sequences, area of native ranges, unifrac score, and unifrac categories (split into int=similar and diff=different).OTU_dataset.csv
DOI: 10.5281/zenodo.18387647
title: The effect of different grazing managements on butterfly abundance, diversity and composition at a calcareous upland site.

description: 1.      Butterfly populations have experienced substantial declines in recent decades due to land-use change, agricultural intensification and climate change. In the UK uplands, the impact of livestock grazing on butterfly populations has not been well documented.

2.      In this study we used long-term monitoring from the Ingleborough National Nature Reserve in the English uplands to examine the impact of sheep grazing, cattle grazing and ungrazed management on butterfly abundance and species diversity across an upland calcareous site.

3.      The lightly cattle-grazed site was found to have 4.9 times the abundance of butterflies compared to sites lightly grazed by sheep. There were 3.6 times as many butterflies on the ungrazed site compared to sheep-grazed sites. The species richness of butterflies was also significantly higher on cattle-grazed and ungrazed sites compared to sheep-grazed sites.

4.      Our study provides evidence of the conservation benefits of low-intensity cattle grazing for butterfly abundance and diversity on calcareous grasslands in the UK uplands.

Practical implication: For effective butterfly conservation, a shift from sheep grazing to light cattle grazing or stock exclusion in upland calcareous landscapes should be considered.
DOI: 10.5281/zenodo.18387648
title: The effect of different grazing managements on butterfly abundance, diversity and composition at a calcareous upland site.

description: 1.      Butterfly populations have experienced substantial declines in recent decades due to land-use change, agricultural intensification and climate change. In the UK uplands, the impact of livestock grazing on butterfly populations has not been well documented.

2.      In this study we used long-term monitoring from the Ingleborough National Nature Reserve in the English uplands to examine the impact of sheep grazing, cattle grazing and ungrazed management on butterfly abundance and species diversity across an upland calcareous site.

3.      The lightly cattle-grazed site was found to have 4.9 times the abundance of butterflies compared to sites lightly grazed by sheep. There were 3.6 times as many butterflies on the ungrazed site compared to sheep-grazed sites. The species richness of butterflies was also significantly higher on cattle-grazed and ungrazed sites compared to sheep-grazed sites.

4.      Our study provides evidence of the conservation benefits of low-intensity cattle grazing for butterfly abundance and diversity on calcareous grasslands in the UK uplands.

Practical implication: For effective butterfly conservation, a shift from sheep grazing to light cattle grazing or stock exclusion in upland calcareous landscapes should be considered.
DOI: 10.5061/dryad.2jc05rt
title: Data from: Interception by two predatory fly species is explained by a proportional navigation feedback controller

description: When aiming to capture a fast-moving target, animals can follow it until
 they catch up, or try to intercept it. In principle, interception is the
 more complicated strategy, but also more energy efficient. To study
 whether simple feedback controllers can explain interception behaviours by
 animals with miniature brains, we have reconstructed and studied the
 predatory flights of the robber fly Holcocephala fusca and killer fly
 Coenosia attenuata. Although both species catch other aerial arthropods
 out of the air, Holcocephala contrasts prey against the open sky, while
 Coenosia hunts against clutter and at much closer range. Thus, their
 solutions to this target catching task may differ significantly. We
 reconstructed in three dimensions the flight trajectories of these two
 species and those of the presented targets they were attempting to
 intercept. We then tested their recorded performances against simulations.
 We found that both species intercept targets on near time-optimal courses.
 To investigate the guidance laws that could underlie this behaviour, we
 tested three alternative control systems (pure pursuit, deviated pursuit
 and proportional navigation). Only proportional navigation explains the
 timing and magnitude of fly steering responses, but with differing gain
 constants and delays for each fly species. Holcocephala uses a
 dimensionless navigational constant of N ≈ 3 with a time delay of ≈28 ms
 to intercept targets over a comparatively long range. This constant is
 optimal, as it minimizes the control effort required to hit the target. In
 contrast, Coenosia uses a constant of N ≈ 1.5 with a time delay of ≈18 ms,
 this setting may allow Coenosia to cope with the extremely high
 line-of-sight rotation rates, which are due to close target proximity, and
 thus prevent overcompensation of steering. This is the first clear
 evidence of interception supported by proportional navigation in insects.
 This work also demonstrates how by setting different gains and delays, the
 same simple feedback controller can yield the necessary performance in two
 different environments.
description: Flightpaths of Predators
 Intercepting Dummy TargetsFlightpaths in XYZ
 coordinates for killer flies (Coenosia attenuata) and a robber fly
 (Holcocephala fusca) intercepting dummy targets. Targets traveled either
 in a linear or erratic fashion. Folders of flightpaths are named both for
 the fly species that is intercepting the target and the style of target
 travel (linear or erratic).Data
 Publishing.zip
DOI: 10.5061/dryad.q5r472k
title: Data from: Divergent rates of change between tree cover types in a tropical pastoral region

description: Context: Forest cover change analyses have revealed net forest gain in
 many tropical regions. While most analyses have focused solely on forest
 cover, trees outside forests are vital components of landscape integrity.
 Quantifying regional-scale patterns of tree cover change, including
 non-forest trees, could benefit forest and landscape restoration (FLR)
 efforts. Objectives: We analyzed tree cover change in Southwestern Panama
 to quantify: 1) patterns of change from 1998-2014, 2) differences in rates
 of change between forest and non-forest classes, and 3) the relative
 importance of social-ecological predictors of tree cover change between
 classes. Methods: We digitized tree cover classes, including dispersed
 trees, live fences, riparian forest, and forest, in very high resolution
 images from 1998-2014. We then applied hurdle models to relate
 social-ecological predictors to the probability and amount of tree cover
 gain. Results: All tree cover classes increased in extent, but gains were
 highly variable between classes. Non-forest tree cover accounted for 21%
 of tree cover gains, while riparian trees constituted 31% of forest cover
 gains. Drivers of tree cover change varied widely between classes, with
 opposite impacts of some social-ecological predictors on non-forest and
 forest cover. Conclusions: We demonstrate that key drivers of forest cover
 change, including topography, road distance and historical forest cover,
 do not explain rates of non-forest tree cover change. Consequently,
 predictions from medium-resolution forest cover change analyses may not
 apply to finer-scale patterns of tree cover. We highlight the opportunity
 for FLR projects to target tree cover classes adapted to local social and
 ecological conditions.
description: Digitized tree cover
 1998This shapefile consists
 of polygons representing tree cover in 150 x 150 m plots. Columns in the
 attribute table indicate the year during which the aerial image used to
 digitize tree cover was acquired (1998), the tree cover type (Dispersed,
 Fallow, Riparian, Fence, and Forest), and the area of each polygon (in
 square meters).digitized_polygons_1998.zipDigitized tree cover 2014This shapefile consists of polygons representing tree cover in 150 x 150 m plots. Columns in the attribute table indicate the year during which the aerial image used to digitize tree cover was acquired (2014), the tree cover type (Dispersed, Fallow, Riparian, Fence, and Forest), and the area of each polygon (in square meters).digitized_polygons_2014.zipSampling squaresThis shapefile represents sampling units for measuring tree cover. Each sampling unit is a 150 x 150 m square. Squares were stratified to properties using a cadastral data set, such that one square represents one property. Within the sampling unit, all tree cover was digitized and categorized into tree cover types. Areas without tree cover were not digitized.USED_squares.zip
DOI: 10.5061/dryad.926bs5d
title: Data from: On the probabilities of branch durations and stratigraphic gaps in phylogenies of fossil taxa when rates of diversification vary over time

description: The time separating the first appearances of species from their
 divergences from related taxa affects assessments of macroevolutionary
 hypotheses about rates of anatomical or ecological change. Branch
 durations necessarily posit stratigraphic gaps in sampling within a clade
 over which we have failed to sample predecessors (ancestors) and over
 which there are no divergences leading to sampled relatives (sister taxa).
 The former reflects only sampling rates whereas the latter reflects
 sampling, origination and extinction rates. Because all three rates vary
 over time, the probability of a branch duration of any particular length
 will differ depending on when in the Phanerozoic that branch duration
 spans. Here, I present a birth death sampling model allowing interval to
 interval variation in diversification and sampling rates. Increasing
 either origination or sampling rates increases the probability of finding
 sister taxa that diverge both during and before intervals of high
 sampling/origination. Conversely, elevated extinction reduces the
 probability of divergences from sampled sister taxa before and during
 intervals of elevated extinction. In the case of total extinction, a
 Signor-Lipps will reduce expected sister-taxa leading up to the
 extinction, with the possible effect stretching back many millions of
 years when sampling is low. Simulations indicate that this approach
 provides reasonable estimates of branch duration probabilities under a
 variety of circumstances. Because our current probability models for
 describing morphological evolution are not as advanced as our methods for
 inferring diversification and sampling rates, branch duration priors
 allowing for time varying diversification and could be a potent tool for
 phylogenetic inference with fossil data.
description: Wagner_R_CodeR code for estimating the probabilities of branch durations on trees of fossil taxa given different origination, extinction & sampling rates from different intervals of time.Supplementary MaterialAnalyses to augment points of the paper, plus code.Supplemantary Material.docx