cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rt8bj147
title: Data from: Immune response increases predation risk

description: Why do individuals have an imperfect immune system? Most studies suggest
 trade-offs associated with immunity and metabolism, and neglect ecological
 factors, such as predation. We provide one of the first experimental
 studies demonstrating a context-dependent survival cost to immune
 activation. In the presence of a predator, immune-challenged male field
 crickets showed significantly lower survival than controls, whilst there
 was no difference in a predator-free environment. Immune-challenged males
 spent more time outside their burrows and reacted slower to a simulated
 predator attack. We conclude that some costs of immunity are expressed via
 increased susceptibility to predation, indicating the importance of
 integrating the ecological context when investigating optimal investment
 in immunity.
description: Capture-recapture
 dataData for Table S1 and
 Figure 1. We would appreciate to be informed about any reuse of our data
 (ootti@mac.com).Otti.etal.Capture-recapture
 data.pdfPredator avoidance trait
 dataData for predator
 avoidance traits analysis and Figure 3. We would appreciate to be informed
 about any reuse of our data (ootti@mac.com).Otti.etal.PAT
 data.pdfOtti.etal.Behavior
 dataData for behavior
 analysis Table S2 and Figure 2c. We would appreciate to be informed about
 any reuse of our data (ootti@mac.com).Otti.etal.Survival
 dataSurvival data for Figure
 2b We would appreciate to be informed about any reuse of our data
 (ootti@mac.com).
DOI: 10.5061/dryad.cp4j7
title: Data from: Dichoptic metacontrast masking functions to infer transmission delay in optic neuritis

description: Optic neuritis (ON) has detrimental effects on the transmission of
 neuronal signals generated at the earliest stages of visual information
 processing. The amount, as well as the speed of transmitted visual signals
 is impaired. Measurements of visual evoked potentials (VEP) are often
 implemented in clinical routine. However, the specificity of VEPs is
 limited because multiple cortical areas are involved in the generation of
 P1 potentials, including feedback signals from higher cortical areas.
 Here, we show that dichoptic metacontrast masking can be used to estimate
 the temporal delay caused by ON. A group of 15 patients with unilateral
 ON, nine of which had sufficient visual acuity and volunteered to
 participate, and a group of healthy control subjects (N = 8) were
 presented with flashes of gray disks to one eye and flashes of gray annuli
 to the corresponding retinal location of the other eye. By asking subjects
 to report the subjective visibility of the target (i.e. the disk) while
 varying the stimulus onset asynchrony (SOA) between disk and annulus, we
 obtained typical U-shaped masking functions. From these functions we
 inferred the critical SOAmax at which the mask (i.e. the annulus)
 optimally suppressed the visibility of the target. ON-associated
 transmission delay was estimated by comparing the SOAmax between
 conditions in which the disk had been presented to the affected and the
 mask to the other eye, and vice versa. SOAmax differed on average by 28
 ms, suggesting a reduction in transmission speed in the affected eye.
 Compared to previously reported methods assessing perceptual consequences
 of altered neuronal transmission speed the presented method is more
 accurate as it is not limited by the observers’ ability to judge subtle
 variations in perceived synchrony.
description: MetacontrastOpticNeuritisThe zip-file includes single subject data for the main study (8 healthy controls, 9 patients) and the control study (4 healthy controls) in MATLAB format. Each data file contains a variable trialMatrix in which each line corresponds to a trial in the experiment. The variable columnLabels describes the columns. Left and right is coded as -1 and 1, respectively. For "side" 1 codes above and 2 codes below fixation.
DOI: 10.5061/dryad.49rd9
title: Data from: Interaction effects of cell diffusion, cell density and public goods properties on the evolution of cooperation in digital microbes

description: Microbial cooperation typically consists in the sharing of secreted
 metabolites (referred to as public goods) within the community. Although
 public goods generally promote population growth, they are also vulnerable
 to exploitation by cheating mutants, which no longer contribute, but still
 benefit from the public goods produced by others. Although previous
 studies have identified a number of key factors that prevent the spreading
 of cheaters, little is known about how these factors interact and jointly
 shape the evolution of microbial cooperation. Here, we address this issue
 by investigating the interaction effects of cell diffusion, cell density,
 public good diffusion and durability (factors known to individually
 influence costs and benefits of public goods production) on selection for
 cooperation. To be able to quantify these effects across a wide parameter
 space, we developed an individual-based simulation platform, consisting of
 digital cooperator and cheater bacteria inhabiting a finite
 two-dimensional continuous toroidal surface. Our simulations, which
 closely mimic microbial microcolony growth, revealed that: (i) either
 reduced cell diffusion (which keeps cooperators together) or reduced
 public good diffusion (which keeps the public goods closer to the
 producer) is not only essential but also sufficient for cooperation to be
 promoted; (ii) the sign of selection for or against cooperation can change
 as a function of cell density and in interaction with diffusion
 parameters; and (iii) increased public goods durability has opposing
 effects on the evolution of cooperation depending on the level of cell and
 public good diffusion. Our work highlights that interactions between key
 parameters of public goods cooperation give rise to complex fitness
 landscapes, a finding that calls for multifactorial approaches when
 studying microbial cooperation in natural systems.
description: Simulation
 dataThe Data folder contains
 all the individual entries used to plot the figures presented in the
 study. The folder contains a parameter legend file describing the meaning
 of each column in the data files.Data.zip
DOI: 10.5061/dryad.m541q
title: Data from: Dynamics of cilia length in left–right development

description: Reduction in the length of motile cilia in the zebrafish left–right
 organizer (LRO), also known as Kupffer's vesicle, has a large impact
 on left–right development. Here we demonstrate through genetic
 overexpression in zebrafish embryos and mathematical modelling that the
 impact of increased motile cilia length in embryonic LRO fluid flow is
 milder than that of short cilia. Through Arl13b overexpression, which
 increases cilia length without impacting cilia beat frequency, we show
 that the increase in cilium length is associated with a decrease in beat
 amplitude, resulting in similar flow strengths for Arl13b overexpression
 and wild-type (WT) embryos, which were not predicted by current theory.
 Longer cilia exhibit pronounced helical beat patterns and, consequently,
 lower beat amplitudes relative to WT, a result of an elastohydrodynamic
 shape transition. For long helical cilia, fluid dynamics modelling
 predicts a mild (approx. 12%) reduction in the torque exerted on the fluid
 relative to the WT, resulting in a proportional reduction in flow
 generation. This mild reduction is corroborated by experiments, providing
 a mechanism for the mild impact on organ situs.
description: Source
 dataSource data is
 identified per FigureArchive.zip
DOI: 10.5061/dryad.3fs82mq
title: Data from: Asymmetric interactions and their consequences for vital rates and dynamics: the smaller tea tortrix as a model system

description: Asymmetric interactions among conspecifics can have diverse effects on
 population dynamics including stabilization, generation of cycles and
 induction of chaotic fluctuations. A difficult challenge, however, is
 establishing the link between the impact of asymmetric interactions on
 life history and the consequences for population dynamics. The smaller tea
 tortrix, Adoxophyes honmai, is a good example. Larval instars differ
 dramatically in size and have a tendency for cannibalism, which suggests
 the potential for strong asymmetric interactions among instars. Yet
 whether these asymmetries have any role in generating the distinct
 single-generation cycles observed in the field and laboratory is unclear.
 Here we report on the development of a new experimental approach to
 characterize the impact of asymmetric interactions on life history that
 can be directly embedded into stage-structured population models. The
 experiments use donor-replacement protocols in which focal individuals are
 challenged to complete their life-cycles in competitive environments where
 the instar and density of the competitors is held constant. The
 experimentally-derived interaction surface contains all the information
 about stage-specific interactions and provides a straightforward framework
 for evaluating alternative ways of abstracting the interactions into
 traditional models of asymmetric competition. Working with the smaller tea
 tortrix, we found strong evidence of asymmetric interactions and
 identified critical ‘tipping points’ in the competitive environment that
 strongly affected survival but not development. We incorporated the
 experimentally-derived interaction surface into a stage-structured
 population model and found that despite the strong impact that asymmetric
 interactions have on tea tortrix life history, they do not scale-up to
 impact the predicted asymptotic population dynamics. Comparing these
 dynamics with two abstracted models of stage-structured interactions
 revealed that while the quantitative details of the emergent dynamics
 depends on the shape of the interaction surface, the qualitative features
 — such as the emergence of single-generation cycles and rapid
 synchronization of development among individuals — are pleasingly robust.
description: Experiment2Data on stage, survival, body length, head width, and pupa mass by age for all individuals in experiment 2.experiment2a2.csvExperiment1Data on stage, survival, body length, head width, and pupa mass by age for all individuals in experiment 1.experiment1a.csv
DOI: 10.5061/dryad.94082
title: Data from: Automated analysis of long-term grooming behavior in Drosophila using a k-nearest neighbors classifier

description: Despite being pervasive, the control of programmed grooming is poorly
 understood. We addressed this gap by developing a high-throughput platform
 that allows long-term detection of grooming in Drosophila melanogaster. In
 our method, a k-nearest neighbors algorithm automatically classifies fly
 behavior and finds grooming events with over 90% accuracy in diverse
 genotypes. Our data show that flies spend ~13% of their waking time
 grooming, driven largely by two major internal programs. One of these
 programs regulates the timing of grooming and involves the core circadian
 clock components cycle, clock, and period. The second program regulates
 the duration of grooming and, while dependent on cycle and clock, appears
 to be independent of period. This emerging dual control model in which one
 program controls timing and another controls duration, resembles the
 two-process regulatory model of sleep. Together, our quantitative approach
 presents the opportunity for further dissection of mechanisms controlling
 long-term grooming in Drosophila.
description: Source Data_Main
 FiguresSource data for main
 figuresSource
 Data_Supplementary FiguresSource data for figure
 supplements
DOI: 10.5061/dryad.67sf15d
title: Data from: Chemical taphonomy and preservation modes of Jurassic spinicaudatans from Patagonia: a chemometric approach

description: Spinicaudatans (‘clam shrimps’) are small branchiopod crustaceans enclosed
 in a chitinous bivalved carapace that is often the only preserved element
 in the fossil record. However, few studies have analyzed the preservation
 of these carapaces, which have been found in continental facies from the
 Devonian to the present. The aim of this study was to contribute to a
 better understanding of the chemical preservation of fossil spinicaudatan
 carapaces, and focused on spinicaudatan carapaces of the Cañadón Asfalto
 Formation from the Jurassic of Argentina. Semi-quantitative
 energy-dispersive X-ray spectrometry (EDS) analysis provided elemental
 composition data that were interpreted using principal component analysis
 (PCA). The results showed a complex chemical mode of preservation for
 spinicaudatan carapaces. In some parts, EDS spectra of the specimens
 exhibits peaks of calcium, phosphorous, aluminum and fluorine,
 representing the retention of original carapace material with some
 diagenetic recrystallization. Certain zones of the carapace show low
 intensity peaks of the elements mentioned above, while silicon and oxygen
 peaks (from the rock matrix) become the dominant spectral signals. These
 modes of preservation modify the interpretations and observations of the
 ornamentation of the carapace, which are used as taxonomic features. Our
 results suggest that specific diagenetic processes play a fundamental role
 in the preservation of spinicaudatans.
description: Appendix -
 1This
 file correspond to tables from PCA analysis of main manuscript. There are
 three tables with captions.Appendix -
 2This
 file represent a complementary PCA anlysis between chemical data from
 fossil and mineral species. There are a paragraph about study description,
 one figure and three tables of analysis.
DOI: 10.5061/dryad.bv88g
title: Data from: DNA barcoding gap: reliable species identification over morphological and geographical scales

description: The philosophical basis, and utility of DNA barcoding has been a subject
 of numerous debates. While most literature embraces it, some studies
 continue to question its use in dipterans, butterflies, and marine
 gastropods. Here, we explore the utility of DNA barcoding in identifying
 spider species that vary in taxonomic affiliation, morphological
 diagnosibility and geographic distribution. Our first test searched for a
 “barcoding gap” by comparing intra- and interspecific means, medians and
 overlap in more than 75,000 computed Kimura 2 parameter (K2P) genetic
 distances in three families. Our second test compared K2P distances of
 congeneric species with high versus low morphological distinctness in 20
 genera of 11 families. Our third test explored the effect of enlarging
 geographical sampling area at a continental scale on genetic variability
 in DNA barcodes within 20 species of nine families. Our results generally
 point towards a high utility of DNA barcodes in identifying spider
 species. However, the size of the barcoding gap strongly depends on
 taxonomic groups and practices. It is becoming critical to define the
 barcoding gap statistically more consistently, and to document its
 variation over taxonomic scales. Our results support models of independent
 patterns of morphological and molecular evolution by showing that DNA
 barcodes are effective in species identification regardless of their
 morphological diagnosibility. We also show that DNA barcodes represent an
 effective tool for identifying spider species over geographic scales, yet
 their variation contains useful biogeographic information.
description: Appendix
 1DNA
 barcodes used in the barcoding gap analysisAppendix_1.xlsxAppendix 2DNA barcodes used in the test of species identification over morphological scales.Appendix_2.xlsxAppendix 3DNA barcodes used in the test of species identification over geographical scales.Appendix_3.xlsx
DOI: 10.5061/dryad.d22q6vh
title: Data from: Combination of the National Early Warning Score (NEWS) and inflammatory biomarkers for early risk stratification in emergency department patients: results of a multi-national, observational study

description: Objectives: The National Early Warning Score (NEWS) helps to estimate
 mortality risk in emergency department (ED) patients. This study aimed to
 investigate whether the prognostic value of the NEWS at ED admission could
 be further improved by adding inflammatory blood markers (i.e. white blood
 cell count (WBC), procalcitonin (PCT), and MR-ProAdrenomedullin
 (MR-proADM). Design: Secondary analysis of a multinational, observational
 study. (TRIAGE study, March 2013 to October 2014) Setting: Three tertiary
 care centers in France, Switzerland, and the USA. Participants: A total of
 1303 adult medical patients with complete NEWS data seeking ED care were
 included in the final analysis. NEWS was calculated retrospectively based
 on admission data. Main outcome measures: The primary outcome was
 all-cause 30-day mortality. Secondary outcome was ICU admission. We used
 multivariate regression analyses to investigate associations of NEWS and
 blood markers with outcomes and area under the receiver operating curve
 (AUC) as a measure of discrimination. Results: Of the 1303 included
 patients, 54 (4.1%) died within 30 days. The NEWS alone showed fair
 prognostic accuracy for all-cause 30-day mortality (AUC 0.73), with a
 multivariate adjusted odds ratio (OR) of 1.26 (95% CI 1.13–1.40,
 p&lt;0.001). The AUCs for the prediction of mortality using the
 inflammatory markers WBC, PCT, and MR-proADM were 0.64, 0.71, and 0.78,
 respectively. Combining NEWS with all three blood markers or only with
 MR-proADM clearly improved discrimination with an AUC 0.82 (p= 0.002).
 Combining the three inflammatory markers with NEWS improved prediction of
 ICU admission (AUC 0.70 vs. 0.65 when using NEWS alone, p=0.006).
 Conclusion: NEWS is helpful in risk stratification of ED patients and can
 be further improved by the addition inflammatory blood markers. Future
 studies should investigate whether risk stratification by NEWS in addition
 to biomarkers improve site-of-care decision in this patient population.
 Trial registration number: ClinicalTrials.gov; Identifier: NCT01768494
description: Combination of NEWS and
 inflammatory biomarkers datafileThis datafile contains
 parts of the data used for our retrospective analyses.NEWS_datafile.xls
DOI: 10.5061/dryad.1qv5t
title: Data from: An automated platform for high-throughput mouse behavior and physiology with voluntary head-fixation

description: Recording neural activity during animal behavior is a cornerstone of
 modern brain research. However, integration of cutting-edge technologies
 for neural-circuit analysis with complex behavioral measurements poses a
 severe experimental bottleneck for researchers. Critical problems include
 a lack of standardization for psychometric and neurometric integration,
 and lack of tools that can generate large, sharable datasets for the
 research community in a time and cost effective way. Here, we introduce a
 novel mouse behavioral-learning platform featuring voluntary head fixation
 and automated high throughput data collection for integrating complex
 behavioral assays with virtually any physiological device. We provide
 experimental validation by demonstrating behavioral training of mice in
 visual discrimination and auditory detection tasks. To examine facile
 integration with physiology systems, we coupled the platform to a
 two-photon microscope for imaging of cortical networks at single-cell
 resolution. Our behavioral learning and recording platform is a prototype
 for the next generation of mouse cognitive studies.
description: CAD
 filesdxf file
 format
DOI: 10.15468/dl.d5h3gc
title: Occurrence Download

description: A dataset containing 71 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of Iberian Plecoptera"
 ]
}

 The dataset includes 71 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000630-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.325r2g3
title: Data from: Conquering the inner couch potato: precommitment is an effective strategy to enhance motivation for effortful actions

description: Letting effort-free gratification derail us from effort-requiring goals is
 one reason why we fail to realize health-relevant intentions like
 ‘exercise regularly’. We tested the effectiveness of the self-control
 strategy precommitment in such effort-related conflicts, using a novel
 laboratory choice paradigm, where participants could precommit to an
 effort-requiring large reward by pre-eliminating an effort-free small
 reward from their choice set. Our participants used precommitment
 frequently and effectively, such that they reached effort-requiring large
 rewards more often. Using computational modelling and Bayesian model
 comparisons, we assessed whether participants employed precommitment to
 avoid anticipated willpower failures (i.e. as a self-regulatory measure)
 or to maximize their motivation to choose the effort-requiring option
 (i.e. as a self-motivational measure). Observed choices and precommitment
 decisions were consistent with the motivation maximization hypothesis, but
 not the willpower hypothesis. Our findings show that offering
 precommitment is effective in helping individuals optimize their
 motivation and choice behaviour and thereby achieve effort-requiring
 goals, and strongly encourage application of precommitment schemes in
 exercise and rehabilitation interventions. This article is part of the
 theme issue ‘Risk taking and impulsive behaviour: fundamental discoveries,
 theoretical perspectives and clinical implications’.
description: Modelling codes and raw
 data for the effort and delay tasksThe zipped folder
 contains the Matlab modelling codes (choice and precommitment models as
 specified in Table 1 of the article) and the respective raw data (one file
 per participant) for each of the two experimental tasksSupplementaryMaterial_ModelingCodes_And_Data.zip
DOI: 10.15468/dl.7vuvwh
title: Occurrence Download

description: A dataset containing 135 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is The InBIO Barcoding Initiative Database: Hemiptera 01"
 ]
}

 The dataset includes 135 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000631-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.