cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7805/hm15-ed29
title: Replication files for "Uncertainty and Change: Survey Evidence of Firms’ Subjective Beliefs"

description: This paper studies how managers plan under uncertainty. In a new panel survey of German manufacturing firms, we observe both forecasts of sales growth and a quantitative measure of subjective uncertainty. We show that subjective uncertainty reflects change experienced by firms: it is high when growth is either unusually low or unusually high. Subjective uncertainty is more than conditional volatility: while more volatile firms are typically more uncertain, experienced change alone increases uncertainty, consistent with a model of learning. Uncertainty over our sample is mostly idiosyncratic but varies substantially over time and leads managers to plan lower employment and prices.
Data access:

The replication code for generating the results - provided you have all the required data sets - is going to be made publicly available for download on this website. A full replication package, which includes program code and data to replicate the results, is only accessible on the premises of the EBDC (on-site) upon written request.
DOI: 10.5061/dryad.92q55
title: Data from: Intruder colour and light environment jointly determine how nesting male stickleback respond to simulated territorial intrusions

description: Variation in male nuptial colour signals might be maintained by negative
 frequency-dependent selection. This can occur if males are more aggressive
 towards rivals with locally common colour phenotypes. To test this
 hypothesis, we introduced red or melanic three-dimensional printed-model
 males into the territories of nesting male stickleback from two optically
 distinct lakes with different coloured residents. Red-throated models were
 attacked more in the population with red males, while melanic models were
 attacked more in the melanic male lake. Aggression against red versus
 melanic models also varied across a depth gradient within each lake,
 implying that the local light environment also modulated the strength of
 negative frequency dependence acting on male nuptial colour.
description: Attack
 countsReadMe details for
 “Bolnick_data.csv” for Bolnick et al. Biology Letters 2016 The file
 Bolnick_data.csv is a comma-delimited ..csv text file. This file contains
 columns necessary to recreate analyses presented in the Biology Letters
 paper. The data in this table is a synthesis of a raw data file containing
 the exact time of each interaction, obtained from the original videos that
 are available upon request from the author (large files). Each column is
 distinct information regarding individual fish (rows). These columns are:
 A) Lake: Blackwater Lake or Gosling Lake B) Fish: an ID number
 corresponding to the camera used to uniquely video tape each interaction
 C) Model_color: Red, Blue, or Control_object (a cylinder the same size as
 our models) D) depth: Resident males’ nest depth (cm) E) N_bites: Number
 of bites directed at the model over a 1 hour video F) N_inspects: Number
 of inspections of the model (focal fish approaching the model to within
 one body length while facing the model) G) Aggressive_interactions: Sum of
 bites and inspections H) Date: date of experiment I)
 Mean.interval.between.bites: the mean duration of time between successive
 bites. Not calculated for Blackwater Lake because too few fish conducted
 more than 2 bites. Measured in seconds. J) Median.interval.between.bites:
 the median duration of time between successive bites. Not calculated for
 Blackwater Lake because too few fish conducted more than 2 bites. Measured
 in seconds. K) SD.interval: the standard deviation of the duration of time
 between successive bites. Not calculated for Blackwater Lake because too
 few fish conducted more than 2 bites. Measured in
 seconds.Bolnick_data.csv
DOI: 10.5061/dryad.fg812n7
title: Data from: Population-level dynamics in experimental mixed infections: evidence for competitive exclusion among bacterial parasites of Paramecium caudatum

description: Parasites frequently share their host populations with other parasites.
 However, little is known about how different parasites respond to
 competition with diverse competitor species in the within-host and
 between-host environments. We explored the repeatability of competition by
 simultaneously exposing microcosm populations of the ciliate Paramecium
 caudatum to pairs of parasites from the Holospora species complex (H.
 undulata, H. caryophila and H. obtusa) affected the persistence and
 prevalence of each compared to single infections, across three host
 genotypes. Three weeks post-inoculation we identified the presence of each
 parasite using fluorescence in situ hybridisation (FISH). Competitive
 exclusion (62/72) was more common than co-existence (10/72) in populations
 inoculated with 2 parasites. There was a clear pattern of competitive
 superiority, with H. caryophila persisting in all doubly inoculated
 populations (with either H. undulata or H. obtusa), and H. undulata
 tending to exclude H. obtusa. This mirrored infection success in single
 infections, with H. caryophila having a higher infection prevalence in
 single inoculations, followed by H. undulata then H. obtusa. The
 probability of persistence in co-inoculations did not change across the
 different host genotypes, and prevalence was the same as in single
 infections. Our results are consistent with superinfection models, which
 assume the competitive exclusion of parasites upon contact within the same
 host. Furthermore, such non-random competitive epidemiological dynamics,
 where one parasites always wins, may be of interest for public health
 management, especially if the winning parasite is avirulent, as is
 seemingly the case here.
description: Duncan_et_al_double_inoculationsDuncan_et_al_single_inoculations
DOI: 10.5061/dryad.k129c
title: Data from: Minimizing polymerase biases in metabarcoding

description: DNA metabarcoding is an increasingly popular method to characterize and
 quantify biodiversity in environmental samples. Metabarcoding approaches
 simultaneously amplify a short, variable genomic region, or “barcode”,
 from a broad taxonomic group via the polymerase chain reaction (PCR),
 using universal primers that anneal to flanking conserved regions. Results
 of these experiments are reported as occurrence data, which provide a list
 of taxa amplified from the sample, or relative abundance data, which
 measure the relative contribution of each taxon to the overall composition
 of amplified product. The accuracy of both occurrence and relative
 abundance estimates can be affected by a variety of biological and
 technical biases. For example, taxa with larger biomass may be better
 represented in environmental samples than those with smaller biomass.
 Here, we explore how polymerase choice, a potential source of technical
 bias, might influence results in metabarcoding experiments. We compared
 potential biases of six commercially available polymerases using a
 combination of mixtures of amplifiable synthetic sequences and real
 sedimentary DNA extracts. We find that polymerase choice can affect both
 occurrence and relative abundance estimates, and that the main source of
 this bias appears to be polymerase preference for sequences with specific
 GC contents. We further recommend an experimental approach for
 metabarcoding based on results of our synthetic experiments.
description: Nichols-et-al-AbovegroundDataAbove-ground data from St Paul Island - rank ordered abundances of plant taxa occurring in sampled sites. Each sample corresponds to a sample used for DNA metabarcoding.
DOI: 10.5061/dryad.2cq2g
title: Data from: Selfish partners: resource partitioning in male coalitions of Asiatic lions

description: Behavioral plasticity within species is adaptive which directs survival
 traits to take multiple pathways under varying conditions. Male-male
 cooperation is an evolutionary strategy often exhibiting an array of
 alternatives between and within species. African male lions coalesce to
 safeguard territories and mate-acquisition. Unique to these coalitions is
 lack of strict hierarchies between partners, who have similar
 resource-securities possibly because of many mating-opportunities within
 large female-groups. Skewed mating and feeding rights have only been
 documented in large coalitions where males were related. However, smaller
 modal prey coupled with less simultaneous mating-opportunities for male
 Asiatic lions in Gir forests, India would likely result in a different
 coalition-structure. Observations on mating-events (n=127) and
 feeding-incidents (n=44) were made on 11 male-coalitions and 9
 female-prides in Gir, to assess resource distribution within- and among-
 different sized male-coalitions. Information from 39 males were used to
 estimate annual tenure-holding probabilities. Single-males had smaller
 tenures and appropriated fewer matings than coalition-males. Pronounced
 dominance-hierarchies were observed within coalitions, with one partner
 getting &gt;70% of all matings and 47% more food. Competition between
 coalition-partners at kills increased with decline in prey-size, increase
 in coalition-size and the appetite-states of the males. However, immediate
 subordinates in coalitions had higher reproductive fitness than
 single-males. Declining benefits to partners with increasing
 coalition-size, with individuals below the immediate subordinates having
 fitness comparable to single-males, suggest to an optimal coalition-size
 of two lions. Lions under higher competitive selection in Gir show
 behavioral plasticity to form hierarchical-coalitions, wherein partners
 utilize resources asymmetrically, yet coalesce for personal gains.
description: Coalition_mating_dataThis file contains number of matings appropriated by coalition males. This was used to compute mating indices and compare that between coalition partners.Singleton_mating_dataThis file contains mating data on single malesFeeding_data_coalitionThis file contains data from coalitions on predation incidents. Time spent on kills were used to compute consumption and skew in consumption between partners. Aggressive encounters on kills have been coded for understanding competition.Male_fitnessThis file contains data on reproductive fitness of males. Tenure holding probabilities and mating events were used to parameterize fitness quotients.
DOI: 10.5061/dryad.3c2v9
title: Data from: Extreme ecological response of a seabird community to unprecedented sea ice cover

description: Climate change has been predicted to reduce Antarctic sea ice but,
 instead, sea ice surrounding Antarctica has expanded over the past 30
 years, albeit with contrasted regional changes. Here we report a recent
 extreme event in sea ice conditions in East Antarctica and investigate its
 consequences on a seabird community. In early 2014, the Dumont
 d'Urville Sea experienced the highest magnitude sea ice cover (76.8%)
 event on record (1982–2013: range 11.3–65.3%; mean±95% confidence
 interval: 27.7% (23.1–32.2%)). Catastrophic effects were detected in the
 breeding output of all sympatric seabird species, with a total failure for
 two species. These results provide a new view crucial to predictive models
 of species abundance and distribution as to how extreme sea ice events
 might impact an entire community of top predators in polar marine
 ecosystems in a context of expanding sea ice in eastern Antarctica.
description: Seabird and seaice
 dataBreeding success data
 and sea ice concentration datascriptR script for the
 segmented analyses and Davies tests
DOI: 10.5061/dryad.t3j32
title: Data from: Haemoglobin-mediated response to hyper-thermal stress in the keystone species Daphnia magna

description: Anthropogenic global warming has become a major geological and
 environmental force driving drastic changes in natural ecosystems. Due to
 the high thermal conductivity of water and the effects of temperature on
 metabolic processes, freshwater ecosystems are among the most impacted by
 these changes. The ability to tolerate changes in temperature may
 determine species long-term survival and fitness. Therefore, it is
 critical to identify coping mechanisms to thermal and hyper-thermal stress
 in aquatic organisms. A central regulatory element compensating for
 changes in oxygen supply and ambient temperature is the respiratory
 protein haemoglobin (Hb). Here, we quantify haemoglobin (Hb) plastic and
 evolutionary response in D. magna (sub)populations resurrected from the
 sedimentary archive of a lake with known history of increase in average
 temperature and recurrence of heat waves. By measuring constitutive
 changes in crude Hb protein content among (sub)populations we assessed
 evolution of the haemoglobin gene family in response to temperature
 increase. To quantify the contribution of plasticity in the response of
 this gene family to hyper-thermal stress, we quantified changes in Hb
 content in all (sub)populations under hyper-thermal stress as compared to
 non-stressful temperature. Further, we tested competitive abilities of
 genotypes as a function of their Hb content, constitutive and induced. We
 found that haemoglobin (Hb)-rich genotypes have superior competitive
 abilities as compared to Hb-poor genotypes under hyper-thermal stress
 after a period of acclimation. These findings suggest that whereas
 long-term adjustment to higher occurrence of heat waves may require a
 combination of plasticity and genetic adaptation, plasticity is most
 likely the coping mechanism to hyper-thermal stress in the short term. Our
 study suggests that with higher occurrence of heat waves Hb-rich genotypes
 may be favoured with potential long-term impact on population genetic
 diversity
description: Cambronero_etal_microsatellite_genotypingCambronero_etal_microsatellite_genotyping: microsatellite genotyping results for the genotypes used in the study obtained from 13 microsatellite loci arranged in two multiplexes. The genotype IDs are as in Orsini et al, 2016 Molecular Ecology. The microsatellite loci were first published in Jansen et al, 2010 Molecular Ecology Resources as part of a panel of 84 microsatellites. -9 indicates missing data.
DOI: 10.5061/dryad.92tt0
title: Data from: Dendritic connectivity shapes spatial patterns of genetic diversity: a simulation-based study

description: Landscape features notoriously affect spatial patterns of biodiversity.
 For instance, in dendritic ecological networks (such as river basins),
 dendritic connectivity has been proposed to create unique spatial patterns
 of biodiversity. Here, we compared genetic datasets simulated under a
 lattice-like, a dendritic and a circular landscape to test the influence
 of dendritic connectivity on neutral genetic diversity. The circular
 landscape had a level of connectivity similar to that of the dendritic
 landscape, so as to isolate the influence of dendricity on genetic
 diversity. We found that genetic diversity and differentiation varied
 strikingly among the three landscapes. For instance, the dendritic
 landscape generated higher total number of alleles and higher global Fst
 than the lattice-like landscape, and these indices also varied between the
 dendritic and the circular landscape, suggesting an effect of dendricity.
 Furthermore, in the dendritic landscape, allelic richness was higher in
 highly connected demes (e.g. confluences in rivers) than in low connected
 demes (e.g. upstream and downstream populations), which was not the case
 in the circular landscape, hence confirming the major role of dendricity.
 This led to bell-shaped distributions of allelic richness along an
 upstream-downstream gradient. Conversely, genetic differentiation (Fst)
 was lower in highly than in low connected demes (which was not observed in
 circular landscape), and significant patterns of isolation-by-distance
 (IBD) were also observed in the dendritic landscape. We conclude that in
 dendritic networks, the combined influence of dendricity and connectivity
 generates unique spatial patterns of neutral genetic diversity, which has
 implications for population geneticists and conservationists.
description: Simcoal 2 and ABCsampler
 input files for the three modelsThis file contains the
 .est and .par input files used for simulating the genetic datasets used in
 this article. There are three different couples of .est/.par files, each
 of them being associated to one of the three models presented in the
 article (i.e. dendritic, lattice and circular models). The event at 40,000
 generations before present (i.e. all genes in the network were send back
 to an unique deme at this date, considering a backwards in time
 timeframe), was used to uniformize coalescence times across simulations
 and models.Simcoal_and_ABCsampler_input_files.zip
DOI: 10.5061/dryad.83bs4jd
title: Data from: Reappraisal of previously reported meta-analyses on antibiotic prophylaxis for low-risk laparoscopic cholecystectomy: an overview of systematic reviews

description: Introduction: Many researchers have addressed over-dosage and
 inappropriate use of antibiotics. Many meta-analyses have investigated
 antibiotic prophylaxis for low-risk laparoscopic cholecystectomy with the
 aim of reducing unnecessary antibiotic use. Most of these meta-analyses
 have concluded that prophylactic antibiotics are not required for low-risk
 laparoscopic cholecystectomies. This study aimed to assess the validity of
 this conclusion by systematically reviewing these meta-analyses. Methods:
 A systematic review was undertaken. Searches were limited to meta-analyses
 and systematic reviews. PubMed and Cochrane Library electronic databases
 were searched from inception until March 2016 using the following keyword
 combinations: “antibiotic prophylaxis”, “laparoscopic cholecystectomy”,
 and “systematic review or meta-analysis”. Two independent reviewers
 selected meta-analyses or systematic reviews evaluating prophylactic
 antibiotics for laparoscopic cholecystectomy. All of the randomized
 controlled trials (RCTs) analyzed in these meta-analyses were also
 reviewed. Results: Seven meta-analyses regarding prophylactic antibiotics
 for low-risk laparoscopic cholecystectomy that had examined a total of 28
 RCTs were included. Reviewing of these meta-analyses revealed 48 miscounts
 of the number of outcomes. Six RCTs were inappropriate for the
 meta-analyses; one targeted patients with acute cholecystitis, another
 measured inappropriate outcomes, the original source of a third was not
 found, and the study protocols of the remaining three were not appropriate
 for the meta-analyses. After correcting the above miscounts and excluding
 the six inappropriate RCTs, pooled risk ratios were recalculated. These
 showed that, contrary to what had previously been concluded, antibiotics
 significantly reduced the risk of postoperative infections. The rates of
 surgical site, distant, and overall infections were all significantly
 reduced by antibiotic administration (risk ratio [95% confidence
 interval]; 0.71 [0.51–0.99], 0.37 [0.19–0.73], 0.50 [0.34–0.75],
 respectively). Conclusions: Prophylactic antibiotics reduce the incidence
 of postoperative infections after elective laparoscopic cholecystectomy.
description: Basic
 dataFundamental data for the
 analysis of the manuscriptData 1Data for the funnel
 plotsData 2Data for the effect
 size. In this data table, the data from the authors, Dobay et al. were
 deleted because their data showed no events both in antibiotics and
 control group.
DOI: 10.5061/dryad.fg3js19
title: Data from: The role of geospatial hotspots in the spatial spread of tuberculosis in rural Ethiopia: a mathematical modelling

description: Geospatial tuberculosis hotspots are hubs of TB transmission both within
 and across community groups. We aimed to quantify the extent to which
 these hotspots account for the spatial spread of TB in a high-burden
 setting. We developed spatially coupled models to quantify the spread of
 TB from geographic hotspots to distant regions in rural Ethiopia. The
 population was divided into three ‘patches’ based on their proximity to
 transmission hotspots, namely hotspots, adjacent regions and remote
 regions. The models were fitted to five-year notification data aggregated
 by the metapopulation structure. Model fitting was achieved with a
 Metropolis-Hastings algorithm using a Poisson likelihood to compare
 model-estimated notification rate with observed notification rates. A
 cross-coupled metapopulation model with assortative mixing by region
 closely fit to notification data as assessed by the Deviance Information
 Criterion. We estimated 45 hotspot-to-adjacent regions transmission events
 and 2 hotspot-to-remote regions transmission events occurred for every
 1000 hotspot-to-hotspot transmission events. Although the degree of
 spatial coupling is weak, the proportion of infections in the adjacent
 region that resulted from mixing with hotspots was high due to the high
 prevalence of TB cases in a hotspot region, with approximately 75% of
 infections attributable to hotspot contact. Our results suggest that the
 role of hotspots in the geospatial spread of TB in rural Ethiopia is
 limited, implying that TB transmission is primarily locally driven.
description: spatial_mathematical_modelThe file contains 1) a system of ordinary differential equations used in the model and 2). a model runner that calls the function
DOI: 10.5061/dryad.6675p
title: Data from: Body ownership and agency altered by an electromyographically-controlled robotic arm

description: Understanding how we consciously experience our bodies is a fundamental
 issue in cognitive neuroscience. Two fundamental components of this are
 the sense of body ownership (the experience of the body as one’s own) and
 the sense of agency (the feeling of control over one’s bodily actions).
 These constructs have been used to investigate the incorporation of
 prostheses. To date, however, no evidence has been provided showing
 whether representations of ownership and agency in amputees are altered
 when operating a robotic prosthesis. Here we investigated a robotic arm
 using myoelectric control, for which the user varied the joint position
 continuously, in a rubber hand illusion task. Fifteen able-bodied
 participants and three trans-radial amputees were instructed to contract
 their wrist flexors/extensors alternately, and to watch the robotic arm
 move. The sense of ownership in both groups was extended to the robotic
 arm when the wrists of the real and robotic arm were flexed/extended
 synchronously, with the effect being smaller when they moved in opposite
 directions. Both groups also experienced a sense of agency over the
 robotic arm. These results suggest that these experimental settings
 induced successful incorporation of the prosthesis, at least for the
 amputees who took part in the present study.
description: data_able-bodiedData for able-bodied participants