cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1jwstqjs2
title: Data from: Are skyline plot-based demographic estimates overly dependent on smoothing prior assumptions?

description: In Bayesian phylogenetics, the coalescent process provides an informative
 framework for inferring changes in the effective size of a population from
 a phylogeny (or tree) of sequences sampled from that population. Popular
 coalescent inference approaches such as the Bayesian Skyline Plot, Skyride
 and Skygrid all model these population size changes with a discontinuous,
 piecewise-constant function but then apply a smoothing prior to ensure
 that their posterior population size estimates transition gradually with
 time. These prior distributions implicitly encode extra population size
 information that is not available from the observed coalescent data i.e.
 the tree. Here we present a novel statistic, Ω, to quantify and
 disaggregate the relative contributions of the coalescent data and prior
 assumptions to the resulting posterior estimate precision. Our statistic
 also measures the additional mutual information introduced by such priors.
 Using Ω we show that, because it is surprisingly easy to over-parametrise
 piecewise-constant population models, common smoothing priors can lead to
 overconfident and potentially misleading inference, even under robust
 experimental designs. We propose Ω as a useful tool for detecting when
 posterior estimate precision is overly reliant on prior choices.
description: This Matlab code was used to produce figures and results for the
 manuscript: "Are skyline plot-based demographic estimates overly
 dependent on smoothing prior assumptions?" The
 main code can be used to compute the omega statistic presented in this
 paper. Key functions/scripts are:  robustDecayTry.m:
 computes a p-correction for GMRF priors to omega
 compLowerBndsDecay.m: computes the bound on omega^2, used for
 model rejection modSelCurve.m, modSel_via_m.m,
 maxpModSel.m and omegaModelSelect.m: use to test model rejection
 algorithms under various conditions robustDecay.m and
 testEllip.m: looks at how Fisher information from prior influences the
 omega statistic and looks at uncertainty ellipses All
 files with the word 'King': computes omega statistic for Kingman
 coalescent *Update: now includes xmls for the
 empirical-based simulations for the bison and HCV examples in the revised
 Fig 5 and 6 of the main text.
DOI: 10.5281/zenodo.18394836
title: Dataset for "First Investigations on WAAM-Printed Adhesive Sockets for Reinforcement Connections" (v1.0)

description: In this study, the WAAM process is investigated using the example of welded connection elements for reinforcing bars, accompanied by centric tensile tests on representative WAAM specimens and pull-out tests on reinforcing bars bonded into different sockets with two different injection mortars. In comparison to this novel approach of connecting steel components with reinforcing bars by bonding sockets produced using WAAM, comparable connection methods such as bolting and welding of the reinforcing bars are investigated. The experimental investigations include pull-out tests of reinforcing bars from two types of sockets, centric tensile tests, and tensile shear tests of the two injection mortars investigated on different surfaces. This data publication includes all test results.
DOI: 10.5281/zenodo.18394837
title: Dataset for "First Investigations on WAAM-Printed Adhesive Sockets for Reinforcement Connections" (v1.0)

description: In this study, the WAAM process is investigated using the example of welded connection elements for reinforcing bars, accompanied by centric tensile tests on representative WAAM specimens and pull-out tests on reinforcing bars bonded into different sockets with two different injection mortars. In comparison to this novel approach of connecting steel components with reinforcing bars by bonding sockets produced using WAAM, comparable connection methods such as bolting and welding of the reinforcing bars are investigated. The experimental investigations include pull-out tests of reinforcing bars from two types of sockets, centric tensile tests, and tensile shear tests of the two injection mortars investigated on different surfaces. This data publication includes all test results.
DOI: 10.5061/dryad.cfxpnvx3f
title: The fungus Leptosphaerulina persists in Anopheles gambiae and induces melanization

description: Anopheles mosquitoes are associated with diverse microorganisms that could
 have important impacts on host biology and vectoral capacity. Eukaryotic
 symbionts such as fungi have been isolated from Anopheles. Whether they
 are stably associated and transstadially transmitted across mosquito life
 history or to their subsequent generation and their fitness cost thereof
 remains largely unexplored. There is need to find anopheline fungal
 symbionts that can be maintained across life stages or vertically
 transmitted, otherwise just conferring protection without intimate
 co-existence may limit their sustainable utilization.  Here, we
 show that Leptosphaerulina sp. fungus isolated from the midgut of
 Anopheles gambiae possess a stable relationship with the host. The fungus
 imposes minimal fitness cost when re-introduced through co-feeding and is
 transstadially transmitted across developmental stages and to their
 subsequent progeny, and is present in field larvae and adult mosquitoes at
 moderate levels across geographical regions. We observe that induction of
 host immunity was necessary for its establishment and persistence in
 Anopheles gambiae. These traits were attributed to systemic infection of
 the midgut and reproductive tissues. We anticipate that this isolate could
 be exploited in paratransgenesis.
description: Fungus was isolated from dissected mosquito guts and reintroduced
 through co-feeding; presence and densities were determined by culture and
 high resolution melting (HRM-qPCR) Aassay. sequencing and resequencing
 were used to confirm isolates in developmental stages and their
 offspring.
DOI: 10.5061/dryad.3bk3j9kgr
title: Crop diversity benefits carabid and pollinator communities in landscapes with semi-natural habitats

description: 1. In agricultural landscapes, arthropods provide essential ecosystem
 services such as biological pest control and pollination. Intensified crop
 management practices and homogenization of landscapes have led to declines
 among such organisms. Semi-natural habitats, associated with high numbers
 of these organisms, are increasingly lost from agricultural landscapes but
 diversification by increasing crop diversity has been proposed as a way to
 reverse observed arthropod declines and thus restore ecosystem services.
 However, whether or not an increase in the diversity of crop types within
 a landscape promotes diversity and abundances of pollinating and
 predaceous arthropods, and how semi-natural habitats might modify this
 relationship, is not well understood. 2. To test how crop diversity and
 the proportion of semi-natural habitats within a landscape are related to
 the diversity and abundance of beneficial arthropod communities, we
 collected primary data from seven studies focusing on natural enemies
 (carabids and spiders) and pollinators (bees and hoverflies) from 154 crop
 fields in Southern Sweden between 2007 and 2017. 3. Crop diversity within
 a 1-km radius around each field was positively related to the Shannon
 diversity index of carabid and pollinator communities in landscapes rich
 in semi-natural habitats. Abundances were mainly affected by the
 proportion of semi-natural habitats in the landscape, with decreasing
 carabid and increasing pollinator numbers as the proportion of this
 habitat type increased. Spiders showed no response to either crop
 diversity or the proportion of semi-natural habitats. 4. Synthesis and
 applications. We show that the joint effort of preserving semi-natural
 habitats and promoting crop diversity in agricultural landscapes is
 necessary to enhance communities of natural enemies and pollinators. Our
 results suggest that increasing the diversity of crop types can contribute
 to the conservation of service-providing arthropod communities,
 particularly if the diversification of crops targets complex landscapes
 with a high proportion of semi-natural habitats.    
description: The dataset is a compilation from seven independent studies
 carried out in the province of Skåne in southern Sweden looking at
 cabadis, spider and wild pollinator abundances. The
 dataset was analised in R and al models were build and analised using lme4
 and glmr packages.
DOI: 10.5061/dryad.d2547d811
title: Data from: Genetic identity and herbivory drive the invasion of a common aquatic microbial invader - phytoplankton and zooplankton abundance

description: Despite the increasing number of species invasions, the factors driving
 invasiveness are still under debate. This is particularly the case for
 ‘invisible’ invasions by aquatic microbial species. Since in many cases
 only a few individuals or propagules enter a new habitat, their genetic
 variation is low and might limit their invasion success, known as the
 genetic bottleneck. Thus, a key question is, how genetic identity and
 diversity of invading species influences their invasion success and,
 subsequently, affect the resident community. We conducted invader-addition
 experiments using genetically different strains of the globally invasive,
 aquatic cyanobacterium Raphidiopsis raciborskii (formerly:
 Cylindrospermopsis raciborskii) to determine the role of invader identity
 and genetic diversity (strain richness) at four levels of herbivory. We
 tested the invasion success of solitary single strain invasions against
 the invader genetic diversity, which was experimentally increased up to
 ten strains (multi-strain populations). By using amplicon sequencing we
 determined the strain-specific invasion success in the multi-strain
 treatments and compared those with the success of these strains in the
 single-strain treatments. Furthermore, we tested for the invasion success
 under different herbivore pressures. We showed that high grazing pressure
 by a generalist herbivore prevented invasion, whereas a specialist
 herbivore enabled coexistence of consumer and invader. We found a weak
 effect of diversity on invasion success only under highly competitive
 conditions. When invasions were successful, the magnitude of this success
 was strain-specific and consistent among invasions performed with
 single-strain or multi-strain populations. A strain-specific effect was
 also observed on the resident phytoplankton community composition,
 highlighting the strong role of invader genetic identity. Our results
 point to a strong effect of the genetic identity on the invasion success
 under low predation pressure. The genetic diversity of the invader
 population, however, had little effect on invasion success in our study,
 in contrast to most previous findings. Instead, it is the interaction
 between the consumer abundance and type together with the strain identity
 of the invader that defined invasion success. This study underlines the
 importance of strain choice in invasion research and in ecological studies
 in general.
description: Phytoplankton and zooplankton biomass was quantified using
 inverted light microscopy, except for the quantification of Synechococcus
 elongatus which was filtered on 0.2 µm membrane filters, stained with
 acridin orange and quantified using fluorescence microscopy. The relative
 contribution of different genotyp in the experiment was quantified using
 Amplicon Amplification and Sequencing on the basis of pre-established
 diagnostic sequences.
DOI: 10.5061/dryad.vx0k6djpc
title: One year after ICU admission for severe community-acquired pneumonia of bacterial, viral or unidentified etiology. What are the outcomes?

description: Introduction: Multiplex polymerase chain reaction (mPCR) for
 respiratory virus testing is increasingly used in community-acquired
 pneumonia (CAP), however data on one-year outcome in intensive care unit
 (ICU) patients with reference to the causative pathogen are
 scarce.  Materials and Methods: We performed a single-center
 retrospective study in 123 ICU patients who had undergone respiratory
 virus testing for CAP by mPCR and with known one-year survival status.
 Functional status including dyspnea (mMRC score), autonomy (ADL Katz
 score) and need for new home-care ventilatory support was assessed at a
 one-year post-ICU follow-up. Mortality rates and functional status were
 compared in patients with CAP of a bacterial, viral or unidentified
 etiology one year after ICU admission. Results: The
 bacterial, viral and unidentified groups included 19 (15.4%), 37 (30.1%),
 and 67 (54.5%) patients, respectively. In multivariate analysis, one-year
 mortality in the bacterial group was higher compared to the viral group
 (HR 2.92, 95% CI 1.71-7.28, p=0.02) and tended to be higher
 compared to the unidentified etiology group (p=0.06); but no difference
 was found between the viral and the unidentified etiology group (p=0.43).
 In 64/83 one-year survivors with a post-ICU follow-up consultation, there
 were no differences in mMRC score, ADL Katz score and new home-care
 ventilatory support between the groups
 (p=0.52, p=0.37, p=0.24, respectively). Severe dyspnea
 (mMRC score = 4 or death), severe autonomy deficiencies (ADL Katz score ≤
 2 or death), and major adverse respiratory events (new home-care
 ventilatory support or death) were observed in 52/104 (50.0%), 47/104
 (45.2%), and 65/104 (62.5%) patients, respectively; with no difference
 between the bacterial, viral and unidentified
 group: p=0.58, p=0.06, p=0.61, respectively.
 Conclusions: CAP of bacterial origin had a poorer outcome than CAP of
 viral or unidentified origin. At one-year, impairment of functional status
 was frequently observed, with no difference according to the etiology.
DOI: 10.15468/dl.85nxz9
title: Occurrence Download

description: A dataset containing 398 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Biancaea sappan",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 398 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002434-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7sqv9s4qf
title: Facial attractiveness data

description: Facial appearance expresses numerous cues about physical qualities as well
 as psychosocial and personality traits. Attractive faces are recognized
 clearly when seen and are often viewed advantageously in professional,
 social and romantic relationships. On the other hand, self-perceived
 attractiveness is not well understood and has been mainly attributed to
 psychological and cognitive factors. Here we study a large young adult
 population (n = 601) to assess the effect of facial appearance on
 self-perceived facial attractiveness.
DOI: 10.5061/dryad.hqbzkh1d0
title: Metagenomics: A viable tool for reconstructing herbivore diet

description: Metagenomics can generate data on the diet of herbivores, without the need
 for primer selection and PCR enrichment steps as is necessary in
 metabarcoding. Metagenomic approaches to diet analysis have remained
 relatively unexplored, requiring validation of bioinformatic steps.
 Currently, no metagenomic herbivore diet studies have utilised both
 chloroplast and nuclear markers as reference sequences for plant
 identification, which would increase the number of reads that could be
 taxonomically informative. Here, we explore how in silico simulation of
 metagenomic datasets resembling sequences obtained from faecal samples can
 be used to validate taxonomic assignment. Using a known list of sequences
 to create simulated datasets, we derived reliable identification
 parameters for taxonomic assignments of sequences. We applied these
 parameters to characterise the diet of western capercaillies (Tetrao
 urogallus) located in Norway, and compared the results with metabarcoding
 trnL P6 loop data generated from the same samples. Both methods performed
 similarly in the number of plant taxa identified (metagenomics 42 taxa,
 metabarcoding 43 taxa), with no significant difference in species
 resolution (metagenomic 24%, metabarcoding 23%). We further observed that
 while metagenomics was strongly affected by the age of faecal samples,
 with fresh samples outperforming old samples, metabarcoding was not
 affected by sample age. On the other hand, metagenomics allowed us to
 simultaneously obtain the mitochondrial genome of the western
 capercaillies, thereby providing additional ecological information. Our
 study demonstrates the potential of utilising metagenomics for diet
 reconstruction but also highlights key considerations as compared to
 metabarcoding for future utilisation of this technique.
DOI: 10.5061/dryad.3j9kd51fr
title: Immigration status, ethnicity, and outcomes following ischemic stroke

description: Objective: To assess the association between immigration status and
 ethnicity and the outcomes of mortality and vascular event recurrence
 following ischemic stroke in Ontario, Canada. Methods: We conducted a
 retrospective cohort study using linked administrative and clinical
 registry-based data from 2002 to 2018 and compared hazards of all-cause
 mortality and vascular event recurrence in immigrants and long-term
 residents using inverse probability of treatment weighting accounting for
 age, sex, income and comorbidities. We stratified analyses by age (≤ 75
 and &gt; 75 years) and used interaction terms to evaluate if the
 association between immigration status and outcomes varied with age or
 ethnicity. Results: We followed 31,918 adult patients, of whom 2740 (8.6%)
 were immigrants, for a median follow-up of 5 years. Immigrants had a lower
 mortality than long-term residents (46.1% vs. 64.5%) which was attenuated
 after adjustment (hazard ratio 0.94; 95% confidence interval 0.88-1.00),
 but persisted in those aged under 75 years (HR 0.82; 0.74-0.91). Compared
 to their respective ethnic long-term resident counterparts, the adjusted
 hazard of death was higher in South Asian immigrants, similar in Chinese
 immigrants, and lower in other immigrants (P value for interaction =
 0.003). The adjusted hazard of vascular event recurrence (HR 1.01;
 0.92-1.11) was similar in immigrants and long-term residents, and this
 observation persisted across all age and ethnic groups. Conclusions:
 Long-term mortality following ischemic stroke is lower in immigrants and
 long-term residents, but is similar after adjustment of baseline
 characteristics, and it is modified by age at the time of stroke and by
 ethnicity.
DOI: 10.5061/dryad.547d7wm61
title: Data from: The size, symmetry, and color saturation of a male guppy’s ornaments forecast his resistance to parasites

description: Sexually selected ornaments range from highly dynamic traits to those that
 are fixed during development and relatively static throughout sexual
 maturity. Ornaments along this continuum differ in the information they
 provide about the qualities of potential mates, such as their parasite
 resistance. Dynamic ornaments enable real-time assessment of the bearer’s
 condition: they can reflect an individual’s current infection status, or
 resistance to recent infections. Static ornaments, however, are not
 affected by recent infection but may instead indicate an individual’s
 genetically-determined resistance, even in the absence of infection. Given
 the typically aggregated distribution of parasites among hosts, infection
 is unlikely to affect the ornaments of the vast majority of individuals in
 a population: static ornaments may therefore be the more reliable
 indicators of parasite resistance. To test this hypothesis, we quantified
 the ornaments of male guppies, Poecilia reticulata, before experimentally
 infecting them with Gyrodactylus turnbulli. Males with more left-right
 symmetrical black coloration and those with larger areas of orange
 coloration, both static ornaments, were more resistant. However, males
 with more saturated orange coloration, a dynamic ornament, were less
 resistant. Female guppies often prefer symmetrical males with larger
 orange ornaments, suggesting parasite-mediated natural and sexual
 selection act in concert on these traits.
description: Details on data collection and processing are given in the
 manuscript and supplement, including R script used.
description: All information for re-use of these data is available in the
 manuscript and supplement.
DOI: 10.5061/dryad.w3r2280nk
title: Shedding light on environmentally transmitted parasites: darker conditions within lakes promote larger epidemics

description: Parasite fitness depends on a successful journey from one host to another.
 For parasites that are transmitted environmentally, abiotic conditions
 might modulate the success of this journey. Here we evaluate how light, a
 key abiotic factor, influences spatiotemporal patterns of zooplankton
 disease where light varies seasonally, across lakes, and with depth in a
 lake. In an in situ experiment using those three sources of variation, we
 tested the sensitivity of spores of two parasites to ambient light.
 Infectivity of both parasites was lower when exposed to ambient light in
 comparison to parasites exposed to otherwise similar conditions in the
 dark. The more sensitive parasite (the fungus, Metschnikowia) was damaged
 even under lower ambient light during late fall (November). With this
 differential sensitivity established, we evaluated links between light
 environment and natural outbreaks in lakes. Consistent with the
 incubations, epidemics of the less sensitive parasite (the bacterium,
 Pasteuria) started earlier in the fall (under higher ambient light), and
 both parasites had smaller outbreaks in more transparent lakes. Overall,
 light environment may impact the timing and size of disease outbreaks.
 Outbreaks could thus become exacerbated by human activities which darken
 waters, including lake browning associated with climate change and
 eutrophication.
description: These files include a dataset (LightExperimentData.txt)
 documenting the numbers of infected and uninfected Daphnia from the
 incubation experiment and a dataset (FieldDataLightEpidemics.txt)
 documenting epidemic size and characteristics of lakes in the field
 study.  We have included two R studio files for
 analysis of the datasets.
description: Use LightPaperExperimentAnalysis.R to analyze the dataset
 LightExperimentData.txt Use LightPaperFieldAnalysis.R
 to analyze the dataset FieldDataLightEpidemics