cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jv3d2
title: Data from: Substandard and falsified medicines in the UK: A retrospective review of drug alerts (2001–2011)

description: Objective: To determine the extent of substandard and falsified medicines
 in the UK. Design: A retrospective review of drug alerts and company-led
 recalls. Setting: The Medicines and Healthcare Products Regulatory Agency
 (MHRA) website search for drug alerts issued between 2001 and 2011.
 Eligibility criteria: Drug alerts related to quality defect in medicinal
 products. Main outcome measure: Relevant data about defective medicines
 reported in drug alerts and company-led recalls, including description of
 the defect, type of formulation, year of the alert and category of the
 alert. Results: There were 280 substandard medicines of which 222 were
 recalled. The two most frequent problems were contamination (74 incidents)
 and issues related to packaging (98 incidents). Formulations for
 parenteral administration (117 incidents) were the formulation most
 frequently affected. There were 11 falsified medicines, as defined by the
 MHRA, reported over the 11 year period. The number of defective medicines
 reported by the MHRA increased tenfold from five in 2001 to 50 in 2011.
 Conclusions: Substandard medicines are a significant problem in the UK. It
 is uncertain whether the increasing number of reports relates to improved
 detection or an increase in the number of substandard medicines.
description: Supplementary
 dataThis file include four
 supplementary tables related to the paper. This data is extracted mainly
 from the Medicines and Healthcare products Regulatory Agency
 (MHRA).
DOI: 10.5061/dryad.33p91
title: Data from: Extinction can be estimated from moderately sized molecular phylogenies

description: Hundreds of studies have been dedicated to estimating speciation and
 extinction from phylogenies of extant species. While it has long been
 known that estimates of extinction rates using trees of extant organisms
 are often uncertain, an influential paper by Rabosky (2010) suggested that
 when birth rates vary continuously across the tree estimates of the
 extinction fraction (i.e., extinction rate/speciation rate) will appear
 strongly bimodal, with a peak suggesting no extinction and a peak implying
 speciation and extinction rates are approaching equality. On the basis of
 these results, and the realistic nature of this form of rate variation, it
 is now generally assumed by many practitioners that extinction cannot be
 understood from molecular phylogenies alone. Here we reevaluated and
 extended the analyses of Rabosky (2010) and come to the opposite
 conclusion – namely, that it is possible to estimate extinction from
 molecular phylogenies, even with model violations due to heritable
 variation in diversification rate. Note that while it may be tempting to
 interpret our study as advocating the application of simple birth-death
 models, our goal here is to show how a particular model violation does not
 necessitate the abandonment of an entire field: use prudent caution, but
 do not abandon all hope.
description: scriptsThe scripts used to conduct the simulations.
DOI: 10.5061/dryad.802bs
title: Data from: Founded: genetic reconstruction of lineage diversity and kinship informs ex situ conservation of Cuban Amazon parrots (Amazona leucocephala)

description: Captive breeding is a widespread conservation strategy, yet such programs
 rarely include empirical genetic data for assessing management assumptions
 and meeting conservation goals. Cuban Amazon parrots (Amazona
 leucocephala) are considered vulnerable, and multiple on-island captive
 populations have been established from wild-caught and confiscated
 individuals of unknown ancestry. Here, we used mitochondrial haplotypic
 and nuclear genotypic data at 9 microsatellite loci to quantify the extent
 and distribution of genetic variation within and among captive populations
 in Zapata Swamp and Managua, Cuba, and to estimate kinship among breeders
 (n = 88). Using Bayesian clustering analysis, we detected 2 distinct
 clusters within the Zapata population, one of which was shared with
 Managua. Individuals from the cluster unique to Zapata possessed
 mitochondrial haplotypes with affinities to Cuban subspecies (A. l.
 leucocephala, A. l. palmarum); the shared cluster was similar, but also
 included haplotypes closely related to the subspecies restricted to Cayman
 Brac (A. l. hesterna). Overall mean kinship was low within each captive
 population (−0.026 to −0.012), with 19 and 11 recommended breeding pairs
 in Zapata and Managua, respectively, ranked according to mean kinship and
 informed by molecular sexing. Our results highlight the importance of
 understanding population history within ex situ management programs, while
 providing genetic information to directly inform Cuban parrot
 conservation.
description: Cuban_Parrot_JOH_DRYAD
DOI: 10.5061/dryad.df1vk
title: Data from: Within-host stochastic emergence dynamics of immune-escape mutants

description: Predicting the emergence of new pathogenic strains is a key goal of
 evolutionary epidemiology. However, the majority of existing studies have
 focussed on emergence at the population level, and not within a host. In
 particular, the coexistence of pre-existing and mutated strains triggers a
 heightened immune response due to the larger total pathogen population;
 this feedback can smother mutated strains before they reach an ample size
 and establish. Here, we extend previous work for measuring emergence
 probabilities in non-equilibrium populations, to within-host models of
 acute infections. We create a mathematical model to investigate the
 emergence probability of a fitter strain if it mutates from a
 self-limiting strain that is guaranteed to go extinct in the long-term. We
 show that ongoing immune cell proliferation during the initial stages of
 infection causes a drastic reduction in the probability of emergence of
 mutated strains; we further outline how this effect can be accurately
 measured. Further analysis of the model shows that, in the short-term,
 mutant strains that enlarge their replication rate due to evolving an
 increased growth rate are more favoured than strains that suffer a lower
 immune-mediated death rate (‘immune tolerance’), as the latter does not
 completely evade ongoing immune proliferation due to inter-parasitic
 competition. We end by discussing the model in relation to within-host
 evolution of human pathogens (including HIV, hepatitis C virus, and
 cancer), and how ongoing immune growth can affect their evolutionary
 dynamics.
description: HartfieldAlizon2015_WithinHost_SimCodeREADME.TXT FOR SIMULATION FILES This file is the source code for the emergence simulations used in the Hartfield and Alizon 2015 paper "Within-host stochastic dynamics of immune-escape mutants". Simulations are written in C and need to be compiled prior to execution. See blurb at start of each program for description and how to execute. Please also note that simulations use routines that are part of the GNU Scientific Library (GSL). Since GSL is distributed under the GNU General Public License (http://www.gnu.org/copyleft/gpl.html), you must download it separately from these files. Comments should be sent to Matthew Hartfield (matt.hartfield@gmail.com).
DOI: 10.5061/dryad.26c4s35
title: Data from: tableone: An open source Python package for producing summary statistics for research papers

description: Objectives: In quantitative research, understanding basic parameters of
 the study population is key for interpretation of the results. As a
 result, it is typical for the first table (“Table 1”) of a research paper
 to include summary statistics for the study data. Our objectives are
 2-fold. First, we seek to provide a simple, reproducible method for
 providing summary statistics for research papers in the Python programming
 language. Second, we seek to use the package to improve the quality of
 summary statistics reported in research papers. Materials and Methods: The
 tableone package is developed following good practice guidelines for
 scientific computing and all code is made available under a permissive MIT
 License. A testing framework runs on a continuous integration server,
 helping to maintain code stability. Issues are tracked openly and public
 contributions are encouraged. Results: The tableone software package
 automatically compiles summary statistics into publishable formats such as
 CSV, HTML, and LaTeX. An executable Jupyter Notebook demonstrates
 application of the package to a subset of data from the MIMIC-III
 database. Tests such as Tukey’s rule for outlier detection and Hartigan’s
 Dip Test for modality are computed to highlight potential issues in
 summarizing the data. Discussion and Conclusion: We present open source
 software for researchers to facilitate carrying out reproducible studies
 in Python, an increasingly popular language in scientific research. The
 toolkit is intended to mature over time with community feedback and input.
 Development of a common tool for summarizing data may help to promote good
 practice when used as a supplement to existing guidelines and
 recommendations. We encourage use of tableone alongside other methods of
 descriptive statistics and, in particular, visualization to ensure
 appropriate data handling. We also suggest seeking guidance from a
 statistician when using tableone for a research study, especially prior to
 submitting the study for publication.
description: Sample data for the
 Python TableOne packageThis is an example
 dataset intended only for demonstrating the Python tableone package. It
 comprises a single CSV file containing sample data collected from 1000
 patients admitted to intensive care units at a hospital in the United
 States. The variables are: age; systolic blood pressure, weight, type of
 intensive care unit, mechanical ventilation flag, length of stay, and
 hospital mortality. The data is a subset of the 2012 PhysioNet Challenge
 Data (https://physionet.org/challenge/2012/), which is itself a subset of
 the MIMIC-III dataset
 (https://www.nature.com/articles/sdata201635).pn2012_demo.csv
DOI: 10.5061/dryad.mc5m6
title: Data from: Population size-structure dependent fitness and ecosystem consequences in Trinidadian guppies

description: 1. Decades of theory and recent empirical results have shown that
 evolutionary, population, community and ecosystem properties are the
 result of feedbacks between ecological and evolutionary processes. The
 vast majority of theory and empirical research on these eco-evolutionary
 feedbacks has focused on interactions among population size and mean
 traits of populations. 2. However, numbers and mean traits represent only
 a fraction of the possible feedback dimensions. Populations of many
 organisms consist of different size classes that differ in their impact on
 the environment and each other. Moreover, rarely do we know the map of
 ecological pathways through which changes in numbers or size structure
 cause evolutionary change. The goal of this study was to test the role of
 size structure in eco-evolutionary feedbacks of Trinidadian guppies and to
 begin to build an eco-evolutionary map along this unexplored dimension. 3.
 We used a factorial experiment in mesocosms wherein we crossed high- and
 low-predation guppy phenotypes with population size structure. We tested
 the ability of changes in size structure to generate selection on the
 demographic rates of guppies using an integral projection model (IPM). To
 understand how fitness differences among high- and low-predation
 phenotypes may be generated, we measured the response of the biomass of
 lower trophic levels and nutrient cycling to the different phenotype and
 size structure treatments. 4. We found a significant interaction between
 guppy phenotype and the size structure treatments for absolute fitness.
 Size structure had a very large effect on invertebrate biomass in the
 mesocosms, but there was little or no effect of the phenotype. The effect
 of size structure on algal biomass depended on guppy phenotype, with no
 difference in algal biomass in populations with more, smaller guppies, but
 a large decrease in algal biomass in mesocosms with phenotypes adapted to
 low-predation risk. 5. These results indicate an important role for size
 structure partially driving eco-evolutionary feedbacks in guppies. The
 changes in the ecosystem suggest that the absence of a steep decline in
 guppy fitness of the low-predation risk populations is likely due to
 higher consumption of algae when invertebrates are comparatively rare.
 Overall, these results demonstrate size structure as a possible dimension
 through which eco-evolutionary feedbacks may occur in natural populations.
description: Guppy
 DataAll Ecosystem
 Data
DOI: 10.5061/dryad.17jn0fq
title: Data from: The association between mitochondrial genetic variation and reduced colony fitness in an invasive wasp

description: Despite the mitochondrion’s long recognised role in energy production,
 mitochondrial DNA (mtDNA) variation commonly found in natural populations
 was assumed to be effectively neutral. However, variation in mtDNA has now
 been increasingly linked to phenotypic variation in life-history traits
 and fitness. We examined whether the relative fitness in native and
 invasive common wasp (Vespula vulgaris) populations in Belgium and New
 Zealand (NZ), respectively, can be linked to mtDNA variation. Social wasp
 colonies in NZ were smaller with comparatively fewer queen cells,
 indicating a reduced relative fitness in the invaded range. Interestingly,
 queen cells in this population were significantly larger leading to larger
 queen offspring. By sequencing 1872 bp of the mitochondrial genome we
 determined mitochondrial haplotypes and detected reduced genetic diversity
 in NZ. Three common haplotypes in NZ frequently produced many queens,
 whereas the four rare haplotypes produced significantly fewer or no
 queens. The entire mitochondrial genome for each of these haplotypes was
 sequenced to identify polymorphisms associated with fitness reduction. We
 found 16 variable sites, however, no non-synonymous mutation that was
 clearly causing impaired mitochondrial function was detected. We discuss
 how detected variants may alter secondary structures, gene expression or
 mito-nuclear interactions, or could be associated with nuclear-encoded
 variation. Whatever the ultimate mechanism, we show reduced fitness and
 mtDNA variation in an invasive wasp population as well as specific mtDNA
 variants associated with fitness variation within this population. Ours is
 one of only a few studies that confirm fitness impacts of mtDNA variation
 in wild non-model populations.
description: Vespula data
 overviewVespula vulgaris nests
 used in the nest analysis and mitochondrial DNA analysis. Sample name:
 internal name used to identify samle; Queen cells and worker cells are
 estimated from queen and worker comb area.;Latitude and longitude give the
 sampling location in New Zealand or Belgium; "DNA from?"
 indicates which DNA extraction method was used.
DOI: 10.5061/dryad.3fr47
title: Data from: Range expansion in asexual dandelions: selection for general-purpose genotypes?

description: Phenotypic plasticity and broad ecological tolerance are hypothesized as
 important traits in the range expansion of asexual species, because
 individual asexual lineages have to face spatial and temporal
 environmental variation with limited opportunity for genetic adaptation.
 The hypothesis that asexual lineages are general-purpose genotypes (GPG)
 has been previously tested, with mixed results, in species that have both
 sexual and asexual variants. Such comparisons can be confounded with
 intra-specific ploidy level differences that are often observed between
 the two reproductive types. Avoiding the confounding effects of ploidy
 differences, we test whether northward range expansion selects for a GPG
 strategy in asexual lineages of the common dandelion (Taraxacum
 officinale), a species that shows geographic parthenogenesis. We compared
 the biomass of asexual lineages that were collected along a geographic
 transect from close to the asexuals’ area of origin (central Europe, where
 asexuals descend from sexual ancestors in mixed populations) towards their
 northern distribution edge (Northern Europe, where only asexual lineages
 occur) in three different experimental environments: optimal, drought and
 shaded conditions. The geometric mean performance across test environments
 did not differ significantly between plants from different regions along
 the transect. However, southern lineages typically showed larger
 differences in biomass between different test environments, mainly caused
 by a relatively high performance in the optimal environment. Northern and
 mid-latitude lineages showed more even performance across the different
 environments. Synthesis. Our results suggest that phenotypic plasticity is
 important in the asexual range expansion of Taraxacum officinale and that
 range shifting in this species is accompanied by a change in phenotypic
 plasticity strategy from lineages with high ability to increase biomass in
 optimal growing conditions (master-of-some strategy) to lineages that
 maintain more constant performance in different environments (GPG or
 jack-of-all-trades strategy) from core to range edge.
description: Oplaat_JECOL_GPGpaper_dataTrait scores of dandelion genotypes that were collected along a transect of historic range expansion in north-western Europe, when grown in a common greenhouse environment under control, drought and shade experimental treatments.
DOI: 10.6084/m9.figshare.19519494
title: Novel H5N6 reassortants bearing the clade 2.3.4.4b HA gene of H5N8 virus have been detected in poultry and caused multiple human infections in China

description: The globally circulating H5N8 avian influenza viruses bearing the clade 2.3.4.4b hemagglutinin (HA) gene are responsible for the loss of more than 33 million domestic poultry since January 2020. Moreover, the H5N8 viruses have reassorted with other avian influenza viruses and formed H5N1, H5N2, H5N3, H5N4, and H5N5 viruses in Europe, Africa, and North America. In this study, we analyzed 15 H5N6 viruses isolated from poultry and seven H5N6 viruses isolated from humans, and found these viruses formed seven different genotypes by deriving the clade 2.3.4.4b HA gene of H5N8 viruses, the neuraminidase of domestic duck H5N6 viruses, and internal genes of different viruses that previously circulated in domestic ducks and wild birds in China. Two of these genotypes (genotype 3 and genotype 6) have caused human infections in multiple provinces. The H5N6 viruses isolated from poultry have distinct pathotypes in mice; some of them replicate systemically and are highly lethal in mice. Although these viruses exclusively bind to avian-type receptors, it is worrisome that they may obtain key mutations that would increase their affinity for human-type receptors during replication in humans. Our study indicates that the novel H5N6 reassortants bearing the clade 2.3.4.4b HA gene of H5N8 viruses were generated through reassortment in domestic ducks and may have spread across a wide area of China, thereby posing a new challenge to the poultry industry and human health. Our findings emphasize the importance of careful monitoring, evaluation, and control of the H5N6 viruses circulating in nature.
DOI: 10.6084/m9.figshare.19519494.v2
title: Novel H5N6 reassortants bearing the clade 2.3.4.4b HA gene of H5N8 virus have been detected in poultry and caused multiple human infections in China

description: The globally circulating H5N8 avian influenza viruses bearing the clade 2.3.4.4b hemagglutinin (HA) gene are responsible for the loss of more than 33 million domestic poultry since January 2020. Moreover, the H5N8 viruses have reassorted with other avian influenza viruses and formed H5N1, H5N2, H5N3, H5N4, and H5N5 viruses in Europe, Africa, and North America. In this study, we analyzed 15 H5N6 viruses isolated from poultry and seven H5N6 viruses isolated from humans, and found these viruses formed seven different genotypes by deriving the clade 2.3.4.4b HA gene of H5N8 viruses, the neuraminidase of domestic duck H5N6 viruses, and internal genes of different viruses that previously circulated in domestic ducks and wild birds in China. Two of these genotypes (genotype 3 and genotype 6) have caused human infections in multiple provinces. The H5N6 viruses isolated from poultry have distinct pathotypes in mice; some of them replicate systemically and are highly lethal in mice. Although these viruses exclusively bind to avian-type receptors, it is worrisome that they may obtain key mutations that would increase their affinity for human-type receptors during replication in humans. Our study indicates that the novel H5N6 reassortants bearing the clade 2.3.4.4b HA gene of H5N8 viruses were generated through reassortment in domestic ducks and may have spread across a wide area of China, thereby posing a new challenge to the poultry industry and human health. Our findings emphasize the importance of careful monitoring, evaluation, and control of the H5N6 viruses circulating in nature.
DOI: 10.5061/dryad.vr165
title: Data from: Group elicitations yield more consistent, yet more uncertain experts in understanding risks to ecosystem services in New Zealand bays

description: The elicitation of expert judgment is an important tool for assessment of
 risks and impacts in environmental management contexts, and especially
 important as decision-makers face novel challenges where prior empirical
 research is lacking or insufficient. Evidence-driven elicitation
 approaches typically involve techniques to derive more accurate
 probability distributions under fairly specific contexts. Experts are,
 however, prone to overconfidence in their judgements. Group elicitations
 with diverse experts can reduce expert overconfidence by allowing
 cross-examination and reassessment of prior judgements, but groups are
 also prone to uncritical “groupthink” errors. When the problem context is
 underspecified the probability that experts commit groupthink errors may
 increase. This study addresses how structured workshops affect expert
 variability among and certainty within responses in a New Zealand case
 study. We find that experts’ risk estimates before and after a workshop
 differ, and that group elicitations provided greater consistency of
 estimates, yet also greater uncertainty among experts, when addressing
 prominent impacts to four different ecosystem services in coastal New
 Zealand. After group workshops, experts provided more consistent ranking
 of risks and more consistent best estimates of impact through increased
 clarity in terminology and dampening of extreme positions, yet probability
 distributions for impacts widened. The results from this case study
 suggest that group elicitations have favorable consequences for the
 quality and uncertainty of risk judgments within and across experts,
 making group elicitation techniques invaluable tools in contexts of
 limited data.
description: Expert data for ranks,
 mode comparison, and interval comparisonMultiple sheets in the
 workbook show data for expert responses ranking and quantifying impacts
 (with uncertainty) on ecosystem services. On ranking sheets, each row
 corresponds to ranking of different experts. On mode comparison,
 "absolute diff" indicates the difference of each expert's
 estimate of impact compared to the mean value. On interval comparison,
 "range" indicates the interval range for each expert's
 uncertainty in the impact score.Expert_data_dryad.xlsx