cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t1g1jwt5c
title: Data for: Increasing information content and diagnosability in family-level classifications

description: Higher-level classifications often must account for monotypic taxa
 representing depauperate evolutionary lineages and lacking synapomorphies
 of their better-known, well-defined sister clades. In a ranked (Linnean)
 or unranked (phylogenetic) classification system, discovering such a
 depauperate taxon does not necessarily invalidate the rank classification
 of sister clades. Named higher taxa must be monophyletic to be
 phylogenetically valid. Ranked taxa above the species level should also
 maximize information content, diagnosability, and utility (e.g., in
 biodiversity conservation). In spider classification, families are the
 highest rank that is systematically catalogued, and incertae
 sedis is not allowed. Consequently, it is important that
 family-level taxa be well defined and informative. We revisit the
 classification problem of Orbipurae, an unranked suprafamilial clade
 containing the spider families Nephilidae, Phonognathidae, and
 Araneidae sensu stricto. We argue that, to maximize
 diagnosability, information content, conservation utility, and practical
 taxonomic considerations, this “splitting” scheme is superior to its
 recently proposed alternative, which lumps these families together as
 Araneidae sensu lato. We propose to redefine Araneidae and
 recognize a monogeneric spider family, Paraplectanoididae fam. nov. to
 accommodate the depauperate lineage Paraplectanoides. We present
 new subgenomic data to stabilize Orbipurae topology which also supports
 our proposed family-level classification. Our example from spiders
 demonstrates why classifications must be able to accommodate depauperate
 evolutionary lineages, for example, Paraplectanoides. Finally,
 although clade age should not be a criterion to determine rank, other
 things being equal, comparable ages of similarly ranked taxa do benefit
 comparative biology. [Classification, family rank, phylogenomics,
 systematics, monophyly, spider phylogeny.]
DOI: 10.5061/dryad.jwstqjqd0
title: Seasonal patterns of dietary partitioning in vertebrates

description: Dietary partitioning plays a central role in biological communities, yet
 the extent of partitioning often varies dramatically over time. Food
 availability may drive temporal variation in dietary partitioning, but
 alternative paradigms offer contrasting predictions about its effect. We
 compiled estimates of dietary overlap between co-occurring vertebrates to
 test whether partitioning is greater during periods of high or low food
 abundance. We found that dietary partitioning was generally greatest when
 food abundance was low, suggesting that competition for limited food
 drives partitioning. The extent of dietary partitioning in birds and
 mammals was also related to seasonality in primary productivity. As
 seasonality increased, partitioning increased during the nonbreeding
 season for birds and the breeding season for mammals. Although some
 hypotheses invoke changes in dietary breadth to explain temporal variation
 in dietary partitioning, we found no association between dietary breadth
 and partitioning. These results have important implications for the
 evolution of dietary divergence.
DOI: 10.7272/q6vm49jf
title: Impairment of endothelial function by cigarette smoke is not caused by a specific smoke constituent, but by vagal input from the airway

description: Background: Exposure to tobacco or marijuana smoke, or e-cigarette
 aerosols, causes vascular endothelial dysfunction in humans and rats. We
 aimed to determine what constituent, or class of constituents, of smoke,
 is responsible for endothelial functional impairment. Methods: We
 investigated several smoke constituents that we hypothesized to mediate
 this effect by exposing rats and measuring arterial flow-mediated dilation
 (FMD) pre- and post-exposure. We measured FMD before and after inhalation
 of sidestream smoke from research cigarettes containing normal and reduced
 nicotine level with and without menthol, as well as two of the main
 aldehyde gases found in both smoke and e-cigarette acrolein (acrolein and
 acetaldehyde), and inert carbon nanoparticles. Results: FMD was reduced by
 all four kinds of research cigarettes, with the extent of reduction
 ranging from 20–46% depending on the cigarette type. While nicotine was
 not required for the impairment, higher nicotine levels in smoke were
 associated with a greater percent reduction of FMD (41.1±4.5% percent
 reduction vs. 19.2±9.5%; p=0.047). Lower menthol levels were also
 associated with a greater percent reduction of FMD (18.5±9.8% vs.
 40.5±4.8%; p=0.048). Inhalation of acrolein or acetaldehyde gases at
 smoke-relevant concentrations impaired FMD by roughly 50% (p=0.001).
 However, inhalation of inert carbon nanoparticles at smoke-relevant
 concentrations with no gas phase also impaired FMD by a comparable amount
 (p&lt;0.001). Bilateral cervical vagotomy blocked the impairment of
 FMD by tobacco smoke. Conclusions: There is no single constituent or class
 of constituents responsible for acute impairment of endothelial function
 by smoke; rather, we propose that acute endothelial dysfunction by
 disparate inhaled products is caused by vagus nerve signaling initiated by
 airway irritation.
description: Raw ultrasound data were collected by a 35 MHz ultrasound
 transducer (Vevo660 and Vevo 3100 LT; VisualSonics, Toronto, Canada).
 Ultrasound images were processed using an automated system (Brachial
 Analyzer; Medical Imaging Applications, Coralville, IA).
description: Use VisualSonics Vevo software for viewing .vsi images and
 Brachial Analyzer for diameter measurements.
DOI: 10.5061/dryad.zgmsbccfk
title: Heat tolerance of marine ectotherms in a warming Antarctica

description: Global warming is affecting the Antarctic continent in complex ways.
 Because Antarctic organisms are specialized to living in the cold, they
 are vulnerable to increasing temperatures, though quantitative analyses of
 this issue are currently lacking. Here we compiled a total of 184
 estimates of heat tolerance belonging to 39 marine species and quantified
 how survival is affected concomitantly by the intensity and duration of a
 thermal stress. Species exhibit thermal limits displaced towards colder
 temperatures, with contrasting strategies between arthropods and fish that
 exhibit low tolerance to acute heat challenges, and brachiopods,
 echinoderms and molluscs that tend to be more sensitive to chronic
 exposure. These differences might be associated with mobility. A dynamic
 mortality model suggests that Antarctic organisms already encounter
 temperatures that might be physiologically stressful and indicate that
 these ecological communities are indeed vulnerable to ongoing rising
 temperatures.
description: We performed an extensive
 review of the literature and built a database of heat tolerance for marine
 organisms distributed in the Southern Ocean (i.e., south of 60° S
 latitude). We started by
 retrieving information published in previous reviews on the
 subject, and combined the
 original sources from these reviews with more recent published references
 found with a Boolean search in ISI Web of Science with the following
 keywords: ‘thermal
 tolerance’ or ‘Antarctic animals’ or ‘CTmax’ or ‘thermal limits’ or ‘heat
 tolerance’. The search for heat tolerance ended in August 2020. The
 resulting dataset was combined with high-resolution ambient temperature
 data records, obtained in intertidal and subtidal Antarctic
 environments, to estimate thermal mortality in field conditions.
description: All analyses were performed with open source R (https://cran.r-project.org/)
DOI: 10.5061/dryad.dz08kps0z
title: Milkweed plants bought at nurseries may expose monarch caterpillars to harmful pesticide residues

description: The decline of monarch butterflies in both the eastern and western United
 States has garnered widespread public interest. Planting milkweeds, their
 larval host plants, has been promoted as one action individuals can take,
 but little is known with respect to potential pesticide contamination of
 store-bought milkweeds. In this study, we collected leaf samples from 235
 milkweed plants purchased at 33 retail nurseries across the US to screen
 for pesticides. Across all samples, we detected 61 different pesticides
 with an average of 12.2 (±5.0) compounds per plant. While only 9 of these
 compounds have been experimentally tested on monarch caterpillars,
 38 % of samples contained a pesticide above a concentration shown
 to have a sub-lethal effect for monarchs. We detected only a modest
 predictive ability of retailer size and milkweed species, and plants with
 labels advertising their value for wildlife did not have fewer pesticides
 at concentrations known to have a negative effect on monarchs. These
 results demonstrate the extensiveness of pesticide exposure within nursery
 milkweeds and the potential impacts on monarchs and other insects exposed
 to store-bought plants.
DOI: 10.5255/ukda-sn-9016-3
title: Mergers and Acquisitions Survey, 2013-2022: Secure Access

description: &lt;p&gt;The &lt;span style="font-style: italic;"&gt;Mergers and Acquisitions Survey&lt;/span&gt; presents information and data on the timing, value, number and methods of funding of Mergers and Acquisitions transactions involving UK businesses with deal values of £1 million and above.&lt;br&gt;&lt;br&gt;The &lt;span style="font-style: italic;"&gt;Mergers and Acquisitions Survey&lt;/span&gt; consists of three categories of investment:&lt;br&gt;&lt;/p&gt;&lt;ul&gt;&lt;li&gt;inward investment (acquisitions of UK companies by foreign companies);&lt;/li&gt;&lt;li&gt;outward investment (UK companies acquisitions of foreign companies);&lt;/li&gt;&lt;li&gt;domestic Mergers and Acquisitions (acquisitions of UK companies by other UK companies).&lt;br&gt;&lt;/li&gt;&lt;/ul&gt;&lt;p&gt;&lt;br&gt;The sampling source for the &lt;span style="font-style: italic;"&gt;Mergers and Acquisitions Survey&lt;/span&gt; was changed in January 2018; Bureau Van Dijk's Zephyr database is now used as the starting point for deal identification.&lt;br&gt;&lt;span style="font-style: italic;"&gt;&lt;br&gt;Linking to other business studies&lt;/span&gt;&lt;br&gt;These data contain Inter-Departmental Business Register (IDBR) reference numbers. These are anonymous but unique reference numbers assigned to business organisations. Their inclusion allows researchers to combine different business survey sources together. Researchers may consider applying for other business data to assist their research.&lt;br&gt;&lt;br&gt;Limited metadata is available about this study but further information about how the data are used, and the latest publications, are available on the &lt;a href="https://www.ons.gov.uk/businessindustryandtrade/changestobusiness/mergersandacquisitions" target="_blank" style="background-color: rgb(255, 255, 255);"&gt;ONS Mergers and Acquisitions&lt;/a&gt; webpages.&lt;br&gt;&lt;br&gt;&lt;span style="font-weight: bold;"&gt;Latest edition information&lt;/span&gt;&lt;br&gt;For the third edition (January 2026), annual inward, outward and domestic 2022 data files have been added to the study. The variable list for 2022 has also been added.&lt;/p&gt;
DOI: 10.5061/dryad.m37pvmd59
title: Drivers of within- and among-individual variation in risk-taking behaviour during reproduction in a long-lived bird

description: Plastic and selective mechanisms govern parental investment adjustments to
 predation threat. We investigated the relative importance of plasticity
 and selection in risk-taking propensity of incubating female common eiders
 Somateria mollissima facing unprecedented predation in SW Finland, Baltic
 Sea. Using a 12-year individual-based dataset, we examined within- and
 among-individual variation in flight initiation distance (FID), in
 relation to predation risk, nest detectability, individual traits and
 reproductive investment (NFID = 1009; Nindividual = 559). We expected
 females nesting in riskier environments (higher predation risk, lower nest
 concealment) to mitigate environmentally-imposed risk by exhibiting longer
 FIDs, and females investing more in current reproduction (older, in better
 condition or laying large clutches) to display shorter FIDs. The target of
 predation - adult or offspring - affected the mechanisms adapting
 risk-taking propensity; females plastically increased their FID under
 higher adult predation risk, while risk-avoiding breeders were predominant
 on islands with higher nest predation risk. Risk-taking females selected
 thicker nest cover, consistent with personality-matching habitat choice.
 Females plastically attenuated their antipredator response (shorter FIDs)
 with advancing age, and females in better body condition were more
 risk-taking, a result explained by selection processes. Future research
 should consider predator type when investigating the fitness consequences
 of risk-taking strategies.
DOI: 10.6084/m9.figshare.30244624
title: Atmospheric Chlorine Wet Deposition in China: National Decreases but Localized Increases in Urban Agglomerations

description: We compiled data from the network and 246 published studies to establish China's first long-term dataset of atmospheric Cl wet deposition from 1990 to 2020. Utilizing an optimized random forest model incorporating multi-source environmental factors, we generated a national Cl wet deposition grid dataset at 0.1° × 0.1° resolution for 2000–2020.
DOI: 10.6084/m9.figshare.30244624.v1
title: Atmospheric Chlorine Wet Deposition in China: National Decreases but Localized Increases in Urban Agglomerations

description: We compiled data from the network and 246 published studies to establish China's first long-term dataset of atmospheric Cl wet deposition from 1990 to 2020. Utilizing an optimized random forest model incorporating multi-source environmental factors, we generated a national Cl wet deposition grid dataset at 0.1° × 0.1° resolution for 2000–2020.
DOI: 10.15468/dl.pzqszb
title: Occurrence Download

description: A dataset containing 2215 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Portugal",
 "OccurrenceStatus is Present",
 "TaxonKey is Podarcis virescens",
 "Year 2000-2026"
 ]
}

 The dataset includes 2215 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003247-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7m0cfxpxs
title: Helpers slow senescence in a Tibetan cooperatively breeding bird

description: Sociality is known to be capable of slowing individual senescence, but it
 is unclear whether the effect differs for reproduction vs. survival in a
 sex-specific way. Here we predict that social benefits are directed toward
 1) somatic maintenance in harsh environments where high survival prospects
 of adults over young intensifies the trade-off between current and future
 reproduction, and 2) females that invest more in reproduction and have a
 greater marginal effect if their survival is improved by reducing the cost
 of reproduction. These two predictions are tested with cooperatively
 breeding Tibetan ground tits (Pseudopodoces humilis). Across the lifetime,
 both mothers and fathers with helpers did not differ in brood size at
 fledging from their counterparts without helpers. The presence of helpers
 reduced survival senescence of both parents, but mothers benefited more
 than fathers from receiving help. Consequently, the inherent sex
 difference in lifespan and along with lifetime reproductive success, as
 expressed in breeders of never-receiving help, became no longer obvious.
 The model of social modulation for senescence should facilitate the
 persistence of cooperative breeding in challenging environments.
DOI: 10.5061/dryad.vx0k6djw0
title: EEG and eyetracking response to static and moving stimuli

description: This dataset contains processed EEG and eyetracking recordings from an
 experiment in which twelve participants viewed a black disk either flashed
 in one position or moving in a straight line in one of six directions.
 Static stimuli were presented at nodes on a hexagonal grid, while moving
 stimuli moved in straight lines along the axes of the grid.
description: See preprint: https://www.biorxiv.org/content/10.1101/2022.06.26.496535v1
description: MATLAB, Python
DOI: 10.5061/dryad.8kprr4xrd
title: Reciprocal transplantation of two ecotypes of two species along a metal pollution gradient

description: This dataset consists of data collected during a field experiment that
 took place from the beginning of June to the end of September 2020,
 covering the entire growing season. This experiment was conducted in the
 former mining area of Sentein (department of Ariège, South West of France,
 42°49'30.3 "N, 0°53'53.3 "E), located at 2000m
 altitude at the subalpine belt of the Pyrenees Mountains on a calcareous
 rock. This dataset contains “Block, Habitat, Species, Ecotype and
 Neighbouring” as explanatory categorical variables and “Target survival”
 as binomial response variable. This data was analyzed in order to
 understand the importance of species and ecotypes stress-tolerance in
 competitive and facilitative responses to neighbours along metal-pollution
 gradients, and to assess both the effect of neighbours at different stress
 levels and the effect of metallic stress with and without neighbours.
description: All data were stored using Microsoft Excel and all the
 statistical analyses were done using R software (R Core Team
 2016).
DOI: 10.34740/kaggle/dsv/14650687
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.3n5tb2rm2
title: A fast machine-learning-guided primer design pipeline for selective whole genome amplification

description: Addressing many of the major outstanding questions in the fields of
 microbial evolution and pathogenesis will require analyses of populations
 of microbial genomes. Although population genomic studies provide the
 analytical resolution to investigate evolutionary and mechanistic
 processes at fine spatial and temporal scales – precisely the scales at
 which these processes occur – microbial population genomic research is
 currently hindered by the practicalities of obtaining sufficient
 quantities of the relatively pure microbial genomic DNA necessary for
 next-generation sequencing. Here we present swga2.0, an optimized and
 parallelized pipeline to design selective whole genome amplification
 (SWGA) primer sets. Unlike previous methods, swga2.0 incorporates active
 and machine learning methods to evaluate the amplification efficacy of
 individual primers and primer sets. Additionally, swga2.0 optimizes primer
 set search and evaluates strategies, including parallelization at each
 stage of the pipeline, to dramatically decrease program runtime from weeks
 to minutes. Here we describe the swga2.0 pipeline, including the empirical
 data used to identify primer and primer set characteristics, that improve
 amplification performance. Additionally, we evaluated the novel swga2.0
 pipeline by designing primers sets that successfully amplify Prevotella
 melaninogenica, an important component of the lung microbiome in cystic
 fibrosis patients, from samples dominated by human DNA.
description: Primer sets designed to amplify <em>P.
 melaninogenica</em> from samples dominated by human DNA were
 empirically tested to evaluate the efficacy of swga2.0. Six primer sets
 were created using <em>P. melaninogenica</em> strain ATCC
 25845 as the target genome with the human genome (GRCh38.p13) as
 background. The six primer sets were evaluated in duplicate on purified
 <em>P. melaninogenica</em> DNA (strain ATCC 25845), diluted to
 1% in purified human genomic DNA (Promega, female, catalog No. G1521).
 Briefly, the 1:99 target:background sample was digested with FspEI (New
 England Biolabs) according to the manufacturer's protocol. The
 digested sample was purified using AmpureXP beads (Beckman Coulter) prior
 to performing selective whole-genome amplification. Reactions were
 performed in a volume of 50 uL using 50 ng of digested DNA, SWGA primers
 (total concentration of all primers together = 3.5mM), 1x Phi29 buffer
 (New England Biolabs), 1 mM dNTPs, and 30 units Phi29 polymerase (New
 England Biolabs). Amplification conditions included a ramp-down from 35 to
 31C (5 min at 35C, 10 min at 34C, 15 min at 33C, 20 min at 32C, 25 min at
 31C), followed by a 16h amplification step at 30C. The polymerase was then
 denatured for 15 min at 65C. Amplified samples were purified using
 AmpureXP beads, prepared for Illumina sequencing, and sequenced on an
 Illumina MiSeq (150 bp, paired end). The unamplified sample was also
 sequenced to assess changes in sequencing coverage due to SWGA.
DOI: 10.6084/m9.figshare.30940052
title: Phylogenetic Data Matrix

description: Phylogenetic data matrix in ".tnt" format.
DOI: 10.6084/m9.figshare.30940052.v1
title: Phylogenetic Data Matrix

description: Phylogenetic data matrix in ".tnt" format.