cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9cnp5hqdj
title: Metrics of diabetes risk are only minimally improved by exercise training in postmenopausal breast cancer survivors

description: Context Insulin resistance is a risk factor for breast cancer recurrence.
 How exercise training changes fasting and post-glucose insulin resistance
 in breast cancer survivors is unknown. Objective To evaluate
 exercise-induced changes in post-glucose ingestion insulin concentrations,
 insulin resistance, and their associations with cancer-relevant biomarkers
 in breast cancer survivors. Setting The University of Massachusetts
 Kinesiology Department. Participants Fifteen postmenopausal breast cancer
 survivors not meeting the physical activity guidelines (150 minutes/week
 of exercise). Intervention a supervised 12-week aerobic exercise program
 (60 min/day, 3-4 days/week). Main outcome measures Post-glucose ingestion
 insulin was determined by peak insulin and area under the insulin curve
 (iAUC) during a five-sample oral glucose tolerance test. Insulin
 sensitivity was estimated from the Matsuda composite insulin sensitivity
 index (C-ISI). Changes in fitness and body composition were determined
 from submaximal VO2peak and dual energy X-ray absorptiometry
 (DEXA). Results Participants averaged 156.8±16.6 minutes/week of
 supervised exercise. Estimated VO2peak significantly increased
 (+2.8±1.4 ml/kg/min, p&lt;0.05) and body weight significantly
 decreased (-1.1±0.8 kg, p&lt;0.05) following the intervention. There
 were no differences in fasting insulin, iAUC, C-ISI or peak insulin
 following the intervention. Insulin was only significantly lower 120
 minutes following glucose consumption (68.8 ± 34.5 vs. 56.2 ± 31.9 uU/ml,
 p&lt;0.05), and there was a significant interaction with past/present
 aromatase inhibitor (AI) use for peak insulin (-11.99 (non-AI) vs +13.91
 (AI) uU/mL) and iAUC (-24.03 (non-AI) vs +32.73 (AI) uU/mL). Conclusions
 Exercise training had limited overall benefits on insulin concentrations
 following glucose ingestion in breast cancer survivors but was strongly
 influenced by AI use.
description: The data represents plasma c-peptide and glucose concentrations
 collected during an oral glucose tolerance test.
DOI: 10.5061/dryad.t4b8gthxf
title: Surveys of crocodilians in the hydroelectric dam, Brazilian Amazonia

description: We counts caimans in the Madeira River, before (2010-2011) and after
 (2012-2014, 2016-2019) hydroelectric dam.
DOI: 10.15468/dl.be2jwh
title: Occurrence Download

description: A dataset containing 89 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-3.2421 42.39047,-1.28006 42.39047,-1.28006 43.14567,-3.2421 43.14567,-3.2421 42.39047))",
 "OccurrenceStatus is Present",
 "TaxonKey is Ranunculus auricomus"
 ]
}

 The dataset includes 89 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002001-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qkx5zc
title: Occurrence Download

description: A dataset containing 265482 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "DatasetKey is one of (EOD – eBird Observation Dataset, iNaturalist Research-grade Observations)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Momotus lessonii",
 "Year 1990-2025"
 ]
}

 The dataset includes 265482 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001955-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.sj3tx961f
title: Data for: Tube feet regeneration and plasticity in the purple sea urchin (Strongylocentrotus purpuratus)

description: Sea urchins are key members of hydrodynamically intense habitats, such as
 open coast intertidal and shallow reefs. Secure attachment to the
 substrata, by means of tube feet and spines, is essential for survival.
 Previous studies suggest that environmental variables (i.e. hydrodynamics,
 substrate) can influence the morphology and adhesive performance of tube
 feet. Catastrophic failure of tube feet occurs often due to strong
 hydrodynamic forces. The time and ability of amputated tube feet to return
 to pre-amputation adhesive performance, and the interaction with
 environmental factors are unknown. To assess the dynamics of adhesive
 performance and re- generation of tube feet, we 1) evaluated phenotypic
 plasticity of disc surface area of two urchin populations inhabiting sites
 with different lithologies (field - in-situ conditions) and, 2) assessed
 regeneration of their functionality (tube foot length, time of disc first
 appearance, disc surface area, and tenacity) after amputation (laboratory
 - ex-situ conditions). Results showed that in the field, tube feet are
 plastic in their phenotype: sea urchins from the two sites differed in
 their disc surface area. Plasticity was also observed in the laboratory,
 where urchins regenerate tube feet that are shorter in length and have
 smaller discs compared to pre-amputation measurements. Thus, sea urchin
 tube feet recovering from amputation events in the intertidal may differ
 in their initial morphology and in the recovery period after amputation.
 Moreover, tube feet that were never amputated also decreased their disc
 area, suggesting that plasticity occurs on tube feet of urchins maintained
 in laboratory conditions. In shallow temperate reef systems, urchins are
 ecosystem engineers that affect the abundance and distribution of many
 other organisms. The plastic nature of morphological and adhesive
 abilities of sea urchin tube feet influences their ability to survive and
 dominate wave-battered habitats.
DOI: 10.5061/dryad.rv15dv44m
title: Data from: Urbanization re-shapes a food web

description: Cities represent humanity’s most intense impact on our Planet, with more
 than half of all humans now residing in urban areas. Indeed, urbanization
 has well understood impacts on both individual species and general
 patterns of biodiversity. However, species do not exist in isolation, but
 are instead members of complex interaction networks that shape patterns of
 diversity and influence ecosystem services. Despite the importance of
 species interaction for creating patterns of diversity, we do not
 understand how urbanization alters these interactions. Here, we
 investigate how an interaction network (food web) is reshaped by
 urbanization. We show that, consistent with theory, cities tend to support
 less diverse ecological communities, and rare species that interact with
 few species are particularly sensitive to urbanization. As a result,
 remnant urban food webs tend to have more interactions per species and
 greater connectance, creating more integrated interaction networks. We
 discuss the implications of this food web reshaping for ecological
 stability, eco-evolutionary dynamics, and the joining of interaction
 networks and conservation planning. The role of cities in reshaping
 interaction networks provides an interesting study of food web
 (dis)assembly, while also shedding light on new approaches to applied
 conservation issues.
DOI: 10.5061/dryad.7d7wm37r0
title: The weakest link: Haploid honey bees are more susceptible to neonicotinoid insecticides

description: Neonicotinoid insecticides are currently of major concern for the health
 of wild and managed insects that provide key ecosystem services like
 pollination. Even though sublethal effects of neonicotinoids are well
 known, there is surprisingly little information on how they possibly
 impact developmental stability, and to what extent genetics are involved.
 This holds especially true for haploid individuals because they are
 hemizygous at detoxification loci and may be more susceptible. Here we
 take advantage of haplodiploidy in Western honey bees,
 Apis mellifera, to show for the first time that neonicotinoids
 affect developmental stability in diploid females (workers), and that
 haploid males (drones) are even more susceptible. Phenotypic fore wing
 venation abnormalities and fluctuating wing asymmetry, as measures of
 developmental instability, were significantly increased under
 field-realistic neonicotinoid-exposure of colonies. The higher
 susceptibility of haploid drones suggests that heterozygosity can play a
 key role in the ability to buffer the sublethal effects of neonicotinoids.
 Aiming to improve conservation efforts, our findings highlight the urgent
 need to better understand the role that genetics plays at enabling
 non-target organisms to cope with insecticide exposure.
DOI: 10.5061/dryad.8w9ghx3gv
title: Seminal fluid-mediated fitness effects in the simultaneously hermaphroditic flatworm Macrostomum lignano

description: As a class, seminal fluid proteins are expected to exert strong effects on
 mating partners due to the selection pressures of sperm competition and
 sexual conflict. But because of the complexity of this secretion, linking
 specific proteins to downstream effects on own fitness – via manipulating
 the reproductive behavior, physiology and ultimately the sperm utilization
 of mating partners – is not straightforward. Here we adopted a systematic
 gene knockdown approach to screen for seminal fluid-mediated fitness
 effects in the simultaneously hermaphroditic flatworm Macrostomum lignano.
 We focused on 18 transcripts in M. lignano seminal fluid, testing how
 their RNA interference-induced knockdown impacted on three aspects of
 donor (male) reproductive success: (i) fertility (offspring production of
 the partner); (ii) defensive sperm competitive ability, P1; and (iii)
 offensive sperm competitive ability, P2. In general, the knockdown of most
 individual transcripts appeared to have only a minor impact on male
 reproductive success, though we found evidence that the knockdown of up to
 five different transcripts impacted on fertility; the knockdown of two
 other transcripts resulted in reduced P2, and knockdown of a further
 transcript actually increased P2. We thus identify a number of candidate
 seminal fluid transcripts that appear to modulate offspring production and
 sperm competitiveness in M. lignano. That only a minority of transcripts
 exhibit such a pattern likely reflects both the difficulty of accurately
 estimating sperm competitiveness and the functional redundancy of seminal
 fluid.
DOI: 10.5061/dryad.wh70rxwhv
title: Data from: Calculation on surface energy and electronic properties of CoS2

description: Density functional theory was employed to investigate the (111), (200),
 (210), (211), and (220) surfaces of CoS2. The surface energy were
 calculated with a sulfur environment using first-principles based
 thermodynamics. It is founded that surfaces with metal atoms at their
 outermost layer are predicted to have higher energy. The stoichiometric
 (220) surface terminated by two layer of sulfur atoms is the most stable
 under the sulfur-rich condition, while the nonstoichiometric (211) surface
 terminated by a layer of Co atoms has the lower energy under the
 decreasingly sulfur-poor environment. A spin-polarized bands were
 calculated on the stoichiometric surfaces. The electric structure results
 showed that there may be some active sites on (200) since it has high
 Fermi energy and its front valence electrons are active. There was an
 energy gap between the stoichiometric (220) and (211), which have low
 Fermi energy, indicating that the electronic structures were dynamically
 stable. These two stoichiometric (200) and (210) surfaces are predicted to
 be noticeably spin-polarized. The results of BFDH method was adopted to
 predict crystal growth habit. It showed that the important crystal planes
 for the CoS2 crystal growth were (111) and (200) planes, and the
 macroscopic morphology of CoS2 crystal may be spherical, cubic,
 octahedral, prismatic or plate-shaped, which have been verified by
 experiments.
DOI: 10.5061/dryad.wh70rxwhw
title: Secondary contacts and genetic admixture shape colonisation by an amphiatlantic epibenthic invertebrate

description: Research on the genetics of invasive species often focuses on patterns of
 genetic diversity and population structure within the introduced range.
 However, a growing body of literature is demonstrating the need to study
 the native range, and how native genotypes affect both ecological and
 evolutionary mechanisms within the introduced range. Here we used
 genotyping-by-sequencing to study both native and introduced ranges [based
 on 1,653 single nucleotide polymorphisms (SNPs)] of the amphiatlantic
 marine invertebrate Ciona intestinalis. A previous study using
 microsatellites analysed samples collected along the Swedish west coast
 and showed the presence of genetically distinct lineages in deep and
 shallow waters. Using our SNP data from newly collected samples (285
 individuals), we first confirmed the presence of this depth-defined
 genomic divergence along the Swedish coast. We then used Approximate
 Bayesian Computation to infer the historical relationship among sites from
 the North Sea, the English Channel and the northwest Atlantic and found
 evidence of ancestral divergence between individuals from deep waters off
 Sweden and individuals from the English Channel. This divergence was
 followed by a secondary contact that led to a genetic admixture between
 the ancestral populations (i.e. deep Sweden and English Channel), which
 originated the genotypes found in shallow Sweden. We then revealed that
 the colonisation of C. intestinalis in the northwest Atlantic was as a
 result of an admixture between shallow Sweden and the English Channel
 genotypes across the introduced range. Our results showed the presence of
 both past and recent genetic admixture events that together may have
 promoted the successful colonisations of C. intestinalis. Our study
 suggests that secondary contacts potentially reshape the evolutionary
 trajectories of invasive species through the promotion of intraspecific
 hybridisation and by altering both colonisation patterns and their
 ecological effects in the introduced range.
description: <strong>Hudson_etal.2019_Ciona_1653loci.vcf</strong> VCF file containing 1653 putatively neutral SNPs as outlined in the associated manuscript.   <strong>Hudson_etal.2019_SampleID.txt</strong> Text file containing sample ID from the VCF files and the appropriate sampling location. Abbreviations as in Table 1 of associated manuscript.
DOI: 10.5061/dryad.bnzs7h464
title: Data from: Rubber agroforestry in Thailand provides some biodiversity benefits without reducing yields

description: Monocultural rubber plantations have replaced tropical forest, causing
 biodiversity loss. While protecting intact or semi-intact biodiverse
 forest is paramount, improving biodiversity value within the 11.4 million
 hectares of existing rubber plantations could offer important conservation
 benefits, if yields are also maintained. Some farmers practice
 agroforestry with high-yielding clonal rubber varieties to increase and
 diversify incomes. Here, we ask whether such rubber agroforestry improves
 biodiversity value or affects rubber yields relative to monoculture. We
 surveyed birds, fruit-feeding butterflies and reptiles in 25 monocultural
 and 39 agroforest smallholder rubber plots in Thailand, the world’s
 biggest rubber producer. Management and vegetation structure data were
 collected from each plot, and landscape composition around plots was
 quantified. Rubber yield data were collected for a separate set of 34
 monocultural and 47 agroforest rubber plots in the same
 region. Reported rubber yields did not differ between agroforests
 and monocultures, meaning adoption of agroforestry in this context should
 not increase land demand for natural rubber. Butterfly richness was
 greater in agroforests, where richness increased with greater natural
 forest extent in the landscape. Bird and reptile richness were similar
 between agroforests and monocultures, but bird richness increased with the
 height of herbaceous vegetation inside rubber plots. Species composition
 of butterflies differed between agroforests and monocultures, and in
 response to natural forest extent, while bird composition was influenced
 by herbaceous vegetation height within plots, the density of non-rubber
 trees within plots (representing agroforestry complexity), and natural
 forest extent in the landscape. Reptile composition was influenced by
 canopy cover and open habitat extent in the landscape. Conservation
 priority and forest-dependent birds were not supported within
 rubber. Synthesis and applications. Rubber agroforestry using
 clonal varieties provides modest biodiversity benefits relative to
 monocultures, without compromising yields. Agroforests may also generate
 ecosystem service and livelihood benefits. Management of monocultural
 rubber production to increase inter-row vegetation height and complexity
 may further benefit biodiversity. However, biodiversity losses from
 encroachment of rubber onto forests will not be offset by rubber
 agroforestry or rubber plot management. This evidence is important for
 developing guidelines around biodiversity-friendly rubber and sustainable
 supply chains, and for farmers interested in diversifying rubber
 production.
description: Sampling protocols are outlined in the paper in <em>Journal
 of Applied Ecology</em>.
description: The accompanying ReadMe.txt file explains the contents of each
 .csv file, including definitions of each column.
DOI: 10.5061/dryad.b8gtht782
title: Transcriptional activation of Arabidopsis zygotes is required for initial cell divisions

description: Commonly referred to as the maternal-to-zygotic transition, the shift of
 developmental control from maternal-to-zygotic genomes is a key event
 during animal and plant embryogenesis. Together with the degradation of
 parental gene products, the increased transcriptional activities of the
 zygotic genome remodels the early embryonic transcriptome during this
 transition. Although evidence from multiple flowering plants suggests that
 zygotes become transcriptionally active soon after fertilization, the
 timing and developmental requirements of zygotic genome activation in
 Arabidopsis thaliana (Arabidopsis) remained a matter of debate until
 recently. In this report, we optimized an expansion microscopy technique
 for robust immunostaining of Arabidopsis ovules and seeds. This enabled
 the detection of marks indicative of active transcription in zygotes
 before the first cell division. Moreover, we employed a live-imaging
 culture system together with transcriptional inhibitors to demonstrate
 that such active transcription is physiologically required in zygotes and
 early embryos. Our results indicate that zygotic genome activation occurs
 soon after fertilization and is required for the initial zygotic divisions
 in Arabidopsis.
DOI: 10.3886/e218342v2-198145
title: National Survey of Drug Use and Health

description: Public Use Files from NSDUH 1979 to 2023
DOI: 10.5061/dryad.n02v6wwsg
title: Data from: A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses

description: Recent high-throughput sequencing endeavors have yielded
 multi-gene/protein phylogenies that confidently resolve several inter- and
 intra-class relationships within the phylum Ciliophora.  We
 leverage the massive sequencing efforts from the Marine Microbial
 Eukaryote Transcriptome Sequencing Project, other SRA submissions, and
 available genome data with our own sequencing efforts to determine the
 phylogenetic position of Mesodinium and to generate the most
 taxonomically-rich phylogenomic ciliate tree to date.  Regardless
 of the data mining strategy, the multi-protein dataset, or the molecular
 models of evolution employed, we consistently recovered the same
 well-supported relationships among ciliate classes, confirming many of the
 higher-level relationships previously identified.  Mesodinium
 always formed a monophyletic group with members of the Litostomatea, with
 mixotrophic species of Mesodinium – M. rubrum, M. major, and M. chamaeleon
 - being more closely related to each other than to the heterotrophic
 member, M. pulex.  The well-supported position of Mesodinium as
 sister to other litostomes contrasts with previous molecular analyses
 including those from phylogenomic studies that exploited the same
 transcriptomic databases.  These topological discrepancies
 illustrate the need for caution when mining mixed-species transcriptomes
 and indicate that identifying ciliate sequences among prey contamination -
 particularly for Mesodinium species where expression from stolen prey
 nuclei appears to dominate – requires thorough and iterative vetting with
 phylogenies that incorporate sequences from a large outgroup of prey.
description: <strong>Final-trees-and-alignments.tar.gz</strong><br> SHA256 67febe6a6cfd0fcc363eed2b0b76c282e6b0a948eafe248c22aa621a8526beb9<br> This file contains Strategy 1 and Strategy 2 Maximum likelihood final trees and alignments (13 files)
DOI: 10.5061/dryad.zw3r22848
title: Data from: A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses

description: Recent high-throughput sequencing endeavors have yielded
 multi-gene/protein phylogenies that confidently resolve several inter- and
 intra-class relationships within the phylum Ciliophora.  We
 leverage the massive sequencing efforts from the Marine Microbial
 Eukaryote Transcriptome Sequencing Project, other SRA submissions, and
 available genome data with our own sequencing efforts to determine the
 phylogenetic position of Mesodinium and to generate the most
 taxonomically-rich phylogenomic ciliate tree to date.  Regardless
 of the data mining strategy, the multi-protein dataset, or the molecular
 models of evolution employed, we consistently recovered the same
 well-supported relationships among ciliate classes, confirming many of the
 higher-level relationships previously identified.  Mesodinium
 always formed a monophyletic group with members of the Litostomatea, with
 mixotrophic species of Mesodinium – M. rubrum, M. major, and M. chamaeleon
 - being more closely related to each other than to the heterotrophic
 member, M. pulex.  The well-supported position of Mesodinium as
 sister to other litostomes contrasts with previous molecular analyses
 including those from phylogenomic studies that exploited the same
 transcriptomic databases.  These topological discrepancies
 illustrate the need for caution when mining mixed-species transcriptomes
 and indicate that identifying ciliate sequences among prey contamination -
 particularly for Mesodinium species where expression from stolen prey
 nuclei appears to dominate – requires thorough and iterative vetting with
 phylogenies that incorporate sequences from a large outgroup of prey.
description: <strong>Protein-trees.tar.gz</strong><br>
 SHA256
 5fa2b2c94f487143dbc866e96cd6382d14694f6ab90a6ce0fb53c7c0874c8799<br>
 This file contains Strategy 1 and Strategy 2 protein trees (401
 files)<br> Strategy 1 tree files have the ending:
 penult.fast.tree<br> Strategy 2 tree files have the ending:
 R.tree