cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.jc5kqe
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((88.86765699999999 24.18423, 88.79067999999999 24.178653, 88.715619 24.162061, 88.644338 24.134866, 88.57860700000001 24.097745, 88.520053 24.051619, 88.47012100000001 23.997633, 88.430036 23.937125, 88.40077700000001 23.871593, 88.38305 23.802656, 88.377274 23.732016, 88.383572 23.661414, 88.40177 23.592586, 88.431403 23.527223, 88.471727 23.466928, 88.521742 23.413178, 88.580214 23.367289, 88.64570500000001 23.33038, 88.716612 23.303355, 88.791203 23.286871, 88.86765699999999 23.281331, 88.94411100000001 23.286871, 89.018702 23.303355, 89.089609 23.33038, 89.1551 23.367289, 89.213572 23.413178, 89.263587 23.466928, 89.303911 23.527223, 89.333544 23.592586, 89.351742 23.661414, 89.35804 23.732016, 89.35226400000001 23.802656, 89.334537 23.871593, 89.305278 23.937125, 89.265193 23.997633, 89.215261 24.051619, 89.156707 24.097745, 89.090976 24.134866, 89.019695 24.162061, 88.94463399999999 24.178653, 88.86765699999999 24.18423))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006383-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9fqk5w
title: Occurrence Download

description: A dataset containing 285858 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Euphorbia prostrata, Lepidium virginicum, Plantago virginica, Sphagneticola trilobata, Paspalum distichum, Amaranthus retroflexus, Ipomoea indica)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 285858 records from 2059 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006320-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6haadh
title: Occurrence Download

description: A dataset listing the 302 species recorded in GBIF matching the query:
{
 "or" : [
 "Geometry POLYGON((1.74278 41.32565,1.76293 41.32565,1.76293 41.34737,1.74278 41.34737,1.74278 41.32565))",
 "Geometry POLYGON((1.74307 41.32536,1.76594 41.32536,1.76594 41.34937,1.74307 41.34937,1.74307 41.32536))"
 ]
}

 The dataset's 302 records were derived from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009608-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2ps14
title: Data from: Imposed work of breathing for flow meters with in-line versus flow-through technique during simulated neonatal breathing

description: Background: The ability to determine airflow during nasal CPAP (NCPAP)
 treatment without adding dead space or resistance would be useful when
 investigating the physiologic effects of different NCPAP systems on
 breathing. The aim of this study was to investigate the effect on pressure
 stability of different flow measuring devices at the in-line and
 flow-through position, using simulated neonatal breathing. Methods: Six
 different flow measure devices were evaluated by recording pressure
 changes and imposed work of breathing for breaths with 16 and 32 ml tidal
 volumes. The tests were performed initially with the devices in an in line
 position and with 5 and 10 L/min using flow through technique, without
 CPAP. The flow meters were then subsequently tested with an Infant Flow
 CPAP system at 3, 5 and 8 cm H2O pressure using flow through technique.
 The quality of the recorded signals was compared graphically. Results: The
 resistance of the measuring devices generated pressure swings and imposed
 work of breathing. With bias flow, the resistance also generated CPAP
 pressure. Three of the devices had low resistance and generated no changes
 in pressure stability or CPAP pressure. The two devices intended for
 neonatal use had the highest measured resistance. Conclusion: The
 importance of pressure stability and increased work of breathing during
 non-invasive respiratory support are insufficiently studied. Clinical
 trials using flow-through technique have not focused on pressure
 stability. Our results indicate that a flow-through technique might be a
 way forward in obtaining a sufficiently high signal quality without the
 added effects of rebreathing and increased work of breathing. The results
 should stimulate further research and the development of equipment for
 dynamic flow measurements in neonates.
description: Flow meter ASL
 testsComplete variable set
 from ASL5000 simulations (identical in xlsx and SPSS data format). A guide
 to calculated variables and labels is included.Flow
 recordingsFlow recordings (xlsx)
 for flow meters in experiments with bias flow and with Infant Flow. An
 example graph is provided for each recording to allow identification of
 variables.
DOI: 10.5061/dryad.6v5tn
title: Data from: Anemia and related nutrient deficiencies after Roux-en-Y gastric bypass surgery: a systematic review and meta-analysis

description: Objective: To obtain a pooled risk estimate on the long-term impact of
 anaemia and related nutritional deficiencies in patients receiving
 Roux-en-Y gastric bypass (RYGB) surgery. Design: Systematic review and
 meta-analysis. Data sources: MEDLINE, EMBASE and Cochrane databases were
 searched to identify English reports published before 16 May 2014.
 Eligibility criteria: Articles with case numbers &gt;100, follow-up
 period &gt;12 months, and complete data from both before and after
 surgery were selected. Outcomes of interest were changes in baseline
 measurements of proportion of patients with anaemia, by haemoglobin,
 haematocrit, ferritin, iron, vitamin B12 and folate levels. Data
 collection and analysis: Two reviewers independently reviewed data and
 selected six prospective and nine retrospective studies with a total of
 5909 patients. A random effect model with inverse variance weighting was
 used to calculate summary estimates of outcomes at 6, 12, 24 and 36 months
 postoperatively. Results: Proportion of patients with anaemia was 12.2% at
 baseline, which, respectively, increased to 20.9% and 25.9% at 12 and
 24 months follow-up, consistent with decreases in haemoglobin and
 haematocrit levels. Although the serum iron level did not change
 substantially after surgery, the frequency of patients with ferritin
 deficiency increased from 7.9% at baseline to 13.4% and 23.0% at 12 and
 24 months, respectively, postoperation. Vitamin B12 deficiency increased
 from 2.3% at baseline to 6.5% at 12 months after surgery in those subjects
 receiving RYGB. There was no obvious increase in folate deficiency.
 Conclusions: RYGB surgery is associated with an increased risk of anaemia
 and deficiencies of iron and vitamin B12, but not folate. Ferritin is more
 sensitive when serum iron level is within normal range.
description: Anemia and Related
 Nutrient Deficiencies after Roux-en-Y Gastric Bypass
 SurgeryStudy characteristics;
 Proportion of study participants with anemia before and after RYGB
 surgery; Proportion of study participants with low ferritin/ serum iron/
 vitamin B12/ folate level before and after RYGB surgery;
 Hemoglobin/Hematocrit level among study participants; Ferritin/ serum
 Iron/ vitamin B12/ folate level among study participants before and after
 RYGB surgery before and after RYGB surgery; Literature search and study
 selection; Forest plot for proportion of study participants with anemia
 before RYGB and 12 months after RYGB; Forest plot for proportion of study
 participants with (A) ferritin (B) serum iron (C) vitamin B12 and (D)
 folate deficiencies before RYGB and 12 months after RYGB; Funnel plot
 comparing log(mean) and s.e. of log(mean) for proportion of study
 participants with anemia 12 months after RYGB; MEDLINE (via PubMed) search
 query with ‘All Fields’; Cochrane Library search query with ‘Search All
 Text’DataSharing_Dryad.docx
DOI: 10.5061/dryad.n6428
title: Data from: Pest control of aphids depends on landscape complexity and natural enemy interactions

description: Aphids are a major concern in agricultural crops worldwide, and control by
 natural enemies is an essential component of the ecological
 intensification of agriculture. Although the complexity of agricultural
 landscapes is known to influence natural enemies of pests, few studies
 have measured the degree of pest control by different enemy guilds across
 gradients in landscape complexity. Here, we use multiple natural-enemy
 exclosures replicated in 18 fields across a gradient in landscape
 complexity to investigate (1) the strength of natural pest control across
 landscapes, measured as the difference between pest pressure in the
 presence and in the absence of natural enemies; (2) the differential
 contributions of natural enemy guilds to pest control, and the nature of
 their interactions across landscapes. We show that natural pest control of
 aphids increased up to six-fold from simple to complex landscapes. In the
 absence of pest control, aphid population growth was higher in complex
 than simple landscapes, but was reduced by natural enemies to similar
 growth rates across all landscapes. The effects of enemy guilds were
 landscape-dependent. Particularly in complex landscapes, total pest
 control was supplied by the combined contribution of flying insects and
 ground-dwellers. Birds had little overall impact on aphid control. Despite
 evidence for intraguild predation of flying insects by ground-dwellers and
 birds, the overall effect of enemy guilds on aphid control was
 complementary. Understanding pest control services at large spatial scales
 is critical to increase the success of ecological intensification schemes.
 Our results suggest that, where aphids are the main pest of concern,
 interactions between natural enemies are largely complementary and lead to
 a strongly positive effect of landscape complexity on pest control.
 Increasing the availability of seminatural habitats in agricultural
 landscapes may thus benefit not only natural enemies, but also the
 effectiveness of aphid natural pest control.
description: MartinetalPeerJ2015_rawdataData collected in a field experiment on cabbage plants in South Korea. Column headings are described in file sheet "Metadata". See the referenced paper (Martin et al 2015 PeerJ) for details on data collection methods and the experiment.
DOI: 10.5061/dryad.t9q11
title: Data from: Computed tomography, anatomical description and three-dimensional reconstruction of the lower jaw of Eusthenopteron foordi Whiteaves, 1881 from the Upper Devonian of Canada

description: The cranial anatomy of the iconic early tetrapod Eusthenopteron foordi is
 probably the best understood of all fossil fishes. In contrast, the
 anatomy of the lower jaw – crucial for both phylogenetics and
 biomechanical analyses – has been only superficially described. Computed
 tomography data of three Eusthenopteron skulls were segmented using
 visualization software to digitally separate bone from matrix and
 individual bones from each other. Here, we present a new description of
 the lower jaw of Eusthenopteron based on microcomputed tomography data,
 including the following: detailed description of sutural morphology and
 the mandibular symphysis; confirmed occurrence of pre- and intercoronoid
 fossae on the dorsal aspect of the lower jaw; and the arrangement of the
 submandibular bones. Furthermore, we identify a novel dermal ossification,
 the postsymphysial, present on the anteromedial aspect of the lower jaw in
 Eusthenopteron and describe its distribution in other stem tetrapod taxa.
 Sutural morphology is used to infer load regimes and, along with overall
 skull and lower jaw morphology, suggests that Eusthenopteron may have used
 biting along with suction feeding to capture and consume large prey.
 Finally, visualization software was used to repair and reconstruct the
 lower jaw, resulting in a three-dimensional digital reconstruction.
description: Appendix
 S1Micro-CT sections
 through the three specimens (left) with black line indicating position on
 corresponding 3D surfaces (right). A, Transverse section through the left
 first intercoronoid fossa of MHMN 06-538. B, Transverse section through
 the right precoronoid fossa of UMZC GN.792. C, Transverse section through
 the anterior lower jaw of UMZC GN.1147.S1
 image.tifAppendix
 S2Transformation matrices
 for three-dimensional surface models of individual bones of the lower jaw
 of Eusthenopteron foordi.S2.docx
DOI: 10.5061/dryad.908
title: Data from: Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries

description: Specific sets of brain-expressed genes, such as aerobic energy metabolism
 genes, evolved adaptively in the ancestry of humans and may have evolved
 adaptively in the ancestry of other large-brained mammals. The recent
 addition of genomes from two afrotherians (elephant and tenrec) to the
 expanding set of publically available sequenced mammalian genomes provided
 an opportunity to test this hypothesis. Elephants resemble humans by
 having large brains and long life spans; tenrecs, in contrast, have small
 brains and short life spans. Thus, we investigated whether the
 phylogenomic patterns of adaptive evolution are more similar between
 elephant and human than between either elephant and tenrec lineages or
 human and mouse lineages, and whether aerobic energy metabolism genes are
 especially well represented in the elephant and human patterns. Our
 analyses encompassed approximately 6000 genes in each of these lineages
 with each gene yielding extensive coding sequence matches in interordinal
 comparisons. Each gene's nonsynonymous and synonymous nucleotide
 substitution rates and dN/dS ratios were determined. Then, from gene
 ontology information on genes with the higher dN/dS ratios, we identified
 the more prevalent sets of genes that belong to specific functional
 categories and that evolved adaptively. Elephant and human lineages showed
 much slower nucleotide substitution rates than tenrec and mouse lineages
 but more adaptively evolved genes. In correlation with absolute brain size
 and brain oxygen consumption being largest in elephants and next largest
 in humans, adaptively evolved aerobic energy metabolism genes were most
 evident in the elephant lineage and next most evident in the human
 lineage.
description: Codeml
 ResultsDAVID Results By
 BinBin DAVID
 output.zipDAVID output (top 5%
 dN/dS)Top 5%
 DAVID output.zipHuman ancestry DAVID
 outputHuman
 Ancestry DAVID output.zip
DOI: 10.5061/dryad.2p66n
title: Data from: The host response to the lung microbiome in Chromic Obstructive Pulmonary Disease

description: Rationale: The relatively sparse but diverse microbiome in human lungs may
 become less diverse in chronic obstructive pulmonary disease (COPD). This
 article examines the relationship of this microbiome to emphysematous
 tissue destruction, number of terminal bronchioles, infiltrating
 inflammatory cells, and host gene expression. Methods: Culture-independent
 pyrosequencing microbiome analysis was used to examine the V3–V5 regions
 of bacterial 16S ribosomal DNA in 40 samples of lung from 5 patients with
 COPD (Global Initiative for Chronic Obstructive Lung Disease [GOLD] stage
 4) and 28 samples from 4 donors (controls). A second protocol based on the
 V1–V3 regions was used to verify the bacterial microbiome results. Within
 lung tissue samples the microbiome was compared with results of
 micro–computed tomography, infiltrating inflammatory cells measured by
 quantitative histology, and host gene expression. Measurements and Main
 Results: Ten operational taxonomic units (OTUs) was found sufficient to
 discriminate between control and GOLD stage 4 lung tissue, which included
 known pathogens such as Haemophilus influenzae. We also observed a decline
 in microbial diversity that was associated with emphysematous destruction,
 remodeling of the bronchiolar and alveolar tissue, and the infiltration of
 the tissue by CD4+ T cells. Specific OTUs were also associated with
 neutrophils, eosinophils, and B-cell infiltration (P &lt; 0.05). The
 expression profiles of 859 genes and 235 genes were associated with either
 enrichment or reductions of Firmicutes and Proteobacteria, respectively,
 at a false discovery rate cutoff of less than 0.1. Conclusions: These
 results support the hypothesis that there is a host immune response to
 microorganisms within the lung microbiome that appears to contribute to
 the pathogenesis of COPD.
description: group.filemothur group file for analysiscombined.groupsname.filename file for mothur analysiscombined.namesfasta.filefasta file for mothur analysiscombined.fasta2nd_Microbiome_Project_SlicetoCoreExtra Meta data for analysisREADMEDescription of uploaded data set.
DOI: 10.5061/dryad.q205m
title: Data from: Visual and odours cues: plant responses to pollination and herbivory affect the behaviour of flower visitors

description: Plants evolved strategies to attract pollinators that are essential for
 reproduction. However, plant defence against herbivores may trade off with
 pollinator attraction. Here, we investigated the role of inducible plant
 secondary metabolites in such a trade-off. Our objective was to reveal the
 mechanisms underlying the effects of induced plant responses to
 pollination and herbivory. We assessed how responses of plants to
 pollination and insect herbivory affect the behaviour of flower visitors.
 Subsequently, we investigated how the production of volatile and
 non-volatile compounds changes after pollination and herbivory. Both
 herbivores and pollinators induced important phenotypic changes in
 flowers. Brassica nigra plants respond to pollination and herbivory with
 changes in the profile of volatiles and non-volatiles of their flowers.
 Our results show that butterflies use different cues when searching for an
 oviposition site or a nectar source. Pollination status influenced the
 behaviour of butterflies, but not that of syrphid flies. We discuss the
 results in the context of the trade-off between defence and reproduction
 in plants and suggest that systemic responses to herbivores can interfere
 with local responses to pollination. Therefore, these responses must be
 addressed in an integrated way because, in nature, plants are
 simultaneously exposed to herbivores and pollinators.
description: raw data volatiles B
 nigra _ effects of herbivory and pollinationInclude raw data related
 to effects of herbivory and pollination on the volatile profile of
 Brassica nigra plantsraw data volatiles B. nigra -
 effects of herbivory and
 pollination.xlsxraw data phenolics B
 nigra _ effects of herbivory and pollinationInclude raw data related
 to effects of herbivory and pollination on the phenolic profile of
 Brassica nigra plantsraw data behaviour
 butterflies on B nigra _ effects of herbivory and
 pollinationInclude raw data related
 to effects of herbivory and pollination on the behavioural responses of
 Pieris brassicae butterflies.raw data behaviour
 syphid flies on B nigra _ effects of herbivory and
 pollinationInclude raw data related
 to effects of herbivory and pollination on the behavioural responses of
 the syrphid fly Episyrphus balteatus.
DOI: 10.5061/dryad.34274
title: Data from: Exon capture phylogenomics: efficacy across scales of divergence

description: The evolutionary histories of species are not measured directly, but
 estimated using genealogies inferred for particular loci. Individual loci
 can have discordant histories, but in general we expect to infer
 evolutionary histories more accurately as more of the genome is sampled.
 High Throughput Sequencing (HTS) is now providing opportunities to
 incorporate thousands of loci in ‘phylogenomic’ studies. Here, we used
 target enrichment to sequence c.3000 protein-coding exons in a group of
 Australian skink lizards (crown group age c.80 Ma). This method uses
 synthetic probes to ‘capture’ target exons that were identified in the
 transcriptomes of selected probe design (PD) samples. The target exons are
 then enriched in sample DNA libraries prior to performing HTS. Our main
 goal was to study the efficacy of enrichment of targeted loci at different
 levels of phylogenetic divergence from the PD species. In taxa sharing a
 common ancestor with PD samples up to c.20 Ma, we detected little
 reduction in efficacy, measured here as sequencing depth of coverage.
 However, at around 80 Myr divergence from the PD species, we observed an
 approximately two-fold reduction in efficacy. A secondary goal was to
 develop a workflow for analysing exon capture studies of phylogenetically
 diverse samples, while minimizing potential bias. Our approach assembles
 each exon in each sample separately, by first recruiting short sequencing
 reads having homology to the corresponding protein sequence. In sum,
 custom exon capture provides a complement to existing, more generic target
 capture methods and is a practical and robust option across low-moderate
 levels of phylogenetic divergence.
description: exon capture
 phylogenomics, data and workflows (dryad_34274)Data and computational
 workflows to accompany "Exon capture phylogenomics: efficacy across
 scales of divergence," by Jason Bragg, Sally Potter, Ke Bi and Craig
 Moritz.dryad_34274.zip
DOI: 10.5281/zenodo.18390008
title: NOVAC_BRAND7_150F_3_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 150F SC sample 3 Novac - EDLC Single - Brand7Part of the Constant Temperature DataBase
DOI: 10.5281/zenodo.18390009
title: NOVAC_BRAND7_150F_3_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 150F SC sample 3 Novac - EDLC Single - Brand7Part of the Constant Temperature DataBase
DOI: 10.5061/dryad.9097
title: Data from: The geographical and institutional distribution of ecological research in the tropics

description: We reviewed 1333 papers published in Biotropica and the Journal of
 Tropical Ecology from 1995 to 2004. Only 62 percent of tropical countries
 were represented in our survey, with 62 percent of the publications based
 on research conducted in only ten countries. Sixty-two percent of papers
 had lead authors that were based at institutions outside the country where
 the research was conducted. Cross-national collaboration was limited,
 accounting for only 28 percent of papers with multiple authors. To
 evaluate if our choice of focal journals could have biased our results, we
 also reviewed 652 papers published in Ecology, Oecologia, Conservation
 Biology, and Biological Conservation for five randomly selected years from
 the same time period. While some differences in authorship and the
 geographic distribution of research existed, the results from these
 journals generally mirrored patterns observed in the two focal ones—almost
 54 percent of publications were based on research conducted in only ten
 countries, and most studies had lead authors from a developed country. The
 results of our review suggest that the geographical distribution of
 research in the tropics is unequal, and that some important regions remain
 understudied. The results also suggest a need for a greater focus on
 establishing collaborative relationships with scientists from tropical
 countries.
description: Stocks_etal_2008_Biotropica_Data