cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d5h62
title: Data from: A database of human exposomes and phenomes from the US National Health and Nutrition Examination Survey

description: The National Health and Nutrition Examination Survey (NHANES) is a
 population survey implemented by the Centers for Disease Control and
 Prevention (CDC) to monitor the health of the United States whose data is
 publicly available in hundreds of files. This Data Descriptor describes a
 single unified and universally accessible data file, merging across 255
 separate files and stitching data across 4 surveys, encompassing 41,474
 individuals and 1,191 variables. The variables consist of phenotype and
 environmental exposure information on each individual, specifically (1)
 demographic information, physical exam results (e.g., height, body mass
 index), laboratory results (e.g., cholesterol, glucose, and environmental
 exposures), and (4) questionnaire items. Second, the data descriptor
 describes a dictionary to enable analysts find variables by category and
 human-readable description. The datasets are available on DataDryad and a
 hands-on analytics tutorial is available on GitHub. Through a new big data
 platform, BD2K Patient Centered Information Commons (http://pic-sure.org),
 we provide a new way to browse the dataset via a web browser
 (https://nhanes.hms.harvard.edu) and provide application programming
 interface for programmatic access.
description: Unifying the US National
 Health and Nutrition Examination Survey: a database of human exposomes and
 phenomesThe National Health and
 Nutrition Examination Survey (NHANES) is an epidemiological survey
 implemented by the Centers for Disease Control and Prevention (CDC) to
 monitor the health of a representative population of the United States.
 While publicly available, analysts need to spend a significant amount of
 time merging and stitching together numerous separate and proprietary
 formatted data files to incorporate the data in their research. This Data
 Descriptor describes a single unified and universally accessible data
 file, merging across 251 separate files and stitching data across 4
 surveys, encompassing 41,474 individuals and 1191 variables. The variables
 consist of phenotype and environmental exposure information on each
 individual, specifically (1) demographic information, physical exam
 results (e.g., height, body mass index), laboratory results (e.g.,
 cholesterol, glucose, and environmental exposures), and (4) questionnaire
 items. Second, the data descriptor describes a dictionary to enable
 analysts find variables by category and human-readable description. The
 datasets are available in .csv and .Rdata format.nh_99-06.zip
DOI: 10.5061/dryad.g8418
title: Data from: Two new synonyms in Heteranthera (Pontederiaceae, Commelinales)

description: Hydrothrix and Scholleropsis, two segregate monospecific genera placed
 within the Heteranthera s.l. clade, are here transferred to Heteranthera
 based on phylogenetic and morphological data. A brief discussion on the
 morphology and affinities of Heteranthera s.l. is given, along with the
 designation of lectotypes for the two new transfers.
description: Fig. 1- Heteranthera
 gardneriHeteranthera gardneri.
 A, habit, showing a flowered population during dry-season; B, detail of
 the stem. C, detail of the flower-like inflorescence, showing how the
 upper perianth-lobes mimic androecium parts. A–B by A.P. Fontana, C by
 C.P. Bove.Fig. 2- Heteranthera
 luteaHeteranthera lutea. A,
 habit, showing an individual with petiolate and sessile leaves; B, habit,
 showing a submerged individual with only sessile leaves; C, detail of the
 one-flowered inflorescence, showing the tetramerous flower. Plate modified
 from the Flore de Madagascar et des Comores, Pontédériacées (1946),
 vol. 38: pp. 5; acquired through the Biodiversity Heritage Library
 (BHL).Fig. 3- Heteranthera
 speciesRelated Heteranthera
 species. A–B, Heteranthera dubia, from the United States: A, habit showing
 submerged individual with sessile and linear leaves; B, detail of the
 one-flowered inflorescence. C–D, Heteranthera rotundifolia, from
 Northeastern Brazil: C, habit, showing; D, detail of the flower; E–F,
 Heteranthera seubertiana, from Northeastern Brazil: E, detail of the
 sessile leave rosette; F, detail of the inflorescence, showing the open
 yellow flowers. G–H, Heteranthera zosterifolia, from Southeastern Brazil:
 G, habit, showing the emerged stem with sessile linear leaves; H, detail
 of the flower. A–B by C.N. Horn, C–D by A. Popovkin, E–F by R. Teobaldo, G
 by G. Oliveira and H by S.S. de Oliveira.
DOI: 10.5281/zenodo.18387238
title: DYNAMIC EARTHQUAKE SOURCE INVERSION
DOI: 10.5061/dryad.48m7c
title: Data from: Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes

description: One of the major unanswered questions in evolutionary biology is when and
 how the transition between diderm (two membranes) and monoderm (one
 membrane) cell envelopes occurred in Bacteria. The Negativicutes and the
 Halanaerobiales belong to the classically monoderm Firmicutes, but possess
 outer membranes with lipopolysaccharide (LPS-OM). Here, we show that they
 form two phylogenetically distinct lineages, each close to different
 monoderm relatives. In contrast, their core LPS biosynthesis enzymes were
 inherited vertically, as in the majority of bacterial phyla. Finally,
 annotation of key OM systems in the Halanaerobiales and the Negativicutes
 shows a puzzling combination of monoderm and diderm features. Together,
 these results support the hypothesis that the LPS-OMs of Negativicutes and
 Halanaerobiales are remnants of an ancient diderm cell envelope that was
 present in the ancestor of the Firmicutes, and that the monoderm phenotype
 in this phylum is a derived character that arose multiple times
 independently through OM loss.
description: Additional-dataRaw data relative to analyses in Antunes et al. 2016.
DOI: 10.5061/dryad.6tq74
title: Data from: Functional traits for carbon access in macrophytes

description: Understanding functional trait distributions among organisms can inform
 impacts on and responses to environmental change. In marine systems, only
 1% of dissolved inorganic carbon in seawater exists as CO2. Thus the
 majority of marine macrophytes not only passively access CO2 for
 photosynthesis, but also actively transport CO2 and the more common
 bicarbonate (HCO3-, 92% of seawater dissolved inorganic carbon) into their
 cells. Because species with these carbon concentrating mechanisms (CCMs)
 are non-randomly distributed in ecosystems, we ask whether there is a
 phylogenetic pattern to the distribution of CCMs among algal species. To
 determine macrophyte traits that influence carbon uptake, we assessed 40
 common macrophyte species from the rocky intertidal community of the
 Northeast Pacific Ocean to a) query whether macrophytes have a CCM and b)
 determine the evolutionary history of CCMs, using ancestral state
 reconstructions and stochastic character mapping based on previously
 published data. Thirty-two species not only depleted CO2, but also
 concentrated and depleted HCO3-, indicative of a CCM. While analysis of
 CCMs as a continuous trait in 30 families within Phylum Rhodophyta showed
 a significant phylogenetic signal under a Brownian motion model, analysis
 of CCMs as a discrete trait (presence or absence) indicated that red algal
 families are more divergent than expected in their CCM presence or
 absence; CCMs are a labile trait within the Rhodophyta. In contrast, CCMs
 were present in each of 18 Ochrophyta families surveyed, indicating that
 CCMs are highly conserved in the brown algae. The trait of CCM presence or
 absence was largely conserved within Families. Fifteen of 23 species
 tested also changed the seawater buffering capacity, or Total Alkalinity
 (TA), shifting DIC composition towards increasing concentrations of HCO3-
 and CO2 for photosynthesis. Manipulating the external TA of the local
 environment may influence carbon availability in boundary layers and areas
 of low water mixing, offering an additional mechanism to increase CO2
 availability.
description: READMEA description of all
 data files in this submission. Please read first.Ochrophyta_family_nOchrophyta_family_pH_13c_raw_dataOchrophyta_family_pH_phylogeny_inputpH_drift_assay_dataset_all_pointsRhodophyta_family_nRhodophyta_family_pH_13c_raw_dataRhodophyta_family_pH_phylogeny_inputsaturation_statesTotalAlkalinity_CO2sys_macroresults_12
DOI: 10.5061/dryad.48636
title: Data from: Wood-inhabiting fungi with tight associations with other species have declined as a response to forest management

description: Research on mutualistic and antagonistic networks, such as
 plant–pollinator and host–parasite networks, has shown that species
 interactions can influence and be influenced by the responses of species
 to environmental perturbations. Here we examine whether results obtained
 for directly observable networks generalize to more complex networks in
 which species interactions cannot be observed directly. As a case study,
 we consider data on the occurrences of 98 wood-inhabiting fungal species
 in managed and natural forests. We specifically ask if and how much the
 positions of wood-inhabiting fungal species within the interaction
 networks influence their responses to forest management. For this, we
 utilize a joint species distribution model that partitions variation in
 species occurrences among environmental (i.e. resource availability) and
 biotic (i.e. species-to-species associations) predictors. Our results
 indicate that in addition to the direct loss of resource-specialised
 species, forest management has indirect effects mediated through
 interactive associations. In particular, species with strong associative
 links to other species are especially sensitive to forest management.
description: Fungal
 dataThis datafile consists
 of the presence-absence data of 326 wood-inhabiting fungal species
 (identified as fruit-bodies) found in 22 418 dead wood units from managed
 and natural forest sites. For each dead wood unit, the decay stage (scalar
 from 1 to 5), diameter (in cm), length (in cm), type (classification
 according to the diameter) are given. For each forest site, the management
 type (managed or natural) and name of the forest site are given. We
 surveyed in each forest site 5-10 randomly located 10 x 10 m sample plots,
 which are indexed in the "plot" column.Fungi
 data.csv
DOI: 10.5061/dryad.rb1pp
title: Data from: Broodstock history strongly influences natural spawning success in hatchery steelhead (Oncorhynchus mykiss)

description: We used genetic parentage analysis of 6200 potential parents and 5497
 juvenile offspring to evaluate the relative reproductive success of
 hatchery and natural steelhead (Onchorhynchus mykiss) when spawning in the
 wild between 2008 and 2011 in the Wenatchee River, Washington. Hatchery
 fish originating from two prior generation hatchery parents had
 &lt;20% of the reproductive success of natural origin spawners. In
 contrast, hatchery females originating from a cross between two natural
 origin parents of the prior generation had equivalent or better
 reproductive success than natural origin females. Males originating from
 such a cross had reproductive success of 26–93% that of natural males. The
 reproductive success of hatchery females and males from crosses consisting
 of one natural origin fish and one hatchery origin fish was 24–54% that of
 natural fish. The strong influence of hatchery broodstock origin on
 reproductive success confirms similar results from a previous study of a
 different population of the same species and suggests a genetic basis for
 the low reproductive success of hatchery steelhead, although environmental
 factors cannot be entirely ruled out. In addition to broodstock origin,
 fish size, return time, age, and spawning location were significant
 predictors of reproductive success. Our results indicate that
 incorporating natural fish into hatchery broodstock is clearly beneficial
 for improving subsequent natural spawning success, even in a population
 that has a decades-long history of hatchery releases, as is the case in
 the Wenatchee River.
description: Sampling data for
 steelhead at Tumwater DamSampling data for adult
 steelhead at Tumwater Dam on the Wenatchee River, Washington, from
 2007-2011. Columns: id = sample id (tied to genotype file), offspring =
 number of offspring assigned to adult via parentage, Sex.Changed =
 indication that the original sex designation was corrected, spawn.year =
 spawning year for fish, date = date fish passed the dam, date-dec31 = day
 of year where Jan1 is "1", final.status = status of fish, age =
 age of fish years, fresh.salt = winter in fresh and salt water based on
 scale analysis, salt.age = years in the ocean, sex = sex, origin =
 hatchery or wild (natural) origin, fkl = fork length in cm, brood.type =
 prior generation cross that produced a hatchery fish, final_stream =
 inferred spawning location, season = season of migration at Tumwater day
 (based on day 160), day-june9 = day of migration based on days after June
 9.adult
 phenotypes.csvgenotypesAdult and juveniles genotypes at 96 single nucleotide polymorphism loci. The "id" column for the adults is tied to the corresponding sample file.
DOI: 10.5061/dryad.4rb47
title: Data from: Nitric oxide signals are interlinked with calcium signals in normal pancreatic stellate cells upon oxidative stress and inflammation

description: The mammalian diffuse stellate cell system comprises retinoid-storing
 cells capable of remarkable transformations from a quiescent to an
 activated myofibroblast-like phenotype. Activated pancreatic stellate
 cells (PSCs) attract attention owing to the pivotal role they play in
 development of tissue fibrosis in chronic pancreatitis and pancreatic
 cancer. However, little is known about the actual role of PSCs in the
 normal pancreas. These enigmatic cells have recently been shown to respond
 to physiological stimuli in a manner that is markedly different from their
 neighbouring pancreatic acinar cells (PACs). Here, we demonstrate the
 capacity of PSCs to generate nitric oxide (NO), a free radical messenger
 mediating, for example, inflammation and vasodilatation. We show that
 production of cytosolic NO in PSCs is unambiguously related to cytosolic
 Ca2+ signals. Only stimuli that evoke Ca2+ signals in the PSCs elicit
 consequent NO generation. We provide fresh evidence for the striking
 difference between signalling pathways in PSCs and adjacent PACs, because
 PSCs, in contrast to PACs, generate substantial Ca2+-mediated and
 NOS-dependent NO signals. We also show that inhibition of NO generation
 protects both PSCs and PACs from necrosis. Our results highlight the
 interplay between Ca2+ and NO signalling pathways in cell–cell
 communication, and also identify a potential therapeutic target for
 anti-inflammatory therapies.
description: Video
 S1Oxidative stress induces
 increase in cytosolic nitric oxide in stellate cells. Pancreatic tissue
 lobule, containing numerous PACs that form the acini, and three PSCs in
 the centre, were loaded with DAF-FM fluorescent NO indicator. The lobule
 followed the challenge with 0.5 mM H2O2, which exerted increase in
 fluorescence in PSCs (time [real-time]: baseline: 00:00:00-04 [3 min],
 stimulation 00:00:04-18 [10.5 min]). See also Fig. S1.Movie
 S1.mov
DOI: 10.5061/dryad.8290n
title: Data from: pcadapt: an R package to perform genome scans for selection based on principal component analysis

description: The R package pcadapt performs genome scans to detect genes under
 selection based on population genomic data. It assumes that candidate
 markers are outliers with respect to how they are related to population
 structure. Because population structure is ascertained with principal
 component analysis, the package is fast and works with large-scale data.
 It can handle missing data and pooled sequencing data. By contrast to
 population-based approaches, the package handle admixed individuals and
 does not require grouping individuals into populations. Since its first
 release, pcadapt has evolved in terms of both statistical approach and
 software implementation. We present results obtained with robust
 Mahalanobis distance, which is a new statistic for genome scans available
 in the 2.0 and later versions of the package. When hierarchical population
 structure occurs, Mahalanobis distance is more powerful than the
 communality statistic that was implemented in the first version of the
 package. Using simulated data, we compare pcadapt to other computer
 programs for genome scans (BayeScan, hapflk, OutFLANK, sNMF). We find that
 the proportion of false discoveries is around a nominal false discovery
 rate set at 10% with the exception of BayeScan that generates 40% of false
 discoveries. We also find that the power of BayeScan is severely impacted
 by the presence of admixed individuals whereas pcadapt is not impacted.
 Last, we find that pcadapt and hapflk are the most powerful in scenarios
 of population divergence and range expansion. Because pcadapt handles
 next-generation sequencing data, it is a valuable tool for data analysis
 in molecular ecology.
description: Simulated SNP data under
 a island and a divergence model.The present archive
 contains 4 subfolders. Each subfolder contains a set of simulations
 relative to a specific model, which are listed in the filenames.txt. For
 each simulation, there are 5 files associated with: - the file without any
 extension contains the genotype matrix encoded with 0, 1 and 2. - the ped
 file. - the map file. - the file with the .gt extension contains the list
 of selected SNPs for the simulation. - the file with the .pop extension
 contains the population labels for each individual.simulations.zip
DOI: 10.5061/dryad.vb6k6
title: Data from: The ontogeny of tolerance curves: habitat quality vs. acclimation in a stressful environment

description: Stressful environments affect life-history components of fitness through
 (i) instantaneous detrimental effects, (ii) historical (carry-over)
 effects and (iii) history-by-environment interactions, including
 acclimation effects. The relative contributions of these different
 responses to environmental stress are likely to change along life, but
 such ontogenic perspective is often overlooked in studies of tolerance
 curves, precluding a better understanding of the causes of costs of
 acclimation, and more generally of fitness in temporally fine-grained
 environments. We performed an experiment in the brine shrimp Artemia to
 disentangle these different contributions to environmental tolerance, and
 investigate how they unfold along life. We placed individuals from three
 clones of A. parthenogenetica over a range of salinities during a week,
 before transferring them to a (possibly) different salinity for the rest
 of their lives. We monitored individual survival at repeated intervals
 throughout life, instead of measuring survival or performance at a given
 point in time, as commonly done in acclimation experiments. We then
 designed a modified survival analysis model to estimate phase-specific
 hazard rates, accounting for the fact that individuals may share the same
 treatment for only part of their lives. Our approach allowed us to
 distinguish effects of salinity on (i) instantaneous mortality in each
 phase (habitat quality effects), (ii) mortality later in life (history
 effects) and (iii) their interaction. We showed clear effects of early
 salinity on late survival and interactions between effects of past and
 current environments on survival. Importantly, analysis of the ontogenetic
 dynamics of the tolerance curve reveals that acclimation affects different
 parts of the curve at different ages. Adopting a dynamical view of the
 ontogeny of tolerance curve should prove useful for understanding niche
 limits in temporally changing environments, where the full sequence of
 environments experienced by an individual determines its overall
 environmental tolerance, and how it changes throughout life.
description: Survival
 timeData structure is as
 follow: {C, S1, S2, A, D}, where C is the clonal line of the individual
 (LM7 = 1, PAM10 = 2 and PAM7 = 3); S1 and S2 are the salinities during
 phase 1 and 2 of the experiment (40, 80, 120 or 180g/L); A is the last day
 the individual was seen alive, after entering the experiment on day 1; D
 is the first day the individual was seen dead (D = 10 000 for censored
 individuals by convention).Survival
 AnalysisMathematica notebook
 implementing the maximum likelihood method of our modified survival
 analysis. Allows parameter estimation and model comparison, as well as
 reproducing the figures in the article.
DOI: 10.5061/dryad.55c8q
title: Data from: Transcriptome modulation during host shift is driven by secondary metabolites in desert Drosophila

description: High-throughput transcriptome studies are breaking new ground to
 investigate the responses that organisms deploy in alternative
 environments. Nevertheless, much remains to be understood about the
 genetic basis of host plant adaptation. Here, we investigate genome-wide
 expression in the fly Drosophila buzzatii raised in different conditions.
 This species uses decaying tissues of cactus of the genus Opuntia as
 primary rearing substrate and secondarily, the necrotic tissues of the
 columnar cactus Trichocereus terscheckii. The latter constitutes a harmful
 host, rich in mescaline and other related phenylethylamine alkaloids. We
 assessed the transcriptomic responses of larvae reared in Opuntia
 sulphurea and T. terscheckii, with and without the addition of alkaloids
 extracted from the latter. Whole-genome expression profiles were massively
 modulated by the rearing environment, mainly by the presence of T.
 terscheckii alkaloids. Differentially expressed genes were mainly related
 to detoxification, oxidation–reduction and stress response; however, we
 also found genes involved in development and neurobiological processes. In
 conclusion, our study contributes new data onto the role of
 transcriptional plasticity in response to alternative rearing
 environments.
description: Developmental time
 analysis in RR script of the
 statistical analysis of developmental timeDT.RDevelopmental time means for the R scriptCSV file of developmental time means used in the statistical analysis in Rtd_means.csvDifferential expression analysis in RR script of the differential expression analysis in R using the package NOISeqDEGs_NOISeq.RDifferential expression data produced by NOIseqData produced in the differential expression analysis by the R package NOISeqDEGs_NOISeq.RData
DOI: 10.5281/zenodo.18386051
title: NOVAC_BRAND7_150F_1_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 150F SC sample 1 Novac - EDLC Single - Brand7Part of the Constant Temperature DataBase
DOI: 10.5281/zenodo.18386052
title: NOVAC_BRAND7_150F_1_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 150F SC sample 1 Novac - EDLC Single - Brand7Part of the Constant Temperature DataBase