cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.12jm63xvf
title: Supplemental Materials: Identification of proteins associated with the early restoration of insulin sensitivity after biliopancreatic diversion

description: ABSTRACT CONTEXT: Insulin resistance (IR) is a risk factor for type 2
 diabetes, diabetic kidney disease, cardiovascular disease and
 non-alcoholic steatohepatitis. Biliopancreatic diversion (BPD) is the most
 effective form of bariatric surgery for improving insulin sensitivity.
 OBJECTIVE: To identify plasma proteins correlating with the early
 restoration of insulin sensitivity after BPD. DESIGN: Prospective single
 centre study including twenty insulin resistant men with morbid obesity
 scheduled for BPD. Patient characteristics and blood samples were
 repeatedly collected from baseline up to four weeks post-surgery. IR was
 assessed by HOMA-IR, Matsuda Index and by studying metabolic profiles
 during meal tolerance tests. Unbiased proteomic analysis was performed to
 identify plasma proteins altered by BPD. Detailed plasma profiles were
 made on a selected set of proteins by targeted multiple reaction
 monitoring mass spectrometry (MRM/MS). Changes in plasma proteome were
 evaluated in relation to metabolic and inflammatory changes. RESULTS: BPD
 resulted in improved insulin sensitivity and reduced body weight.
 Proteomic analysis identified 29 proteins changed following BPD. Changes
 in plasma levels of afamin, apolipoprotein A-IV (ApoA4) and apolipoprotein
 A-II (ApoA2) correlated significantly with changes in IR. CONCLUSION:
 Circulating levels of afamin, ApoA4 and ApoA2 were associated with and may
 contribute to the rapid improvement in insulin sensitivity after BPD.
DOI: 10.5281/zenodo.18395476
title: Resources for Alloo et al. "....A Fokker-Planck approach to grating interferometry"

description: This repository contains experimental datasets (courtesy of Florian Scaff) and the corresponding retrieved phase and dark-field images of a test phantom sample. Results are obtained using both the conventional grating interferometry image-retrieval approach and our developed Fokker–Planck–based method. Python scripts used to process the data are also provided, including the Fokker–Planck algorithm code written by Samantha Alloo and the conventional sinusoidal algorithm code by Florian Scaff.

The repository also includes retrieved dynamic-phase and dark-field image sequences (videos) of the mouse chest sample presented in the manuscript, generated using both approaches.
DOI: 10.5281/zenodo.18395475
title: Resources for Alloo et al. "....A Fokker-Planck approach to grating interferometry"

description: This repository contains experimental datasets (courtesy of Florian Scaff) and the corresponding retrieved phase and dark-field images of a test phantom sample. Results are obtained using both the conventional grating interferometry image-retrieval approach and our developed Fokker–Planck–based method. Python scripts used to process the data are also provided, including the Fokker–Planck algorithm code written by Samantha Alloo and the conventional sinusoidal algorithm code by Florian Scaff.

The repository also includes retrieved dynamic-phase and dark-field image sequences (videos) of the mouse chest sample presented in the manuscript, generated using both approaches.
DOI: 10.5061/dryad.dncjsxkwz
title: Data from: Invasive dominance and resident diversity: unpacking the impact of plant invasion on biodiversity and ecosystem function

description: Plant invasions have consistently been shown to cause significant
 reductions in the diversity of recipient plant communities; an effect that
 can cascade through ecosystems to impact the stocks and flows of nutrients
 and energy as well as the diversity of higher trophic levels. However, the
 manner in which invasive plants alter ecosystem functioning and trophic
 interactions is highly variable can occur through the direct effects of
 the invader’s abundance and its indirect effects via changes in community
 diversity. Understanding the nature of these interactions between plant
 invasion, community diversity and ecosystem functioning can provide
 insight for ecosystem managers. We evaluated whether plant invasion alters
 the relationship between biodiversity and ecosystem function (BEF) by
 comparing BEF models that either include or subtract the diversity and
 function values associated with the invasive vine, Vincetoxicum rossicum.
 To do this, we 1) characterize V. rossicum within the functional trait
 space of the regional species pool; 2) assess how different components of
 plant biodiversity vary along a V. rossicum invasion gradient; and 3)
 examine how V. rossicum invasion affects BEF relationships and trophic
 interactions, both at the plot-scale and incrementally along a site-level
 invasion gradient. In general, we found that V. rossicum invasion was
 associated with significant declines in plant community diversity across a
 suite of biodiversity measures; a consequence of V. rossicum’s functional
 trait structure (height and specific leaf area). We also found that V.
 rossicum invasion resulted in significantly greater productivity (i.e.
 dominance effects in the inclusion model), but also that the diversity of
 the remaining resident community was positively associated with
 productivity (i.e. niche complementarity in the subtraction model).
 Further, we observed that while the relationship between flower cover and
 pollinator diversity was positive for both the inclusion and subtraction
 models, this relationship was stronger in the absence of V. rossicum. Our
 findings suggest that while plant invasion can result in enhanced
 productivity via dominance effects, this comes at the cost of significant
 declines in diversity. However, it is also the case that remaining
 resident diversity can exhibit positive effects on multiple functions and
 support for higher trophic levels.
description: Please refer to methods described in the manuscript.
DOI: 10.5061/dryad.sqv9s4n1v
title: Data from: Using artificial intelligence classification of videos to examine the environmental, evolutionary and physiological constraints on provisioning behavior

description: The use of artificial intelligence (AI) technologies can revolutionize how
 we approach data collection and analysis in behavioral ecology. One such
 example is in provisioning behavior. Parents of altricial species are
 selected to provide parental care (such as food provisioning) for their
 offspring, but there is substantial variation in the level of this care.
 Provisioning rate may be determined environmentally, by the physiological
 ability of parents and needs of nestlings, or by evolutionary
 incentives.  We quantified provisioning rate in 20 purple martin
 (Progne subis) nests in the context of an experimental reduction of nest
 ectoparasites. 10 nests had a parasite reduction treatment, and 10 nests
 were controls. By using AI to automate the analysis of nest camera videos
 we were able to obtain nearly-continuous provisioning rate information at
 a high temporal resolution for the first half of the nestling period. We
 used random forest modeling to assess the factors determining provisioning
 rate and found evidence for environmental, evolutionary and physiological
 constraints and incentives on provisioning. Birds appeared to be
 environmentally limited in their provisioning in cool, wet conditions,
 especially later in the breeding season; but adjusted their provisioning
 according to the changing physiological needs of nestlings. We found
 evidence for a compensatory response to increased parasite load, in which
 parents increased provisioning to more heavily parasitized nests.
DOI: 10.5061/dryad.vmcvdncqn
title: Data from: Trait-based variation in host contribution to pathogen transmission across species and resource supplies

description: Two key knowledge gaps currently limit the development of more predictive
 and general models of pathogen transmission: (1) the physiological basis
 of heterogeneity in host contribution to pathogen transmission (reservoir
 potential) remains poorly understood, and (2) a general means of
 integrating the ecological dynamics of host communities has yet to emerge.
 If the traits responsible for differences in reservoir potential also
 modulate host community dynamics, these traits could be used to predict
 pathogen transmission as host communities change. In two greenhouse
 experiments, across 23 host species and two levels of resource supply, the
 reservoir potential of plant hosts increased significantly along the Leaf
 Economic Spectrum, a global axis of plant physiological trait covariation
 that features prominently in models of plant community ecology. This
 indicates that the traits of the Leaf Economic Spectrum underlie broad
 differences in reservoir potential across host species and resource
 supplies. Therefore, host traits could be used to integrate
 epidemiological models of pathogen transmission with ecological models of
 host community change.
description: See associated manuscript for detials.
description: Missing values are explined in the associated manuscript. See
 Appendix S5 of the associated manuscript for sample sizes. Column headings
 are explained in the second sheet of the data set
 ("notes").
DOI: 10.58024/aguma5dc78b8
title: Ar-Ar Geochronology of Volcanics from the Bulga Plateau, NSW
DOI: 10.5061/dryad.w3r2280nj
title: Cadmium exposure persistently modulates the gut-liver axis in an Alzheimer’s disease mouse model

description: The human Apolipoprotein E4 (ApoE4) variant is the strongest known genetic
 risk factor for Alzheimer’s disease (AD).  Cadmium (Cd) has been
 shown to impair learning and memory at a greater extent in humanized ApoE4
 knock-in (ApoE4-KI) mice as compared to the ApoE3 (common allele)-KI mice.
 In this study, we determined the extent that cadmium interacts with the
 ApoE4 gene variants to modify the gut-liver axis, which is important for
 xenobiotic biotransformation and nutrient homeostasis. Large intestinal
 content bacterial 16S rDNA sequencing, serum lipid metabolomics, and
 hepatic transcriptomics were analyzed in ApoE3- and ApoE4-KI mice orally
 exposed to vehicle, a low dose, or a high dose of Cd in drinking water.
  Aligning with the previous report showing that the ApoE4-KI
 males are more susceptible to cadmium-induced memory deficit, ApoE4-KI
 males had the most prominent changes in gut microbiota, including an
 up-regulation of A. muciniciphila, which is a biomarker for AD in humans,
 as well as predicted down-regulation of many essential microbial pathways
 involved in nutrient and energy homeostasis.  Serum lactate was
 lower only in ApoE4-KI males following Cd exposure. In the host liver,
 cadmium-exposed ApoE4-KI males had the most differentially regulated
 pathways; specifically there was an enrichment in several pathways
 involved in platelet activation, which is known to amplify liver damage
 and inflammation. These pathways were associated with up-regulated
 Prevotella and A. muciniphila in intestine at the Cd low dose. 
 Cadmium-exposed ApoE4-KI mice also had the most differentially regulated
 hepatic drug processing genes, and in particular, the up-regulation of
 Cyp2 family, Ugts, Gsts, and Slco1b2 in liver associated with the
 up-regulation of Clostridiaceae in the intestine at the Cd high
 dose.  In conclusion, Cd exposure profoundly modified the
 gut-liver axis in the most susceptible mouse strain to neurological
 damage, (ApoE4-KI males) evidenced by up-regulation in microbial AD
 biomarkers, reduction in energy supply-related pathways in gut and blood,
 and up-regulation in hepatic pathways involved in inflammation and
 xenobiotic biotransformation.
description: Total DNA was isolated from the large intestinal content of male
 and female ApoE3-KI and ApoE4-KI mice (n=4-5).  Briefly, samples were
 prepared using an E.Z.N.A. DNA Stool Kit (Omega Bio-tek Inc., Norcross,
 GA) per the manufacturer’s instructions. The V4 hypervariable region of
 16S rDNA was amplified and sequenced using a HiSeq 2500 second generation
 sequencing platform (250-bp paired-end) (Novogene Corporation Inc.,
 Sacramento, CA). Total RNA was isolated from livers of
 Cd or vehicle exposed ApoE3-KI and ApoE4-KI mice (n=4 per exposure per
 sex) using RNA zol Bee reagent (Tel-Test Inc., Friendswood, TX). cDNA
 libraries were prepared using a Clontech cDNA library prep kit (Clontech
 Laboratories Inc., Mountain View CA), and were sequenced using a NextSeq
 500 sequencing platform (75 bp paired end).
DOI: 10.7280/d1s38h
title: Physical processes determine spatial structure in water temperature and residence time on a wide reef flat

description: On coral reefs, flow determines residence time of water, influencing
 physical and chemical environments and creating observable microclimates
 within the reef structure. Understanding the physical mechanisms driving
 variability on coral reefs, which distinguishes them from the open ocean,
 can be important for understanding what contributes to thermal resilience
 of coral communities and predicting their response to future anomalies. In
 June 2014, a field experiment was conducted at Dongsha Atoll in the
 northern South China Sea to study the physical forces that drive flow over
 a broad shallow reef flat. Instrumentation included current and pressure
 sensors, and a distributed temperature sensing system, which resolved
 spatially and temporally continuous temperature measurements over a 3-km
 cross-reef section from the lagoon to the reef crest. Spectral analysis
 shows that while diurnal variability in temperature was significant across
 the entire reef flat - a result expected from daily solar heating - water
 temperature also varied at higher frequencies near the reef crest. These
 thermal microclimates are shaped by circulation on the wide reef flat,
 with spatially and temporally variable contributions from tides, wind, and
 waves. Through particle tracking simulations, we find the residence time
 of water is short near the reef crest (2.8 hours) and longer near the
 lagoon (7.7 hours). Tidal variability in flow direction leads to patterns
 in residence time that are different than what would be predicted from
 unidirectional flow conditions. Circulation on the reef also governs the
 source (originating from offshore vs. the lagoon) of the water dominant
 across the reef flat.
description: Dataset was collected in June 2014. It includes distributed
 temperature sensing data, currents and pressure measurements from the
 Dongsha east reef flat. Locations and instruments are outlined below, and
 also in more detail in info sheets within the zip folders. 
 Across the reef flat and slope - distributed temperature sensing
 fiber optic cable, as well as 4 SBE-56 calibration loggers and 4
 validation loggers. E1 - AWAC Profiler, located at
 18.1m depth, measuring currents and waves E2 - SBE-26
 pressure gauge E3 - Nortek Aquadopp Profiler, measuring
 currents and pressure.  E4 - SBE-26 pressure
 gauge E5 - Nortek Aquadopp Profiler, measuring currents
 and pressure.  E6 - SBE-26 pressure gauge
DOI: 10.15468/dl.e3rerw
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bauhinia tomentosa",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002427-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.56rnjm
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-100.99114 20.50417,-100.95234 20.50417,-100.95234 20.52096,-100.99114 20.52096,-100.99114 20.50417))",
 "OccurrenceStatus is Present",
 "TaxonKey is Amphibia"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002428-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kmvtev
title: Occurrence Download

description: A dataset containing 145113 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((18 -22,17 -22,17 -23,18 -23,18 -22))",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 145113 records from 140 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002396-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dhc82f
title: Occurrence Download

description: A dataset containing 364597 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Belgium",
 "TaxonKey is one of (Aponogeton distachyos, Arthurdendyus triangulatus, Cabomba caroliniana, Callosciurus finlaysonii, Cherax destructor, Corvus splendens, Crassula helmsii, Elodea densa, Eriocheir sinensis, Erythranthe guttata, Faxonius immunis, Faxonius juvenilis, Faxonius rusticus, Faxonius virilis, Gambusia affinis, Heracleum mantegazzianum, Heracleum persicum, Heracleum pubescens, Houttuynia cordata, , Impatiens glandulifera, Koenigia polystachya, Lagarosiphon major, Lepomis gibbosus, Limnoperna fortunei, Ludwigia grandiflora, Ludwigia peploides, Lysichiton americanus, Morone americana, Muntiacus reevesi, Myriophyllum aquaticum, Myriophyllum heterophyllum, Pacifastacus leniusculus, Petasites japonicus, Pontederia cordata, Procambarus acutus, Procambarus clarkii, Procambarus virginalis, Pseudorasbora parva, Pycnonotus cafer, Saururus cernuus, Sciurus carolinensis, Sciurus niger, Solenopsis invicta, Solenopsis richteri, Threskiornis aethiopicus, Vespa velutina, Zizania latifolia)",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 364597 records from 88 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002386-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.d51c5b00j
title: Phylogenomics, origin and diversification of anthozoans (Phylum Cnidaria)

description: Anthozoan cnidarians (corals and sea anemones) include some of the
 world's most important foundation species, capable of building
 massive reef complexes that support entire ecosystems. Although previous
 molecular phylogenetic analyses have revealed widespread homoplasy of the
 morphological characters traditionally used to define orders and families
 of anthozoans, analyses using mitochondrial genes or rDNA have failed to
 resolve many key nodes in the phylogeny. With a fully resolved,
 time-calibrated phylogeny for 234 species constructed from hundreds of
 ultraconserved elements and exon loci, we explore the evolutionary origins
 of the major clades of Anthozoa and some of their salient morphological
 features. The phylogeny supports reciprocally monophyletic Hexacorallia
 and Octocorallia, with Ceriantharia as the earliest diverging hexacorals;
 two reciprocally monophyletic clades of Octocorallia; and monophyly of all
 hexacoral orders with the exception of the enigmatic sea anemone
 Relicanthus daphneae. Divergence dating analyses place Anthozoa in the
 Cryogenian to Tonian periods (648–894 Ma), older than has been suggested
 by previous studies. Ancestral state reconstructions indicate that the
 ancestral anthozoan was a solitary polyp that had bilateral symmetry and
 lacked a skeleton. Colonial growth forms and the ability to precipitate
 calcium carbonate evolved in the Ediacaran (578 Ma) and Cambrian (503 Ma)
 respectively; these hallmarks of reef-building species have subsequently
 arisen multiple times independently in different orders. Anthozoans formed
 associations with photosymbionts by the Devonian (383 Ma), and
 photosymbioses have been gained and lost repeatedly in all orders.
 Together, these results have profound implications for interpretation of
 the Precambrian environment and the early evolution of metazoans.
DOI: 10.5061/dryad.m37pvmd06
title: Incorporating hierarchical characters into phylogenetic analysis

description: Popular optimality criteria for phylogenetic trees focus on sequences of
 characters that are applicable to all the taxa. As studies grow in
 breadth, it can be the case that some characters are applicable for a
 portion of the taxa and inapplicable for others.  Past work has
 explored the limitations of treating inapplicable characters as missing
 data, noting that this strategy may favor trees where interval nodes are
 assigned impossible states, where the arrangement of taxa within subclades
 is unduly influenced by variation in distant parts of the tree, and/or
 where taxa that otherwise share most primary characters are grouped
 distantly. Approaches that avoid the first two problems have recently been
 proposed. Here, we propose an alternative approach which avoids all three
 problems. In the spirit of maximum parsimony, the proposed criterion seeks
 the phylogenetic tree with the minimal changes across any tree branch, but
 where changes are defined in terms of dissimilarity metrics that weigh the
 affects of inapplicable characters. The approach can accommodate binary,
 multistate, ordered, unordered, and polymorphic characters.  We
 give a polynomial-time algorithm, inspired by Fitch's algorithm, to
 score trees under a family of dissimilarity metrics, and prove its
 correctness.  We show that the resulting optimality criteria is
 computationally hard, by reduction to the NP-hardness of the maximum
 parsimony optimality criteria.  We demonstrate our approach using
 synthetic and empirical data sets and compare the results with other
 recently proposed methods for choosing optimal phylogenetic trees when the
 data includes inapplicable characters.
description: There are three different data sets: * The
 first is a character matrix of brachiopods (Cusask et al, 1999), recoded
 using redundant coding (the original matrix was coded using a mixture of
 non-additive binary coding and composite coding).  A file of character
 dependencies has also been added. * The second is a
 character matrix of myriapods (Fernandez et al, 2016) that had been
 previously modified for use as a case study for managing inapplicable
 characters for disparity analysis (Hopkins and St. John, 2018).  A file of
 character dependencies has also been added. * The third
 are synthetic data sets on 8 taxa with 13 and 20 characters.  A file of
 character dependencies has also been included.
 Supplementary material, including data files and additional
 discussion and figures, are in SOM.pdf.