cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dfn2z34zx
title: Natural history of model organisms: the secret (group) life of Drosophila melanogaster larvae and why it matters to developmental ecology

description: Model organisms such as Drosophila melanogaster have been key tools for
 advancing our fundamental and applied knowledge in biological and
 biomedical sciences. However, model organisms have become intertwined with
 the idea of controlled and stable laboratory environments, and their
 natural history has been overlooked. In holometabolous insects, lack of
 natural history information on larval ecology has precluded major advances
 in the field of developmental ecology, especially in terms of
 manipulations of population density early in life (i.e., larval density).
 This is because of relativistic and to some extent, arbitrary
 methodologies employed to manipulate larval densities in laboratory
 studies. As a result, these methodologies render comparisons between
 species impossible, precluding our understanding of macroevolutionary
 responses to population densities during development that can be derived
 from comparative studies. We recently proposed a new conceptual framework
 to address this issue and here, we provide the first natural history
 investigation of Drosophila melanogaster larval density under such
 framework. First, we characterised the distribution of larval densities in
 wild population of D. melanogaster using rotting apples as breeding
 substrate in a suburban area in Sweden. Next, we compiled the commonly
 used methodologies for manipulating larval densities in laboratory studies
 from the literature and found that the  majority of laboratory
 studies did not manipulate larval densities below or above the densities
 observed in nature, suggesting that we have yet to study true life-history
 and physiological responses to low and high population densities during D.
 melanogaster development. This is, to our knowledge, the first direct
 natural history account of larval density in nature for this model
 organism. Our study paves the way for a more integrated view of organismal
 biology which re-incorporates natural history of model organisms into
 hypothesis-driven research in developmental ecology.
description: Details provided in the publication
description: ReadMe file uploaded with the dataset
DOI: 10.5061/dryad.j9kd51c9q
title: Increased signal diversity/complexity of spontaneous EEG, but not evoked EEG responses, in ketamine-induced psychedelic state in humans

description: How and to what extent electrical brain activity reflects
 pharmacologically altered states and contents of consciousness, is not
 well understood. Therefore, we investigated whether measures of evoked and
 spontaneous electroencephalographic (EEG) signal diversity are altered by
 sub-anaesthetic levels of ketamine compared to normal wakefulness, and how
 these measures relate to subjective experience. High-density 62-channel
 EEG was used to record spontaneous brain activity and responses evoked by
 transcranial magnetic stimulation (TMS) in 10 healthy volunteers before
 and during administration of sub-anaesthetic doses of ketamine in an
 openlabel within-subject design. Evoked signal diversity was assessed
 using the perturbational complexity index (PCI), calculated from EEG
 responses to TMS perturbations. Signal diversity of spontaneous EEG, with
 eyes open and eyes closed, was assessed by Lempel Ziv complexity (LZc),
 amplitude coalition entropy (ACE), and synchrony coalition entropy (SCE).
 Although no significant difference was found in TMS-evoked complexity
 (PCI) between the sub-anaesthetic ketamine condition and normal
 wakefulness, all measures of spontaneous EEG signal diversity (LZc, ACE,
 SCE) showed significantly increased values in the sub-anaesthetic ketamine
 condition. This increase in signal diversity correlated with subjective
 assessment of altered states of consciousness. Moreover, spontaneous
 signal diversity was significantly higher when participants had eyes open
 compared to eyes closed, both during normal wakefulness and during
 influence of subanaesthetic ketamine. The results suggest that PCI and
 spontaneous signal diversity may reflect distinct, complementary aspects
 of changes in brain properties related to altered states of consciousness:
 the brain’s capacity for information integration, assessed by PCI, might
 be indicative of the brain’s ability to sustain consciousness, while
 spontaneous complexity, as measured by EEG signal diversity, may be
 indicative of the complexity of conscious content. Thus, sub-anaesthetic
 ketamine may increase the complexity of the conscious content and the
 brain activity underlying it, while the level or general capacity for
 consciousness remains largely unaffected.
description: Raw and TMS-evoked EEG data were collected from healthy
 volunteers in normal wakefulness and under the effects of low doses of
 intravenous ketamine. The data available here have since been preprocessed
 in accordance with the description in the manuscript (available on
 BioRxiv, and is under review in PLOS ONE). 
description: The data have been preprocessed in matlab. The raw data were
 preprocessed using EEGLAB, and are available as .set files. The evoked
 data were published using scripts from the Massimini lab (SSP, the
 SiSyPhus project written largely by Casali and colleagues), and are
 available as raw matlab arrays. Please get in touch with the authors for
 further information
DOI: 10.5061/dryad.x69p8czgp
title: Characteristics of non-neoplastic epithelium that appears within gastric cancer with and without Helicobacter pylori eradication

description: A non-neoplastic epithelium (NE) often appears in gastric cancer (GC). We
 explored the histological features of NE in comparison between
 HP-eradicated and HP-infected GCs. We enrolled 40 HP-eradicated and 40
 HP-infected GCs matched by size, macroscopic and histological type. NE was
 classified into full gland type and surface type; the former was a
 non-neoplastic gland isolated within cancer, and the latter was NE on the
 surface of the cancer. Surface type was additionally divided into NE at
 the cancer margin (marginal surface type) and NE inside cancer (internal
 surface type). The primary endpoints were the frequency and the length
 ratio (the ratio to cancer length) of NE in each GC. The secondary
 endpoints were the relationships between NE and clinicopathological
 factors, including endoscopic findings of a gastritis-like appearance
 (GLA), multiple white elevated lesions (MWELs), reddish depressed lesion
 (RDL), and white nodular mucosa (WNM). The frequency and length ratio of
 the internal surface type in HP-eradicated GCs were significantly higher
 (82.5% vs 50%, P = 0.005) and larger (11.6 ± 10.6 vs 4.2 ± 9.9, P &lt;
 0.001) than those in HP-infected GCs. The frequency and length ratio of
 marginal surface type and full gland type were not significantly different
 between the two GC groups, but the coexistence of internal surface and
 full gland types was statistically significant (p &lt; 0.001). The
 frequencies of GLA, RDLs, and WNM in HP-eradicated GCs were significantly
 higher than those in HP-infected GCs. Moreover, GLA-positive GCs were
 covered more widely by internal surface type than GLA-negative GCs (13.3%
 vs. 6.6%, P = 0.003). Various types of NE were noted in gastric cancer,
 and the internal surface type of NE was shown to be significantly linked
 to HP-eradicated cancer and GLA.
DOI: 10.15468/dl.eb7bpq
title: Occurrence Download

description: A dataset containing 3046 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thymallus arcticus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3046 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002618-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7272/q6cc0xxj
title: DNA scaffolds enable efficient and tunable functionalization of biomaterials for immune cell modulation

description: Biomaterials can improve the safety and presentation of therapeutic agents
 for effective immunotherapy, and a high level of control over surface
 functionalization is essential for immune cell modulation. Here, we
 developed biocompatible immune cell engaging particles (ICEp) that use
 synthetic short DNA as scaffolds for efficient and tunable protein
 loading. To improve the safety of chimeric antigen receptor (CAR) T cell
 therapies, micron-sized ICEp were injected intratumorally to present a
 priming signal for systemically administered AND-gate CAR-T cells. Locally
 retained ICEp presenting a high density of priming antigens activated
 CAR-T cells, driving local tumor clearance while sparing uninjected tumors
 in immunodeficient mice. The ratiometric control of costimulatory ligands
 (anti-CD3 and anti-CD28 antibodies) and the surface presentation of a
 cytokine (IL-2) on ICEp were shown to significantly impact human primary T
 cell activation phenotypes. This modular and versatile biomaterial
 functionalization platform can provide new opportunities for
 immunotherapies.
DOI: 10.5061/dryad.sj3tx9636
title: Mechanistic dissection of increased enzymatic rate in a phase-separated compartment

description: Biomolecular condensates concentrate macromolecules into discrete cellular
 foci without an encapsulating membrane.  Condensates are often
 presumed to increase enzymatic reaction rates through increased
 concentrations of enzymes and substrates (mass action), although this idea
 has not been widely tested and other mechanisms of modulation are
 possible.  Here we describe a synthetic system where the
 SUMOylation enzyme cascade is recruited into engineered condensates
 generated by liquid-liquid phase separation of multidomain scaffolding
 proteins.  SUMOylation rates can be increased up to 36-fold in
 these droplets compared to the surrounding bulk, depending on substrate
 KM. This dependency produces substantial specificity among different
 substrates.  Analyses of reactions above and below the phase
 separation threshold lead to a quantitative model in which reactions in
 condensates are accelerated by mass action and by changes in substrate KM,
 likely due to scaffold-induced molecular organization. Thus, condensates
 can modulate reaction rates both by concentrating molecules and by
 physically organizing them.
DOI: 10.5061/dryad.z34tmpgbm
title: Cryptic speciation in the Warbling Vireo (Vireo gilvus)

description: Eastern (Vireo gilvus gilvus) and  western (V. g. swainsoni)
 forms of the Warbling Vireo have essentially allopatric breeding ranges
 across north-central North America, but come into contact in central
 Alberta, Canada.  In 1986, Jon Barlow presented preliminary
 morphological and song evidence suggesting that the Warbling Vireo complex
 might comprise more than one valid species.  However, to date
 Barlow’s suggestion is supported by only limited DNA evidence,
 demonstration of molt and migration differences between the taxa, and
 anecdotal accounts of differences in song, morphology, plumage, and
 ecology.  We analyzed variation in both mitochondrial and nuclear
 DNA in birds from Alberta and surrounding areas to determine the levels of
 genetic differentiation and  hybridization occurring in the
 contact zone, and whether the two taxa warrant recognition as separate
 biological species.  Our analyses reveal that Warbling Vireos in
 Alberta and the surrounding areas are separated into two well-defined,
 genetically-differentiated, and monophyletic clades corresponding to
 previously-recognized taxonomic groups.  The two taxa come into
 contact in a narrow (~85 km) zone in Barrhead County, northwest of
 Edmonton, Alberta.  They show evidence of limited
 hybridization.  The distinct genetic differences are maintained
 in the contact zone, where individuals of the two taxa may occupy
 neighboring territories.  Differences in spring arrival dates,
 molt schedules and migration routes indicate that a migratory divide may
 play an important role in reproductive isolation.  We suggest
 that the two taxa are distinct cryptic species: an eastern form, Vireo
 gilvus, and a western form, Vireo swainsoni.
description: Data spreadsheets: AFLP data set (<strong>Lovell et al
 AFLP.csv</strong>); Cline analyses data set (AFLP frequencies for
 all loci across a contact zone transect between Warbling Vireos.)
 (<strong>HZARgenFreq.csv</strong>) R Scripts for cline analyses
 using HZAR: <b>RunHZAR.R</b>; <b>params.R</b>;
 <b>modelLoader.R</b>; <b>mleHelper.R</b>
 <b>; mcmcHelper.R</b> <strong>README_for_Lovell
 et al_WAVI_DNA.docx</strong>
DOI: 10.5061/dryad.7h44j0zsh
title: Amyloid PET imaging in self-identified non-Hispanic Blacks from the Anti-Amyloid in Asymptomatic Alzheimer’s Disease (A4) Study – Supplementary Data

description: The goal of the manuscript was to examine whether amyloid PET in CN
 individuals that were screened for the Anti-Amyloid in Asymptomatic AD
 (A4) study differed across self-identified, non-Hispanic White and Black
 (NHW and NHB) groups.  We examined 3685 NHW and 144 NHB that
 passed initial screening for the A4 study and underwent amyloid PET. The
 effect of race on amyloid PET was examined using logistic (dichotomous
 groups) and linear (continuous values) regression controlling for age,
 sex, and number of APOE ε4 and APOE ε2 alleles. Lifestyle factors and
 medical conditions were available for the majority of individuals that
 received an amyloid PET scan. Additional sensitivity analyses were run to
 examine potential effects between amyloid and lifestyle as well as
 self-reported medical conditions that differed by race. Reduced amyloid
 was observed in self-identified non-Hispanic Blacks that passed initial
 eligibility criteria for the A4 Study, but lifestyle and vascular factors
 did not impact this effect. This work stresses the importance of
 investigating AD biomarkers in ancestrally diverse samples as well as the
 need for careful consideration regarding study eligibility criteria in AD
 prevention trials.
DOI: 10.15468/dl.4cxsqp
title: Occurrence Download

description: A dataset containing 216 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Anaphalis javanica",
 "Year 1000-2005"
 ]
}

 The dataset includes 216 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002619-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.crjdfn32v
title: Observation of separated dynamics of charge and spin in the Fermi-Hubbard model

description: Strongly correlated quantum systems give rise to many exotic physical
 phenomena, including high-temperature superconductivity. Simulating these
 systems on quantum computers may avoid the prohibitively high
 computational cost incurred in classical approaches. However, systematic
 errors and decoherence effects presented in current quantum devices make
 it difficult to achieve this. Here, we simulate the dynamics of the
 one-dimensional Fermi-Hubbard model using 16 qubits on a digital
 superconducting quantum processor. We observe separations in the spreading
 velocities of charge and spin densities in the highly excited regime, a
 regime that is beyond the conventional quasiparticle picture. To minimize
 systematic errors, we introduce an accurate gate calibration procedure
 that is fast enough to capture temporal drifts of the gate parameters. We
 also employ a sequence of error-mitigation techniques to reduce
 decoherence effects and residual systematic errors. These procedures allow
 us to simulate the time evolution of the model faithfully despite having
 over 600 two-qubit gates in our circuits. Our experiment charts a path to
 practical quantum simulation of strongly correlated phenomena using
 available quantum devices.
description: These contain raw data collected from Google's Sycamore
 superconducting quantum processor as well as processed data with
 associated metadata.  The code that used to process the data can be found
 at https://github.com/quantumlib/ReCirq.
description: A README file is included. Data are stored in Cirq compatible
 JSON format.
DOI: 10.5061/dryad.bvq83bk6z
title: Deep reefs are not refugium for shallow-water fish communities in the southwestern Atlantic

description: 1. The deep reef refugia hypothesis (DRRH) predicts that deep reef
 ecosystems may act as refugium for the biota of disturbed shallow waters.
 Because deep reefs are amongst the most understudied habitats on Earth,
 formal tests of the DRRH remain scarce. If the DRRH is valid at the
 community level, the diversity of species, functions and lineages of fish
 communities of shallow reefs should be encapsulated in deep reefs. 2. We
 tested the DRRH by assessing the taxonomic, functional and phylogenetic
 diversity of 22 Brazilian fish communities between 2 and 62m depth. We
 partitioned the gamma diversity of shallow (&lt;30m) and deep reefs
 (&gt;30m) into independent alpha and beta components, accounted for
 species’ abundance, and assessed if beta patterns were mostly driven by
 spatial turnover or nestedness. 3. We recorded 3821 fishes belonging to 85
 species and 36 families. Contrary to DRRH expectations, only 48% of the
 species occurred in both shallow and deep reefs. Alpha diversity of rare
 species was higher in deep reefs as expected, but alpha diversity of
 typical and dominant species did not vary with depth. Alpha functional
 diversity was higher in deep reefs only for rare and typical species, but
 not for dominant species. Alpha phylogenetic diversity was consistently
 higher in deep reefs, supporting DRRH expectations. 4. Profiles of
 taxonomic, functional, and phylogenetic beta diversity indicated that deep
 reefs were not more heterogeneous than shallow reefs, contradicting
 expectations of biotic homogenization near sea surface. Furthermore,
 pairwise beta diversity analyses revealed that the patterns were mostly
 driven by spatial turnover rather than nestedness at any depth. 5.
 Conclusions: Although some results support the DRRH, most
 indicate that the shallow-water reef fish diversity are not fully
 encapsulated in deep reefs. Every reef contributes significantly to the
 regional diversity and must be managed and protected accordingly.
DOI: 10.5061/dryad.gqnk98skg
title: Phylogenomic analysis reveals dispersal-driven speciation and divergence with gene flow in Lesser Sunda Flying Lizards (Genus Draco)

description: The Lesser Sunda Archipelago offers exceptional potential as a model
 system for studying the dynamics of dispersal-driven diversification. The
 geographic proximity of the islands suggests the possibility for
 successful dispersal, but this is countered by the permanence of the
 marine barriers and extreme intervening currents that are expected to
 hinder gene flow. Phylogenetic and species delimitation analyses of flying
 lizards (genus Draco) using single mitochondrial genes, complete
 mitochondrial genomes, and exome-capture data sets identified 9–11 deeply
 divergent lineages both within and between islands, with the largest
 islands each containing parapatrically-distributed non-sister lineages.
 Population clustering and demographic analyses confirmed these genetic
 boundaries and suggest the occurrence of 9–10 cryptic and non-cryptic
 species rather than the two species currently recognized. These analyses
 indicate initial entry of Draco into the archipelago at 5.5–7.5 Ma, with
 most inter-island colonization events having occurred between 1–3 Ma.
 Biogeographical model testing favors scenarios integrating geographic
 distance and historical island connectivity, including an initial
 stepping-stone dispersal process from the Greater Sunda Shelf through the
 Sunda Arc as far eastward as Lembata Island. However, rather than reaching
 the adjacent island of Pantar by dispersing over the 15-km wide Alor
 Strait, Draco ultimately reached Pantar (and much of the rest of the
 archipelago) by way of a circuitous route involving dispersal from either
 Sumbawa or Flores south to Sumba, east to Timor (across a 300-km marine
 barrier), north to Wetar, and then westward back to Pantar. These findings
 suggest that historical geological and oceanographic conditions heavily
 influenced dispersal pathways and gene flow, which in turn drove species
 formation and shaped species boundaries.
description: This data repository contains Supplementary Matarials, software
 input files, and the probe design file. For information on how the dataset
 was collected see the 'Supplementary Methods' section of the
 file.
DOI: 10.5061/dryad.8gtht76n6
title: Data from: Whole-genome analyses provide no evidence for dog introgression in Fennoscandian wolf populations

description: Hybridisation and admixture can threaten the genetic integrity of
 populations and be of particular concern to endangered species.
 Hybridisation between grey wolves and dogs has been documented in many
 wolf populations worldwide and is a prominent example of human-mediated
 hybridisation between a domesticated species and its wild relative. We
 analysed whole-genome sequences from &gt;200 wolves and &gt;100
 dogs to study admixture in Fennoscandian wolf populations. A principal
 component analysis of genetic variation as well as Admixture showed that
 wolves and dogs were well separated, without evidence for introgression.
 Analyses of local ancestry revealed that wolves had &lt;1% mixed
 ancestry, levels comparable to the degree of mixed ancestry in many dogs,
 and likely not resulting from recent wolf-dog hybridisation. We also show
 that the founders of the Scandinavian wolf population were genetically
 inseparable from Finnish and Russian Karelian wolves, pointing at the
 geographical origin of contemporary Scandinavian wolves. Moreover, we
 found Scandinavian-born animals among wolves sampled in Finland,
 demonstrating bi-directional gene flow between the Scandinavian peninsula
 and eastern countries. The low incidence of admixture between wolves and
 dogs in Fennoscandia may be explained by that feral dogs are rare in this
 part of Europe, and that careful monitoring and management act to remove
 hybrids before they backcross into wolf populations.
DOI: 10.5061/dryad.31zcrjdjg
title: Data from: Numerical models for assessing the risk of leaflet thrombosis post-transcatheter aortic valve-in-valve implantation

description: Leaflet thrombosis has been suggested as the reason for the reduced
 leaflet motion in cases of hypoattenuated leaflet thickening of
 bioprosthetic aortic valves. This work aimed to estimate the risk of
 leaflet thrombosis in two post-ViV configurations, using five different
 numerical approaches. Realistic ViV configurations were calculated by
 modeling the deployments of the latest version of transcatheter aortic
 valve devices (Medtronic Evolut PRO, Edwards SAPIEN 3) in the surgical
 Sorin Mitroflow. Computational fluid dynamics simulations of blood flow
 followed the dry models. Lagrangian and Eulerian measures of near-wall
 stagnation were implemented by particle and concentration tracking,
 respectively, to estimate the thrombogenicity and to predict the risk
 locations. Most of the numerical approaches indicate on a higher leaflet
 thrombosis risk in the Edwards SAPIEN 3 device because of its
 intra-annular implantation. The Eulerian approaches estimated high-risk
 locations in agreement with the WSS separation points. On the other hand,
 the Lagrangian approaches predicted high-risk locations at the proximal
 regions of the leaflets matching the low WSS magnitude regions of both
 TAVI models and reported clinical and experimental data. The proposed
 methods can help optimizing future designs of transcatheter aortic valves
 with minimal thrombotic risks.
description: The results were exported from ANSYS Fluent and processed in
 Matlab and Paraview.