cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7272/q6kk991s
title: Phenotypic analysis of the unstimulated in vivo HIV CD4 T cell reservoir

description: The latent reservoir is a main barrier for curing HIV. But because
 latently-infected cells cannot be phenotyped directly, the features of the
 in vivo reservoir have remained elusive. Here, we describe a method that
 leverages high-dimensional phenotyping using CyTOF to trace
 latently-infected cells reactivated ex vivo to their original
 pre-activation states. Our results suggest that contrary to common
 assumptions, the reservoir is not randomly distributed among cell subsets,
 and is remarkably conserved between individuals. However, reservoir
 composition differs between tissues and blood, as do cells successfully
 reactivated by different latency reversing agents. By selecting 8-10 of
 our 39 original CyTOF markers, we were able to isolate highly purified
 populations of unstimulated in vivo latent cells. These purified
 populations were highly enriched for replication-competent and intact
 provirus, transcribed HIV, and displayed clonal expansion. The ability to
 isolate unstimulated latent cells from infected individuals enables
 previously impossible studies of HIV persistence.
description: Included are the raw CSV files for the atlas CD4+ T cells
 ("atlas") and kNN latent cells ("kNN") for specimens
 in the study analyzed by PP-SLIDE. Each row corresponds to a cell,  and
 each column indicates the arcsinh-transformed values for each measured
 protein parameter. Zero values correspond to instances where the
 corresponding metal-conjugated antibody was not detected by the CyTOF
 instrument.
DOI: 10.5061/dryad.jh9w0vt8d
title: Data from: Joint effect of phylogenetic relatedness and trait selection on the elevational distribution of Rhododendron species

description: Congeneric species may coexist at ﬁne spatial scales through niche
 diﬀerentiation, however, the magnitude to which the eﬀects of functional
 traits and phylogenetic relatedness contribute to their distribution along
 elevational gradients remains understudied. To test the hypothesis that
 trait and elevational range overlap can aﬀect local speciesʼ coexistence,
 we ﬁrst compared phylogenetic relatedness and trait (including
 morphological traits and leaf elements) divergence among closely related
 species of Rhododendron L. on Yulong Mountain, China. We then assessed
 relationships between the overlap of multiple functional traits and the
 degree of elevational range overlap among species pairs in a phylogenetic
 context. We found that phylogeny was a good predictor for most functional
 traits, where closely related species showed higher trait similarity and
 occupied diﬀerent elevational niches at our study site. Species pairs of
 R. subgen. Hymenanthes (Blume) K. Koch showed low elevational range
 overlap and some species pairs of R. subgen. Rhododendron showed obvious
 niche diﬀerentiation. Trait divergence is greater for species in R.
 subgen. Rhododendron, and it plays an important role between species pairs
 with low elevational range overlap. Trait convergent selection takes place
 between co-occurring closely related species that have high elevational
 range overlap, which share more functional trait space due to
 environmental ﬁltering or ecological adaptation in more extreme habitats.
 Our results highlight the importance of evolutionary history and trait
 selection for species coexistence at ﬁne ecological scales along
 environmental gradients.
description: We extracted 76 common protein-coding genes from plastid genome
 of all our sampled <em>Rhododendron</em> species. Multiple
 sequence alignments for each gene were performed using MAFFT v7.22 and
 sequences of these 76 genes were concatenated by AMAS to generate a
 supermatrix (58,131 bp in length).
DOI: 10.15468/j8ebtr
title: Two new species of monitor lizards (Squamata: Varanus) endemic to the Louisiade and Tanimbar Archipelagos with a key to the subgenus Euprepiosaurus

description: This dataset contains the digitized treatments in Plazi based on the original journal article Weijola, Valter, Kraus, Fred (2023): Two new species of monitor lizards (Squamata: Varanus) endemic to the Louisiade and Tanimbar Archipelagos with a key to the subgenus Euprepiosaurus. Journal of Natural History 57 (13 - 16): 947-975, DOI: 10.1080/00222933.2023.2218574, URL: http://dx.doi.org/10.1080/00222933.2023.2218574ABSTRACTWe describe two new species of Varanus, one each endemic to the Louisiade and Tanimbar Archipelagos in Papua New Guinea and Indonesia, respectively. The new species belong to the subgenus Euprepiosaurus and, therein, to the widely distributed and relatively species-rich Varanus indicus group. They can be distinguished from all other recognised species by scalation, colour-pattern and genetic differences. The new species from Tanimbar is most closely related to V. indicus and V. melinus, from which it can be distinguished by its dark blue/grey tongue and higher middorsal and midventral scale counts. The new species from the Louisiades can be distinguished from its phylogenetically and geographically nearest relative, V. chlorostigma, by the presence of dorsal crossbands, the mostly pink tongue mottled with grey, and higher midbody scale count. The Louisiades constitute the easternmost archipelago of Milne Bay Province in eastern Papua New Guinea, and they host a diverse herpetofauna with a high degree of endemism; Varanus louisiadensis sp. nov. increases the known number of herpetofaunal endemics in that archipelago to 60. The Tanimbar Islands are situated in the southern part of Maluku Province (Moluccas), Indonesia, and are a minor centre of vertebrate endemism; Varanus tanimbar sp. nov. increases the number of known herpetofaunal endemics there to six.KEYWORDSMelanesia; Wallacea; endemic; reptile; lizard; taxonomyhttp://www.zoobank. org/ urn:lsid:zoobank.org:pub: E06BDE2A-0B24-4CB5-B46E-6B93476CC3EB
DOI: 10.5061/dryad.sf7m0cg3k
title: Tumor control via targeting PD-L1 with chimeric antigen receptor modified NK cells

description: Failed T cell-based immunotherapies in the presence of genomic alterations
 in antigen presentations pathways may be overcome by NK cell-based
 immunotherapy. This approach may still be limited by the presence of
 immunosuppressive myeloid populations. Here we demonstrate that NK cells
 (haNKs) engineered to express a PD-L1 chimeric antigen receptor (CAR)
 haNKs killed a panel of human and murine head and neck cancer cells at low
 effector-to-target ratios in a PD-L1-dependent fashion. Treatment of
 syngeneic tumors resulted in CD8 and PD-L1-dependent tumor rejection or
 growth inhibition and a reduction in myeloid cells endogenously expressing
 high levels of PD-L1. Treatment of xenograft tumors resulted in PD-L1
 dependent tumor growth inhibition. PD-L1 CAR haNKs reduced levels of
 macrophages and other myeloid cells endogenously expressing high PD-L1 in
 peripheral blood from patients with head and neck cancer. The clinical
 study of PD-L1 CAR haNKs is warranted.
DOI: 10.5061/dryad.rr4xgxd69
title: Data from: Factors related to time of stroke onset versus time of hospital arrival: A SITS registry-based study in an Egyptian Stroke Center

description: Background: high-quality data on time of stroke onset and time of hospital
 arrival is required for proper evaluation of points of delay that might
 hinder access to medical care after the onset of stroke symptoms. Purpose:
 Based on (SITS Dataset) in Egyptian stroke patients, we aimed to explore
 factors related to time of onset versus time of hospital arrival for acute
 ischemic stroke (AIS). Material and Methods: We included 1,450 AIS
 patients from two stroke centers of Ain Shams University, Cairo, Egypt. We
 divided the day to four quarters and evaluated relationship between
 different factors and time of stroke onset and time of hospital arrival.
 The factors included: age, sex, duration from stroke onset to hospital
 arrival, type of management, type of stroke (TOAST classification),
 National Institute of Health Stroke Scale (NIHSS) on admission and
 favorable outcome modified Rankin Scale (mRS ≤2).  Results:
 Pre-hospital: highest stroke incidence was in the first and fourth
 quarters. There was no significant difference in the mean age, sex, type
 of stroke in relation to time of onset. NIHSS was significantly less in
 onset in third quarter of the day. Percentage of patients who received
 thrombolytic therapy was higher with onset in the first 2 quarters of the
 day (p=&lt;0.001). In-hospital: there was no difference in percentage
 of patients who received thrombolytic therapy nor in outcome across 4
 quarters of arrival to hospital. Conclusion: pre-hospital factors still
 need adjustment to improve percentage of thrombolysis, while in-hospital
 factors showed consistent performance.
DOI: 10.25338/b8s612
title: Generic injuries are sufficient to induce ectopic Wnt organizers in Hydra

description: During whole-body regeneration, a bisection injury can trigger two
 different types of regeneration. To understand the transcriptional
 regulation underlying this adaptive response we characterized transcript
 abundance and chromatin accessibility during oral and aboral regeneration
 in the cnidarian Hydra vulgaris. We found that the initial response to
 amputation at both wound sites is identical and includes widespread
 apoptosis and the activation of the oral-specifying Wnt signaling pathway.
 By 8 hours post-amputation, Wnt signaling became restricted to oral
 regeneration. Wnt pathway genes were also upregulated in puncture wounds
 and these wounds induced the formation of ectopic oral structures if
 pre-existing organizers were simultaneously amputated. Our work suggests
 that oral patterning is activated as part of a generic injury response in
 Hydra, and that alternative injury outcomes are dependent on signals from
 the surrounding tissue. Furthermore, Wnt signaling is likely part of a
 conserved wound response predating the split of cnidarians and
 bilaterians.
description: Please refer to the README.pdf file for usage notes.
DOI: 10.5281/zenodo.18395562
title: An unexpected snake fossil (Pythonidae, Python) from Taiwan

description: The fossil record of Taiwan has produced various major clades (e.g. mammals, turtles, crocodiles and birds), but the lepidosaur/squamate fossil remains poorly known from Taiwan. Here, we report an unexpected snake fossil, a large single trunk vertebra, from the Pleistocene of Taiwan. This fossil vertebra from the Pleistocene of Taiwan shows a combination of morphological features, indicating its taxonomic assignment to the genus Python. No extant members of the genus Python inhabit the main island of Taiwan. Our discovery of a Pleistocene Python (up to 4 m long), with recent palaeontological progress on large predators including the longirostrine crocodylians and sabre-toothed cat, highlights the presence of a palaeo-ecosystem, which greatly differs from the present and further underscores a radical faunal turnover to the modern biodiversity in Taiwan. Interestingly, the modern ecosystems of Taiwan are devoid of top predators, but the large Python from the Pleistocene of Taiwan coexisted with other top predators, such as Homotherium and Toyotamaphimeia. We hypothesise that the modern ecosystem of Taiwan may have yet to recover from the Pleistocene extinction event. Further fossil collecting with updated large-scale analyses should promise to reveal more about the faunal turnover, resulting in the emergence of modern biodiversity.
DOI: 10.5281/zenodo.18395561
title: An unexpected snake fossil (Pythonidae, Python) from Taiwan

description: The fossil record of Taiwan has produced various major clades (e.g. mammals, turtles, crocodiles and birds), but the lepidosaur/squamate fossil remains poorly known from Taiwan. Here, we report an unexpected snake fossil, a large single trunk vertebra, from the Pleistocene of Taiwan. This fossil vertebra from the Pleistocene of Taiwan shows a combination of morphological features, indicating its taxonomic assignment to the genus Python. No extant members of the genus Python inhabit the main island of Taiwan. Our discovery of a Pleistocene Python (up to 4 m long), with recent palaeontological progress on large predators including the longirostrine crocodylians and sabre-toothed cat, highlights the presence of a palaeo-ecosystem, which greatly differs from the present and further underscores a radical faunal turnover to the modern biodiversity in Taiwan. Interestingly, the modern ecosystems of Taiwan are devoid of top predators, but the large Python from the Pleistocene of Taiwan coexisted with other top predators, such as Homotherium and Toyotamaphimeia. We hypothesise that the modern ecosystem of Taiwan may have yet to recover from the Pleistocene extinction event. Further fossil collecting with updated large-scale analyses should promise to reveal more about the faunal turnover, resulting in the emergence of modern biodiversity.
DOI: 10.5061/dryad.3xsj3txd5
title: Temporary Allee effects among non-stationary recruitment dynamics in depleted gadid and flatfish populations

description: We investigated whether low-abundance recruitment dynamics can
 change in time between compensation and depensation, the latter
 implying the presence of the Allee effect. For this, we
 studied the stock-recruitment time series of 17 gadid
 and flatfish populations in the RAM Legacy Stock Assessment
 Database using a Bayesian change point model. The
 recruitment dynamics were represented with the sigmoidal
 Beverton-Holt and the Saila-Lorda stock-recruitment models, and
 the parameters of the models were allowed to shift at a priori
 unknown change points.
description: The stock-recruitment data were extracted from the RAM Legacy
 Stock Assessment Database. The data set contains the spawning stock
 biomass (SSB) and recruit time series of the studied populations.
   The S-R models were fitted to the data with the
 Bayesian online change point detection method (BOCPD), combined with
 simulation-based filtering. The data were divided into segments by
 calculating their most likely segmentation (MLS). The methods are
 described more in detail in the supplementary material of the
 article.
description: The folder RAMLegacy contains the main scripts for fitting the
 change point model to the empirical data. The folder method_validation
 contains scripts for simulating S-R data and fitting the change point
 model to the simulated time series for method validation. Consider
 parallel computing for efficiency.
DOI: 10.5061/dryad.jh9w0vt8f
title: Data from: Functional traits determine why species belong to the dark diversity in a dry grassland fragmented landscape

description: A challenge for nature conservation is to know why many species are absent
 from suitable habitats and whether they might be able to disperse and to
 establish. Here, we used 272 dry grassland patches within a fragmented
 landscape to investigate the role of local abiotic conditions and
 dispersal filtering in determining the likelihood of vascular plants to
 belong to the dark diversity (i.e. absent portion of the species pool).
 First, we quantified the species (SD), functional (FD) and phylogenetic
 (PD) diversity of both observed and dark communities. Second, we
 determined the roles of abiotic, present-day and historical landscape
 configuration variables in shaping their patterns. Third, we evaluated the
 importance of each variable in determining their species compositions.
 Environmental filtering was assessed as effects of local abiotic
 conditions and dispersal filtering as the effects of present-day and
 historical landscape configuration. Dispersal filtering was also estimated
 by comparing dispersal traits of observed and dark diversity. Finally, we
 assessed community completeness to determine how much of the species pool
 was realized within a local community. We found higher SD in the observed
 compared to the dark communities, but PD did not differ. Contrary to
 expectations, dark communities resembled higher FD compared to the
 observed communities. Species with low dispersal capacity, low competitive
 abilities and high stress-tolerance were more often absent. Observed and
 dark diversities were mostly affected by local abiotic variables. In the
 observed communities, present-day landscape configuration variables
 affected SD while historical landscape configuration variables explained
 FD and PD. In the dark communities, we found the opposite pattern.
 Completeness was affected by present-day and historical patch size. Our
 results explain why dry grassland species may belong to the dark diversity
 and highlight the importance of local abiotic and dispersal traits of the
 species to conserve dry grasslands in changing landscapes.
DOI: 10.15468/dl.en8j9n
title: Occurrence Download

description: A dataset containing 594 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Berlinia bracteosa",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 594 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002429-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4j0zpc88c
title: Intra-specific variation in plant associated herbivore communities is phylogenetically structured in Brassicaceae

description: As a result of co-evolution between plants and herbivores, related plants
 often interact with similar herbivore communities. Variation in
 plant-herbivore interactions is determined by variation in underlying
 functional traits and by ecological and stochastic processes. Hence,
 typically only a subset of possible interactions is realized on individual
 plants. We show that insect herbivore communities assembling on individual
 plants are structured by plant phylogeny among twelve species in two
 phylogenetic lineages of Brassicaceae. This community sorting to plant
 phylogeny was retained when splitting the community according to herbivore
 feeding guilds. Relative abundance of herbivores as well as the size of
 the community structured community dissimilarity among plant species.
 Importantly, the amount of intra-specific variation in realized
 plant-herbivore interactions is also phylogenetically structured. We argue
 that variability in realized interactions that is not directly structured
 by plant traits is ecologically relevant and must be considered in the
 evolution of plant defences.
description: Data originates from a common garden field-experiment, recording
 plant phenotype and herbivore communities on individual plants. Community
 development on plants was surveyed from 4-week-old plants until seed set.
 To allow the community to fully develop, insects were identified
 <i>in situ</i> to the highest taxonomic resolution possible
 (species or family level). The Ecology Letters manauscript has a detailed
 methods section that outlines data collection and methodology.
 Field observations: Raw herbivore
 abundance observations of herbivores individual plants. Observations
 present cumulative abundance over all monitoring rounds (see detailed
 methodology in the Ecology Letters manuscript).
 Phenotypic parameters: Plant height (measured from
 the ground to the top of the plant), diameter (measured as the distance
 between the two most distal leaves), length of the largest leaf, number of
 true leaves, and number of flowering branches. We present the maximum
 observed parameter values for each plant individual to represent its
 specific phenotype. Phylogeny:
 Phylogenetic dissimilarity among 12 brassicaceous plant species, based on
 ITS (see detailed methodology in the Ecology Letters
 manuscript).
description: Our Excel
 sheet contains a Read-Me file explaining the abbreviations, usage, and
 type of data collected. The Ecology Letters manauscript has a detailed
 methods section that outlines data collection and methodology. 
 We appreciate notification of data re-use. Please use the contact
 Daan.Mertens@wur. nl and/or Erik.Poelman@wur.nl
DOI: 10.5061/dryad.w6m905qmx
title: Staphylococcus aureus phenol soluble modulin aggregation kinetics

description: The infective ability of the opportunistic pathogen Staphylococcus aureus,
 recognized as the most frequent cause of biofilm-associated infections, is
 associated with biofilm mediated resistance to host immune response.
 Phenol-soluble modulins (PSM) comprise the structural scaffold of S.
 aureus biofilms through self-assembly into functional amyloids, but the
 role of individual PSMs during biofilm formation remains poorly understood
 and the molecular pathways of PSM self-assembly have yet to be identified.
 Here, we demonstrate high degree of cooperation between individual PSMs
 during functional amyloid formation. PSMα3 initiates the aggregation,
 forming unstable aggregates capable of seeding other PSMs resulting in
 stable amyloid structures. Using chemical kinetics we dissect the
 molecular mechanism of aggregation of individual PSMs showing that PSMα1,
 PSMα3 and PSMβ1 display secondary nucleation whereas PSMβ2 aggregates
 through primary nucleation and elongation. Our findings suggest that the
 various PSMs have evolved to ensure fast and efficient biofilm formation
 through cooperation between individual peptides.
description: The dataset was collected using Thioflavin T fluoresence for the
 detection of protien aggregates using a plate-reader assay.
 The dataset was processed using chemical kinetics from the
 amylofit webserver (www.amylofit.ch.cam.ac.uk).
DOI: 10.5061/dryad.r4xgxd294
title: Data from: In situ glacial survival maintains high genetic diversity of Mussaenda kwangtungensis on continental islands in subtropical China

description: Generally, island populations are predicted to have less genetic variation
 than their mainland relatives. However, there has been exceptions,
 indicating that the relationships were impacted by several factors, e.g
 historical processes. In the present study, we chose a group of
 subtropical islands located in South China as the study system, which are
 quite younger and much closer to the mainland than most of the previous
 studied island systems, to test the hypothesis that in situ glacial
 survival contributes to high levels of genetic diversity in island
 populations. We conducted a comparison of genetic variation between 12
 island and 11 nearby mainland populations of Mussaenda kwangtungensis
 using eleven nuclear microsatellite and three chloroplast markers,
 evaluated effects of the island area and distance to mainland on genetic
 diversity of island populations, and simulated the potential distribution
 over the past by ecological niche modelling, together with the genetic
 data to detect the role of islands during the glacial periods. The island
 populations displayed comparable levels of genetic diversity and
 differentiation with mainland populations, overall high levels of unique
 polymorphisms, and the greatest values of specific within-population
 genetic diversity. No significant correlation was detected between genetic
 diversity of island populations and distance to mainland, as well as area
 of islands, except that allelic richness was significantly positively
 correlated with the area of islands. Nuclear microsatellites revealed two
 main clusters, largely corresponding to islands and inland populations,
 which divergence dated to a time of island formation by ABC analysis.
 Ecological Niche Modelling predicted a highly climatic suitability on
 islands during the Last Glacial Maximum (LGM). Our results suggest that
 the islands have acted as refugia during the LGM and highlight the role of
 in situ glacial survival in maintaining high levels of genetic diversity
 of M. kwangtungensis in continental islands of subtropical China.