cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.z08kprrj1
title: IgLON5 immunoprecipitation files of binding partners in rat granullar cells of the cerebellum

description: Background: Anti-IgLON5 disease is a rare neurological disorder
 characterized by autoantibodies against IgLON5, and pathological evidence
 of neurodegeneration. IgLON5 is a cell adhesion molecule but its
 physiological function is unknown. Our aim was to investigate the IgLON5
 interactome and to determine if IgLON5 antibodies (IgLON5-abs) affect
 these protein interactions. Methods: IgLON5 interactome was investigated
 by mass spectrometry sequencing of proteins immunoprecipitated by IgLON5
 autoantibodies using cultures of rat cerebellar granular neurons (CGNs).
 Shedding of IgLON5 was explored using HEK cells transfected with human
 IgLON5 plasmid and in CGNs. Interactions of IgLON5 with identified binding
 partners and IgLON5-abs effects were confirmed by immunofluorescence in
 transfected HEK cells and rat hippocampal neurons. Results: 
 Patients’ IgLON5 antibodies co-precipitated all members of the IgLON
 family and three 3 additional surface proteins. IgLON5 predominantly
 establishes homomeric and heteromeric cis (within the cell) and trans
 (between cells)-interactions with other IgLON family members and undergoes
 spontaneous ectodomain shedding. Antibodies from patients with anti-IgLON5
 disease prevent trans-interactions in hippocampal neurons independently of
 the IgLON5 IgG subclass distribution. Conclusions: We show a potentially
 novel pathogenic mechanism of IgLON5-abs that consists in blocking IgLON5
 interactions with its binding partners. These findings extend our
 knowledge about the physiological role of IgLON5 and pave the way to
 future understanding of the pathological mechanisms of anti-IgLON5
 disease.
description: This dataset was collected by Centre de Regulació Genomica,
 Barcelona, Spain
DOI: 10.5061/dryad.7m0cfxq06
title: Disposable platform for bacterial lysis and nucleic acid amplification based on a single USB-powered printed circuit board

description: Recent advances in electronics and microfluidics have enabled several
 research groups to develop fully integrated, sample-to-result isothermal
 nucleic acid amplification test (NAAT) platforms for the point of care.
 However, high component counts and costs have limited translation of these
 platforms beyond the clinic to low-resource settings—including homes. Many
 NAATs include complex, multi-component heater electronics based on flex
 circuits or multiple printed circuit boards (PCBs) to support essential
 NAAT steps such as lysis, sample deactivation, and nucleic acid
 amplification. In contrast, current commercial assays for home use, such
 as those for pregnancy or ovulation that include electronics, typically
 have just one onboard PCB. This work describes a generalizable strategy to
 integrate all heaters and the electronics needed to control them onto a
 single low-cost, USB-powered PCB. We built a multiplexable disposable NAAT
 (“MD NAAT”) platform that applies these principles, integrating small-area
 heaters that heat small regions to near-boiling (for pathogen lysis and
 deactivation) and large-area heaters (for amplification) on the same PCB.
 We show that both classes of heaters have high intra-board and
 inter-device reproducibility despite only heating a NAAT cartridge from
 below. We validated the small-area heaters by lysing methicillin-resistant
 Staphylococcus aureus (MRSA) cells and the large-area heaters by
 performing two types of isothermal NAATs (isothermal strand displacement
 amplification (iSDA) and loop-mediated isothermal amplification (LAMP)).
 These results demonstrate the merit of integrating NAAT heaters and
 control electronics onto a single printed circuit board and are a step
 toward translating NAATs to the home.
description: EAGLE
DOI: 10.5061/dryad.6wwpzgn3d
title: Data for: Defining the relationship between phylogeny, clinical manifestation and phenotype for Trichophyton mentagrophytes/interdigitale complex; a literature review and taxonomic recommendations

description: This study looked for correlations between molecular identification,
 clinical manifestation and morphology for Trichophyton interdigitale and
 T. mentagrophytes. For this purpose, a total of 110 isolates were obtained
 from Czech patients with various clinical manifestations of
 dermatophytosis. Micro- and macromorphology and physiology were analysed,
 and the strains were characterized using multilocus sequence typing. Among
 the 12 measured/scored phenotypic features, statistically significant
 differences between species were found only in growth rates at 37°C and in
 the production of spiral hyphae but none of these features was diagnostic.
 Correlations were found between T. interdigitale and higher age of
 patients and between clinical manifestations such as tinea pedis or
 onychomychosis. The MLST approach showed that ITS genotyping of
 T. mentagrophytes isolates has limited practical benefits because of
 extensive gene flow between sublineages. Based on our results and previous
 studies, there are few taxonomic arguments for preserving both
 species' names. The species show a lack of monophyly and unique
 morphology. On the other hand, some genotypes are associated with
 predominant clinical manifestations and sources of infections, which keep
 those names alive. This practice is questionable because the use of both
 names confuses identification, leading to difficulty in comparing
 epidemiological studies. The current identification method using ITS
 genotyping is ambiguous for some isolates and is not user-friendly.
 Additionally, identification tools such as MALDI-TOF MS fail to
 distinguish these species. To avoid further confusion and simplify
 identification in practice, we recommend using the name T. mentagrophytes
 for the entire complex. When clear differentiation of populations
 corresponding to T. interdigitale and T. indotineae is possible based on
 molecular data, we recommend optionally using a variety rank: T.
 mentagrophytes var. interdigitale and T. mentagrophytes var. indotineae.
DOI: 10.5061/dryad.51c59zwcx
title: Data for: Low protease activity in B cell follicles promotes retention of intact antigens after immunization

description: The structural integrity of vaccine antigens is critical to the generation
 of protective antibody responses, but the impact of protease activity on
 vaccination in vivo is poorly understood. We characterized protease
 activity in lymph nodes and found that antigens were rapidly degraded in
 the subcapsular sinus, paracortex, and interfollicular regions, whereas
 low protease activity and antigen degradation rates were detected in the
 vicinity of follicular dendritic cells (FDCs). Correlated with these
 findings, immunization regimens designed to target antigen to FDCs led to
 germinal centers dominantly targeting intact antigen, whereas traditional
 immunizations led to much weaker responses that equally targeted the
 intact immunogen and antigen breakdown products. Thus, spatially
 compartmentalized antigen proteolysis affects humoral immunity and can be
 exploited.
description: The files are in "tif" format and can be opened with
 any image viewer.
DOI: 10.5061/dryad.bnzs7h4g6
title: Data from: Evaluating single-cell variability in proteasomal decay

description: Gene expression is a stochastic process that leads to variability in mRNA
 and protein abundances even within an isogenic population of cells grown
 in the same environment. This variation, often called
 gene-expression noise, has typically been attributed to transcriptional
 and translational processes while ignoring the contributions of protein
 decay variability across cells. Here we estimate the single-cell
 protein decay rates of two degron GFPs in \textit{Saccharomyces
 cerevisiae} using time-lapse microscopy. We find substantial
 cell-to-cell variability in the decay rates of the degron GFPs.We evaluate
 cellular features that explain the variability in the proteasomal decay
 and find that the amount of 20s catalytic beta subunit of the proteasome
 marginally explains the observed variability in the degron GFP
 half-lives. We propose alternate hypotheses that might explain
 the observed variability in the decay of the two degron GFPs.Overall, our
 study highlights the importance of studying the kinetics of the decay
 process at single-cell resolution and that decay rates vary at the
 single-cell level, and that the decay process is stochastic. A
 complex model of decay dynamics must be included when modeling stochastic
 gene expression to estimate gene expression noise.
description: The data submitted here are raw fluorescent microscopy images
 from Nikon TiE.
description: Fiji to open the raw images. Imaris suite version 9.8 (or any
 version) to open the ".ims" files. The CSV files are to be used
 with RMDs on the GitHub repo mentioned in the README file.
DOI: 10.15468/dl.45p2fh
title: Occurrence Download

description: A dataset containing 67395 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Parkinsonia aculeata"
 ]
}

 The dataset includes 67395 records from 547 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002860-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6hdr7sr55
title: Neoisoptera repeatedly colonised Madagascar after the Middle Miocene climatic optimum

description: Madagascar is home to many endemic plant and animal species owing to its
 ancient isolation from other landmasses. This unique fauna includes
 several lineages of termites, a group of insects known for their key role
 in organic matter decomposition in many terrestrial ecosystems. How and
 when termites colonised Madagascar remains unknown. In this study, we used
 601 mitochondrial genomes, 93 of which were generated from Malagasy
 samples, to infer the global historical biogeography of Neoisoptera, a
 lineage containing more than 80% of described termite species. Our results
 indicate that Neoisoptera colonised Madagascar between seven to ten times
 independently during the Miocene, between 8.4-16.6 Ma (95% HPD: 6.1-19.9
 Ma). This timing matches that of the colonization of Australia by
 Neoisoptera. Furthermore, the taxonomic composition of the Neoisopteran
 fauna of Madagascar and Australia are strikingly similar, with Madagascar
 harbouring an additional two lineages absent from Australia. Therefore,
 akin to Australia, Neoisoptera colonised Madagascar during the global
 expansion of grasslands, possibly helped by the ecological opportunities
 arising from the spread of this new biome.
DOI: 10.5061/dryad.ncjsxkt09
title: Asymmetric effects of daytime and nighttime warming on alpine treeline recruitment

description: Trees at their upper range limits are highly sensitive to climate change,
 and thus alpine treelines worldwide have changed their recruitment
 patterns in response to climate warming. However, previous studies focused
 only on daily mean temperature, neglecting the asymmetric influences of
 daytime and nighttime warming on recruitments in alpine treelines. Here,
 based on the compiled dataset of tree recruitment series from 172 alpine
 treelines across the Northern Hemisphere, we quantified and compared the
 different effects of daytime and nighttime warming on treeline recruitment
 using four indices of temperature sensitivity, and assessed the responses
 of treeline recruitment to warming-induced drought stress. Our analyses
 demonstrated that even in different environmental regions, both daytime
 and nighttime warming could significantly promote treeline recruitment,
 however, treeline recruitment was much more sensitive to nighttime warming
 than to daytime warming, which could be attributable to the presence of
 drought stress. The increasing drought stress primarily driven by daytime
 warming rather than by nighttime warming would likely constrain the
 responses of treeline recruitment to daytime warming. Our findings
 provided compelling evidence that nighttime warming rather than daytime
 warming could play a primary role in promoting the recruitment in alpine
 treelines, which was related to the daytime warming-induced drought
 stress. Thus, daytime and nighttime warming should be considered
 separately to improve future projections of global change impacts across
 alpine ecosystems.
DOI: 10.5061/dryad.n02v6wx21
title: Scalable Bayesian divergence time estimation with ratio transformations

description: Divergence time estimation is crucial to provide temporal signals for
 dating biologically important events, from species divergence to viral
 transmissions in space and time. With the advent of high-throughput
 sequencing, recent Bayesian phylogenetic studies have analyzed hundreds to
 thousands of sequences. Such large-scale analyses challenge
 divergence time reconstruction by requiring inference on
 highly-correlated internal node heights that often become
 computationally infeasible. To overcome this limitation, we
 explore a ratio transformation that maps the original N - 1
 internal node heights into a space of one height parameter and N
 - 2 ratio parameters. To make the analyses scalable, we develop a
 collection of linear-time algorithms to compute the gradient and
 Jacobian-associated terms of the log-likelihood with respect to these
 ratios. We then apply Hamiltonian Monte Carlo sampling with the ratio
 transform in a Bayesian framework to learn the divergence times in four
 pathogenic viruses (West Nile virus, rabies virus, Lassa virus
 and Ebola virus) and the coralline red algae.  Our
 method both resolves a mixing issue in the West Nile virus example and
 improves  inference efficiency by at least 5-fold for
 the Lassa and rabies virus examples as well  as for the
 algae example. Our method now also makes it computationally feasible
 to  incorporate mixed-effects molecular clock models for
 the Ebola virus example, confirms  the findings from the
 original study and reveals clearer multimodal distributions of
 the  divergence times of some clades of interest.
DOI: 10.5061/dryad.sn02v6x86
title: Directly dating Plio-Pleistocene climate change in the terrestrial record

description: This is the Supporting Information for Dröllner et al. "Directly
 dating Plio-Pleistocene climate change in the terrestrial record"
 published in Geophysical Research Letters. The data comes from a
 ferruginous induration in the arid landscapes of the Nullarbor Plain in
 southern Australia (30° 54' 33.84'' S, 132° 13'
 5.88'' E). The data provides constraints on the timing of
 Plio-Pleistocene aridification in the continental realm and supports the
 use of ferruginous indurations as targets to obtain absolute ages on
 landscape evolution. The dataset includes chemical-mineralogical results,
 which suggest that the formation of ferruginous indurations was linked
 with a decline of the groundwater table. (U-Th)/He geochronology of
 goethite from ferruginous indurations provides age constraints that link
 the textural and chemical-mineralogical observations to a rapid climatic
 shift from humid Late Pliocene to arid Early Pleistocene conditions.
 Specifically, this Supporting Information includes a pdf file (available
 through Zenodo; https://doi.org/10.5281/zenodo.7739575) with detailed
 analytical methods for X-ray powder diffraction (XRD, Text S1),
 energy-dispersive spectroscopy (Text S2), Raman spectroscopy (Text S3),
 and (U-Th)/He geochronology (Text S4). This pdf file also includes
 Supporting Figures S1 (sample material, and fragments used for dating) and
 S2 (XRD spectra), as well as Supporting Tables S1 (XRD bulk mineralogy),
 S2 ((U-Th)/He data), S3 (XRD instrument parameters), and the captions for
 Table S4 (Raman data) and Table S5 (XRD data). The latter two datasets are
 provided as separate files available through Dryad (this data).
description: Methods are detailed in the pdf file available through Zenodo
 (https://doi.org/10.5281/zenodo.7739575).
DOI: 10.6078/d1wm6t
title: Supplementary data for: Hummingbird ingestion of low-concentration ethanol within artificial nectar

description: Both frugivores and nectarivores are potentially exposed to dietary
 ethanol produced by fermentative yeasts which metabolize sugars. Some
 nectarivorous mammals exhibit preference for low-concentration ethanol
 solutions compared to controls of comparable caloric content, but
 behavioral responses to ethanol by nectar-feeding birds are unknown. We
 investigated dietary preference by Anna's Hummingbirds (Calypte anna)
 for ethanol-enhanced sucrose solutions. Via binary-choice experiments,
 three male hummingbirds were exposed to sucrose solutions containing 0%,
 1%, or 2% ethanol; rates of volitional nectar consumption were measured
 over a 3-hour interval. Hummingbirds did not discriminate between 0% and
 1% ethanol solutions but exhibited significantly reduced rates of
 consumption of a 2% ethanol solution. Opportunistic measurements of
 ethanol concentrations within hummingbird feeders registered values
 peaking at about 0.05%. Ethanol at low concentrations (i.e., around 1%) is
 not aversive to Anna's Hummingbirds and may be characteristic of both
 natural and anthropogenic nectars from which they feed. Given high daily
 amounts of nectar consumption by hummingbirds, chronic physiological
 exposure to ethanol may thus be substantial, although naturally occurring
 concentrations within floral nectar are unknown.
description: See the original publication in Proceedings of the Royal Society
 B titled "Hummingbird Ingestion of Low-concentration Ethanol within
 Artificial Nectar", to which these files are supplementary.
description: Three (3) data tables provided as separate sheets in spreadsheet
 format (.xlsx).
DOI: 10.5061/dryad.x3ffbg7px
title: Female reproductive fluids ‘rescue’ sperm from phenotypic ageing in an external fertilizer

description: Female reproductive fluids (FRF) serve key reproductive functions in
 sexually reproducing animals, including modifying the way sperm swim and
 detect eggs, and influencing sperm lifespan. Despite the central role of
 FRF during fertilisation, we know surprisingly little about sperm-FRF
 interactions under different environmental conditions. Theory suggests
 that, in external fertilisers, FRF may ‘rescue’ sperm from ageing effects
 as they search to fertilise eggs. Here, we test the interaction between
 these two fundamental properties of the fertilisation environment,
 ejaculate age (i.e., time since ejaculation) and FRF, on a range of
 functional sperm phenotypes in a broadcast spawning mussel, Mytilus
 galloprovincialis. We found that the effects of ejaculate age on
 multivariate sperm motility traits and total sperm motility were altered
 by FRF, and that longer-lived sperm exhibit stronger, likely more
 advantageous, responses to FRF after periods of ageing. We also detected
 significant among-male variation in the relationship between sperm
 motility traits and ejaculate age; notably, these patterns were only
 revealed when sperm encountered FRF. Collectively these findings
 underscore the importance of considering female reproductive physiology
 when interpreting ageing-related declines in sperm motility, as doing so
 may expose important sources of variation in sperm phenotypic plasticity
 among males and environments.
DOI: 10.5061/dryad.zgmsbcch3
title: Novel finding of Paulownia fortunei endophytic rhizobia in China

description: Previous research has mainly focused on breeding, timber supply, and
 physiological-biochemical characteristics of Paulownia fortunei. However,
 there has been limited attention given to its endophytic rhizobia and its
 potential benefits for plant growth due to a lack of knowledge about the
 existence of root nodules. In this study, we extracted 9
 bacterial strains from the root nodules after occasionally discovering the
 nodular-like structure in uncultivated 3-year P. fortunei roots and then
 sequenced the 16S rDNA and nifA sequencing to conduct the bacterial strain
 identifications. We then determined the carbon use capability and
 nitrogenase activity of the bacterial strains. The result of 16S rDNA
 sequencing indicated that the endophytic rhizobia belongs to the genus
 Agrobacterium, Rhizobium, Herbaspirillum, and Burkholderia. The results of
 nifA sequencing indicated that the nifA gene was sequenced in strain PG-3,
 PG-5, PG-6, PG-7, PG-8, rather than in strain PG-1, PG-2, and PG-4.
 Besides, the nitrogenase activity of strain PG-9 was significantly higher
 than other bacterial strains. RDA results indicated that
 fructose, glucose, and sucrose were significantly related to the plant
 height, diameter, and biomass rather than other carbon sources and
 nitrogenase activity. Our research revealed that the majority of bacterial
 strains isolated from P. fortunei exhibited a broad carbon utilization
 pathway and have the potential to promote plant growth after
 re-Inoculation. This study aims to investigate the phylogeny of endophytic
 rhizobia in P. fortunei, and expand the range of non-legume hosts studied
 for future research on biological N fixation.
description: We used a vernier caliper,
 band tape, and length rod to measure the plant height, stem diameter and
 dry biomass three months after planting to investigate the effects of
 bacterial strain applications on <em>Paulownia</em> seedling growth. The nitrogenase activity of 9
 endophytic rhizobia strains was measured colorimetrically at 450 nm (N =
 3) using the nitrogenase ELISA kit (Jining, Tongwei, Shanghai, China)
 according to the manufacturer’s instructions.
description: # **Novel finding of *Paulownia fortunei* endophytic rhizobia in China**
 ## Description of the data
 and file structure The raw data contains plant diameter (unit: mm), height
 (unit: cm), and dry biomass (unit: g) after bacterial applications, as
 well as nitrogenase activity (unit: μL/g/h) of nine bacterial strains.
 Someone who uses the data to do further analysis will need to take the
 fact that the bacterial strains are isolated from Paulownia fortunei into
 consideration. ## Sharing/Access information The raw data are archived
 from our research.