cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7272/q6z60m99
title: Autoantigen profiling reveals a shared post-COVID signature in fully recovered and long COVID patients

description: Some individuals do not return to baseline health following SARS-CoV-2
 infection, leading to a condition known as Long COVID. The underlying
 pathophysiology of Long COVID remains unknown. Given that autoantibodies
 have been found to play a role in severity of COVID infection and certain
 other post-COVID sequelae, their potential role in Long COVID is important
 to investigate. Here we apply a well-established, unbiased, proteome-wide
 autoantibody detection technology (PhIP-Seq) to a robustly phenotyped
 cohort of 121 individuals with Long COVID, 64 individuals with prior
 COVID-19 who reported full recovery, and 57 pre-COVID controls. While a
 distinct autoreactive signature was detected which separates individuals
 with prior COVID infection from those never exposed to COVID, we did not
 detect patterns of autoreactivity that separate individuals with Long
 COVID relative to individuals fully recovered from SARS-CoV-2 infection.
 These data suggest that there are robust alterations in autoreactive
 antibody profiles due to infection; however, no association between
 autoreactive antibodies and Long COVID was apparent by this assay.
DOI: 10.5061/dryad.ns1rn8pz4
title: Colonial coral resilience by decreasing size: reaction to increased detrital influx during onset of the late Palaeozoic Ice Age

description: Modern coral reefs and associated biodiversity are severely threatened by
 increasing terrestrial runoff. Similar scenarios could be suspected for
 geological times, but reef coral resilience is still an enigma. In late
 Visean-Serpukhovian (Mississippian foraminiferal zones/MFZ 14-16) times, a
 major glaciation phase of the late Palaeozoic Ice Age (LPIA) associated
 with enhanced terrestrial weathering and runoff coincides with a
 biodiversity crisis and coral reef decline. In this study, the impact of
 enhanced terrestrial runoff is tested on size variations of colonial
 corals Aulina rotiformis and Lithostrotion decipiens along a gradient of
 contemporaneous (Serpukhovian) open marine carbonate to nearshore
 siliciclastic facies in South China. Along this gradient, their sizes
 decrease from carbonate, through intermediate carbonate-siliciclastic, to
 siliciclastic facies. This is consistent with increasing abundance of
 terrestrial materials of high silicon, aluminium, and phosphorus values.
 On a larger million-year-long interval (MFZ14-16) and for several
 palaeocontinents, size data of Lithostrotion decipiens and Siphonodendron
 pauciradiale show a distinct decline in late Visean, when enhanced
 terrestrial weathering occurred commonly with palaeosols developed during
 regression. This suggests that terrestrial sediment and nutrient input may
 have mainly controlled phenotypic plasticity in Mississippian reef corals,
 with a decrease in size as a component of resilience across the LPIA
 onset.
DOI: 10.5061/dryad.v41ns1s1v
title: Toward understanding insect species introduction and establishment: a community-level barcoding approach using island beetles

description: Since Darwin put forward his opposing hypotheses to explain the successful
 establishment of species in areas outside their native ranges, the
 preadaptation and competition-relatedness hypotheses, known as Darwin’s
 naturalisation conundrum, numerous studies have sought to understand the
 relative importance of each. Here we take advantage of well-characterised
 beetle communities across laurel forests of the Canary Islands for a first
 evaluation of the relative support for Darwin’s two hypotheses within
 arthropods. We generated a mitogenome backbone tree comprising nearly half
 of the beetle genera recorded within the Canary Islands for the
 phylogenetic placement of native and introduced species sampled in laurel
 forests, using cytochrome c oxidase I (COI) sequences. For comparative
 purposes, we also assembled and phylogenetically placed a data set of COI
 sequences for introduced beetle species that were not sampled within
 laurel forests. Our results suggest a stronger effect of species
 preadaptation over resource competition, while also revealing an
 underappreciated shortfall in arthropod biodiversity data – knowledge of
 endemic species. We name this the Humboldtean shortfall, and suggest that
 similar studies using arthropods should incorporate DNA barcode sequencing
 to mitigate this problem.
description: <em><strong>Coleoptera sampling by active and passive
 methods</strong></em> Extraction and
 amplification of DNA using Jerry-Spat (COI-3P) and folmer (COI-5P) primers
 to obtain COI sequences of each species sampled in the laurel forest.
 Completion of the species dataset with GenBank and/or BOLD Systems
 sequences of records of species introduced to the Canary Islands but not
 sampled by us in the laurel forest. Generation of
 mitogenomes using the TruSeq Nano DNA kit and Illumina sequencing.
 Mitogenomes assembled with IDBA, celera, ray, and SPAdes methods. 
 Mitogenome species list completed with mitogenomes available in
 GenBank. <em><strong>Generation of the
 Mitogenome backbone tree using
 Phylobayes</strong></em> Phylogenetic
 placement of COI sequences into the mitogenome backbone tree using CIPRES
 Science Gateway.
DOI: 10.5061/dryad.18931zd2m
title: Dementia mortality rates at the provincial level in Italy from 2012-2019 in the form of Standardized Mortality Ratios (SMR)

description: Dementia is becoming increasingly prevalent in the global population and
 has been designated as a worldwide public health priority by the World
 Health Organization. In Italy, it is projected that by 2051, there will be
 280 elderly individuals for every 100 young individuals, resulting in a
 rise in all age-related chronic diseases, including dementia. Presently,
 the estimated number of individuals suffering from dementia is over 1
 million, predominantly with Alzheimer's disease and Parkinson's
 disease. Comprehensive investigations into the causes of dementia pose
 challenges due to the intricate nature of these conditions and their
 prolonged course. This database presents mortality rates for AD and PD at
 the provincial level in Italy over an 8-year period (2012-2019) in the
 form of Standardized Mortality Ratios (SMR). Access to long-term,
 spatially detailed, and easily accessible data could promote both health
 monitoring and the exploration of new treatments, drugs, and innovative
 methodologies for early dementia diagnosis.
description: Updated version 11 July 2023 has updated variable names, but data
 has not changed.
DOI: 10.15468/dl.ju6q7j
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pteronotus pristinus"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003489-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.05qfttf7g
title: Data from: Immune challenge reduces daily activity period in free-living birds for three weeks

description: Non-lethal infections are common in free-living animals and the associated
 sickness behaviours can impact crucial life-history trade-offs. However,
 little is known about the duration and extent of such sickness behaviours
 in free-living animals, and consequently how this affects life-history
 decisions. Here, free-living Eurasian blackbirds Turdus merula were
 immune-challenged with lipopolysaccharide (LPS) to mimic a bacterial
 infection, and their behaviour was monitored for up to 48 days using
 accelerometers. As expected, immune-challenged birds were less active than
 controls within the first 24 hours. Unexpectedly, this reduced activity
 remained detectable for 20 days, before both groups returned to similar
 activity levels. Furthermore, activity was positively correlated with a
 pre-experimental index of complement activity, but only in
 immune-challenged birds, suggesting that sickness behaviors are modulated
 by constitutive immune function. Differences in daily activity levels
 stemmed from immune-challenged birds resting earlier at dusk than control
 birds, while activity levels between groups were similar during core
 daytime hours. Overall, activity was reduced by 19% in immune-challenged
 birds and they were on average almost 1 hour less active per day for 20
 days. This unexpected longevity in sickness behaviour may have severe
 implications during energy-intense annual-cycle stages (e.g., breeding,
 migration, winter). Thus, our data help to understand the consequences of
 non-lethal infections on free-living animals.
description: Version 1 has the unit associated with the variable
 'handling' as hours, but it is in minutes. Version 2 is updated
 correctly.
DOI: 10.5061/dryad.zpc866td0
title: Data for: Human endogenous oxytocin and its neural correlates

description: Both oxytocin (OT) and touch are key mediators of social attachment. In
 rodents, tactile stimulation elicits endogenous release of OT, potentially
 facilitating attachment and other forms of prosocial behavior, yet the
 relationship between endogenous OT and neural modulation remains
 unexplored in humans. Using serial sampling of plasma hormone levels
 during functional neuroimaging across two successive social interactions,
 we show that contextual circumstances of social touch influence not only
 current hormonal and brain responses but also later responses. Namely,
 touch from a male to his female romantic partner enhanced her subsequent
 OT release for touch from an unfamiliar stranger, yet females’ OT
 responses to partner touch were dampened following stranger touch.
 Hypothalamus and dorsal raphe activation reflected plasma OT changes
 during the initial social interaction. In the subsequent interaction,
 precuneus and parietal-temporal cortex pathways tracked time- and
 context-dependent variables in an OT-dependent manner. This OT-dependent
 cortical modulation included a region of medial prefrontal cortex that
 also covaried with plasma cortisol, suggesting an influence on stress
 responses. These findings demonstrate that modulation between hormones and
 the brain during human social interactions can flexibly adapt to features
 of social context over time.
description: Plasma samples for OT analysis
 were extracted using acetonitrile precipitation (Merck Millipore: Human
 Neuropeptide Magnetic Bead Panel 96-Well Plate Assay Cat. # HNPMAG-35K)
 and OT concentrations were then determined using the Oxytocin ELISA kit
 (Enzo Life Sciences; sensitivity &gt; 15.0 pg/ml, intra-assay
 precision 10.2-13.3 % CV, inter-assay precision 11.8–20.9 %
 CV). Plasma cortisol levels were determined using the
 Cortisol Parameter Assay Kit according to the manufacturer’s
 recommendations (R&D Systems, Minneapolis, Minnesota, USA)
 (sensitivity 0.071 ng/mL, precision 10.4%). Cortisol analysis serum
 samples were diluted 60 times preceding analysis. Pretreatment steps of
 the serum samples resulted in a dilution factor of three and the
 pretreated serum samples required an additional 20-fold dilution in
 Calibrator Diluent RD5-43. For both the OT and cortisol analyses, standards
 and controls were implemented according to manufacturer recommendations.
 Washing procedures were performed using a Wellwash™ Microplate Washer
 (ThermoFisher Scientific, Waltham, Massachusetts, USA) and the absorbance
 was read using a Multiskan™ FC Microplate Photometer (ThermoFisher
 Scientific, Waltham, Massachusetts, USA). The color development of the
 samples was read for OT at 405 nm (background correction at 571 nm) and
 for cortisol at 450 nm (background correction at 571 nm). SkanIt™ Software
 was used for creation of standard curves, curve fitting and calculation of
 concentrations (ThermoFisher Scientific, Waltham, Massachusetts,
 USA).
DOI: 10.4231/z1d3-d689
title: Data for unwrapping a dodecaboranes’ B12 core: A structure, electronic property, and chemical reactivity study over the holistic series of [B12In]– (n = 11–1)

description: &lt;p&gt;Successively stripping the exohedral substituents from the stable &lt;i&gt;closo&lt;/i&gt;-dodecaborate anion [B&lt;sub&gt;12&lt;/sub&gt;I&lt;sub&gt;12&lt;/sub&gt;]&lt;sup&gt;2&ndash;&lt;/sup&gt; results in structural transformations of the icosahedral B&lt;sub&gt;12&lt;/sub&gt;&lt;sup&gt; &lt;/sup&gt;into a (quasi-)planar unsubstituted B&lt;sub&gt;12&lt;/sub&gt;&lt;sup&gt;0/&ndash;&lt;/sup&gt; unit. Previous studies have finally pinpointed the first ions with an open B&lt;sub&gt;12&lt;/sub&gt; unit to [B&lt;sub&gt;12&lt;/sub&gt;I&lt;sub&gt;7&lt;/sub&gt;]&lt;sup&gt;&ndash;&lt;/sup&gt;, but further transitions in geometry, electronic structure and chemical reactivity across the whole range of fragments [B&lt;sub&gt;12&lt;/sub&gt;I&lt;sub&gt;n&lt;/sub&gt;]&lt;sup&gt;&ndash;&lt;/sup&gt; (n = 11&ndash;1) remained elusive. Herein, we report a systematic investigation to explore the chemical properties of these intermediate structures using negative ion photoelectron spectroscopy (NIPES), ion mobility spectrometry (IMS), ion-molecule reactions, and quantum chemical calculations. [B&lt;sub&gt;12&lt;/sub&gt;I&lt;sub&gt;n&lt;/sub&gt;]&lt;sup&gt;&ndash;&lt;/sup&gt; ions can be categorized into three groups: (1) very reactive fragments with intact (quasi-)icosahedral B&lt;sub&gt;12&lt;/sub&gt;-cages (n = 11&ndash;8), (2) less reactive open structures (n = 7&ndash;4), and (3) almost unreactive (quasi-)planar structures (n = 3&ndash;1). Preparative mass spectrometry shows that the unsaturated B&lt;sub&gt;12&lt;/sub&gt; core of category (2) ions tends to form smaller fully substituted &lt;i&gt;closo&lt;/i&gt;-borate anions [B&lt;sub&gt;m&lt;/sub&gt;X&lt;sub&gt;m&lt;/sub&gt;]&lt;sup&gt;2&ndash;&lt;/sup&gt; (m=6-11 with X=I, H, OH) on surfaces. In contrast, category (3) ions fully decay, and no ions were found on surfaces. This research provides fundamental insights into physical and chemical properties of B&lt;sub&gt;12&lt;/sub&gt; units depending on their substitution level and paves the way for the rational design of boron-rich compounds using unconventional [B&lt;sub&gt;12&lt;/sub&gt;I&lt;sub&gt;n&lt;/sub&gt;]&lt;sup&gt;&ndash;&lt;/sup&gt; building blocks.&lt;/p&gt;

&lt;p&gt;The raw data was collected on a Thermo linear quadrupole ion trap mass spectrometer and the files are named in the following order: mode of ionization, ionization source, name of the neutral reagent, targeted ion of interest and the isolation steps. &lt;/p&gt;
description: This research provides fundamental insights into physical and chemical properties of B12 units depending on their substitution level and paves the way for the rational design of boron-rich compounds using unconventional [B12In]– building blocks.
DOI: 10.15468/dl.zp9p3f
title: Occurrence Download

description: A dataset containing 2752 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Notocrypta curvifascia"
 ]
}

 The dataset includes 2752 records from 71 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003487-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0zpc8672t
title: Raw microscopy data of split-GFP and immunofluorescence experiments

description: Mitochondria critically rely on protein import and its tight regulation.
 Here, we found that the complex I assembly factor NDUFAF8 follows a
 two-step import pathway linking IMS and matrix import systems. A weak
 targeting sequence drives TIM23-dependent NDUFAF8 matrix import, and en
 route allows exposure to the IMS disulphide relay which oxidizes NDUFAF8.
 Import is closely surveyed by proteases: YME1L prevents accumulation of
 excess NDUFAF8 in the IMS, while CLPP degrades reduced NDUFAF8 in the
 matrix. Therefore, NDUFAF8 can only fulfil its function in complex I
 biogenesis if both oxidation in the IMS and subsequent matrix import work
 efficiently. We propose that the two-step import pathway for NDUFAF8
 allows to integrate the activity of matrix complex I biogenesis pathways
 with the activity of the mitochondrial disulphide relay system in the IMS.
 Such coordination might not be limited to NDUFAF8 as we identified further
 proteins that can follow such a two-step import pathway. The raw
 microscopy data provided in this dataset were obtained to visualize the
 localization of NDUFAF8 and further proteins following a two-step import
 pathway.
description: For the image acquisition the
 microscope LSM 980 with Airyscan 2 and multiplex from Carl Zeiss
 Microscopy was used with a Plan-Apochromat 63x/1,4 Oil DIC objective and
 the GaAsP-PMT, Multi-Alkali-PMT detector. The cells were imaged at room
 temperature with oil as imaging medium.The following fluorochromes were
 used: GFP, Mitotracker CMXRos and Alexa Fluor488. Images were displayed using the acquisition
 software ZEN 3.3. and were processed using the software
 OMERO.insight. <br>
DOI: 10.5061/dryad.5x69p8d82
title: Micro-evolutionary response of spring migration timing in a wild seabird

description: In the context of rapid climate change, phenological advance is a key
 adaptation for which evidence is accumulating across taxa. Among
 vertebrates, phenotypic plasticity is known to underlie most of this
 phenological change, while evidence for micro-evolution is very limited
 and challenging to obtain. In this study, we quantified phenotypic and
 genetic trends in timing of spring migration using 8032 dates of arrival
 at the breeding grounds obtained from observations on 1715 individual
 common terns (Sterna hirundo) monitored across 27 years, and tested
 whether these trends were consistent with predictions of a
 micro-evolutionary response to selection. We observed a strong phenotypic
 advance of 9.3 days in arrival date, of which c. 5% was accounted for by
 an advance in breeding values. The Breeder’s equation and Robertson’s
 Secondary Theorem of Selection predicted qualitatively similar
 evolutionary responses to selection, and these theoretical predictions
 were largely consistent with our estimated genetic pattern. Overall, our
 study provides rare evidence for micro-evolution underlying (part of) an
 adaptive response to climate change in the wild and illustrates how a
 combination of adaptive micro-evolution and phenotypic plasticity
 facilitated a shift towards earlier spring migration in this free-living
 population of common terns.
description: Data used for models presented in:
 Micro-evolutionary response of spring migration timing in a wild
 seabird by Moiron M, Teplitsky C, Haest B, Charmantier A†, Bouwhuis S†  (†
 = shared last authors) published in Evolution Letters.
 for information regarding the analyses, please
 contact mariamoironc@gmail.com for information
 regarding the data, please contact
 sandra.bouwhuis@ifv-vogelwarte.de if you'd like
 to use the data, please also contact
 sandra.bouwhuis@ifv-vogelwarte.de These
 data are part of those collected in an ongoing individual-based
 longitudinal population study additional data are likely to be available,
 and we are often very happy to collaborate provided that none of our own
 staff or students is working on a conflicting project.
DOI: 10.5066/p1mtwgsv
title: Pathology of lesions in corals from the US Virgin Islands data release

description: Stony coral tissue loss disease (SCTLD) was first documented in Florida in 2014 and has since spread through the Caribbean causing unprecedented mortality in over 20 species of corals. The cause of SCTLD is unknown, but bacteria are suspected based on regression of gross lesions in some corals treated with antibiotics. Limited pathology studies on SCTLD exist, but it is likely that ‘SCTLD’ is a general term encompassing tissue loss disease of unexplained origin. Here, we examined pathology of lesions in corals from the USVI where SCTLD has recently emerged. The typical histologic lesion of SCTLD in Florida corals was lytic necrosis comprising vacuolation and necrosis of mucus cells with erosion of mesoglea and misshapen endosymbionts with variably sized intracytoplasmic granules and common occurrence of filamentous viral-like particles in endosymbionts visible on electron microscopy (EM). In contrast, USVI corals had mainly mucus cell lytic hypertrophy and necrosis with no involvement of mesoglea, endosymbiont pathology at the light microscopy level was less evident, and VLP were rarely seen on EM. We suspect SCTLD is likely more complex with multiple presentations and potential etiologies depending on geographic region. Further pathological studies from other regions might help refine the case definition of SCTLD.
DOI: 10.5061/dryad.d2547d86h
title: The Cauchy Process on phylogenies: a tractable model for pulsed evolution

description: Phylogenetic comparative methods use random processes, such as the
 Brownian Motion, to model the evolution of continuous traits on
 phylogenetic trees. Growing evidence for non-gradual evolution motivated
 the development of complex models, often based on Lévy processes. However,
 their statistical inference is computationally intensive and currently
 relies on approximations, high dimensional sampling, or numerical
 integration. We consider here the Cauchy Process (CP), a particular
 pure-jump Lévy process in which the trait increment along each branch
 follows a centered Cauchy distribution with a dispersion proportional to
 its length. In this work, we derive an exact algorithm to compute both the
 joint probability density of the tip trait values of a phylogeny under a
 CP and the ancestral trait values and branch increments posterior
 densities in quadratic time. A simulation study shows that the CP
 generates patterns in comparative data that are distinct from any Gaussian
 process and that Restricted Maximum Likelihood (REML) parameter estimates
 and root trait reconstruction are unbiased and accurate for trees with 200
 tips or less. The CP has only two parameters but is rich enough to capture
 complex pulsed evolution. It can reconstruct posterior ancestral trait
 distributions that are multimodal, reflecting the uncertainty associated
 with the inference of the evolutionary history of a trait from extant taxa
 only. Applied to empirical datasets taken from the Evolutionary Ecology
 and Virology literature, the CP suggests nuanced scenarios for the body
 size evolution of Greater Antilles Lizards and for the geographical spread
 of the West Nile Virus epidemics in North America, both consistent with
 previous studies using more complex models. The method is efficiently
 implemented in C with an R interface in package cauphy, which is open
 source and freely available online.
DOI: 10.5061/dryad.d7wm37q5k
title: Threatened and endangered bird species and critical habitats in US cities

description: Cities have classically been viewed as biologically impoverished,
 homogenized, and simplified systems that harbor low value for
 biodiversity. However, recent work has demonstrated that cities are
 critical ecological systems that provide important services to humanity
 and biodiversity. Cities can play vital roles in conserving biodiversity
 as well as habitats, providing system stability, and offering direct
 opportunities for people to engage with nature. In a rapidly changing
 world with biodiversity loss at an all-time high, cities have the
 potential to act as sanctuaries for biodiversity conservation. Here, we
 propose a “cities as sanctuaries” concept, which demonstrates the
 importance of cities for ecology and conservation, and provide the
 groundwork for advancing this novel field of study.