cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sj3tx9617
title: Genetic affinities and biogeography of putative Levantine-endemic seaweed Treptacantha rayssiae (Ramon) M.Mulas, J.Neiva & A.Israel, comb. nov. (Phaeophyceae)

description: Cystoseira sensu lato C.Agardh (Ochrophyta) forests are important
 habitat formers in the Mediterranean Sea, but they have mostly been
 studied in the western basin where many species are under decline due to
 human pressures. In the eastern basin, where fewer species occur,
 Cystoseira rayssiae Ramon was described in the year 2000 as an
 endemic species, based on morphological characteristics from herbaria
 samples collected on the Israeli coast. No further investigations have
 been conducted on this peculiar species since, but recently it has been
 recorded in contiguous Lebanon and outside the Mediterranean. Our work was
 aimed at confirming the taxonomic validity and endemic nature of this
 species, including its position among recently split Cystoseira sensu
 stricto, Carpodesmia Greville and Treptacantha Kützing
 genera, by sequencing the mitochondrial COI gene and by examining
 morphological characterics using samples from three different sites in
 northern Israel. Nothwithstanding considerable morphological plasticity,
 molecular analyses revealed a single unique COI sequence. Phylogenetic
 analyses show that Cystoseira rayssiae belongs to the resurrected
 genus Treptacantha and hence, the new combination
 Treptacantha rayssiae (Ramon) M.Mulas, J.Neiva & A.Israel, comb.
 nov. is proposed. Unique sequences and a restricted range support its
 Levantine-endemic status. Intriguing extra-Mediterranean reports from the
 Red Sea and the Persian Gulf are probably misidentifications rather than
 reflecting a disjunct distribution or recent invasion.  *MM and
 JN contributed equally to this work.
DOI: 10.5061/dryad.0vt4b8gtp
title: Data from: Social context alters spatial memory performance in free-living male prairie voles

description: Spatial memory is crucial for mating success because it enables males to
 locate potential mates and potential competitors in space. Intraspecific
 competition and its varying intensity under certain conditions are
 potentially important for shaping spatial memory. For example, spatial
 memory could enable males to know where competitors are (contest
 competition), it could help males find mating partners (scramble
 competition), or both. We manipulated the intensity of intraspecific
 competition in two distinct contexts by altering the operational sex ratio
 of prairie voles (Microtus ochrogaster) living in outdoor enclosures by
 creating male- and female-biased sex ratios. After living freely under
 these contexts for four weeks, we compared males’ performance in a
 laboratory spatial memory test. Males in the male-biased context
 demonstrated better spatial memory performance than males in the
 female-biased context. Notably, these data show that in spite of
 experiencing equally complexspatialcontexts (i.e., natural outdoor
 enclosures), it was the social context that influenced
 spatial cognition, and it did so in a manner consistent with the
 hypothesis that spatial memory is particularly relevant for male-male
 interactions. Attached are the supporting data for this project.
DOI: 10.5061/dryad.t1g1jwsxv
title: Data from: No biotic homogenisation across decades but consistent effects of landscape position and pH on macrophyte communities in boreal lakes

description: It has been predicted that spatial beta diversity shows a decreasing trend
 in the Anthropocene due to increasing human impact, causing biotic
 homogenisation. We aimed to discover if vascular aquatic macrophyte
 communities show different spatial patterns in beta diversity in relation
 to land use and environmental characteristics in different decades from
 1940s to 2010s. We aimed to discover if spatial structures differ between
 species-, phylogeny- and functional-based beta diversity. We used
 presence-absence data of aquatic macrophytes from five decades from small
 boreal lakes. We utilized generalised dissimilarity modelling to analyse
 spatial patterns in beta diversity in relation to environmental gradients.
 We found that lake elevation and pH were the most important variables in
 each decade, while land use was not particularly important in shaping beta
 diversity patterns. We did not find signs of a decreasing trend in spatial
 beta diversity in our study area during the past 70 years. We did not find
 signs of either biotic homogenisation or biotic differentiation
 (taxonomic, phylogenetic or functional). Vascular aquatic macrophyte
 communities showed only slightly different beta diversity patterns in
 relation to human impact across decades. The patterns of different facets
 of beta diversity diverged only slightly from each other. Lake position in
 the landscape, reflecting both natural connectivity and lake
 characteristics, explained the patterns found in beta diversity, probably
 because our study area has faced only modest changes in land use from
 1940s to 2010s when compared globally. Our study highlights the fact that
 biotic homogenisation is not an unambiguous process acting similarly at
 all spatial and temporal scales or in different environments and different
 organism groups.
description: Macrophyte species and environmental data from the 1940s to the
 2010s from boreal lakes. More detailed description of the data, macrophyte
 sampling and environmental variables can be found from the Lindholm et al.
 2019, doi:10.1111/ecog.04757. This data consists of two
 csv-files: Lindholm_et_al_2019_Ecography_Macrophytes_1940_2010.csv and
 Lindholm_et_al_2019_Ecography_Environmental_variables_1940_2010.csv. More information about the data files in Lindholm_et_al_2019_readme.txt-file.
DOI: 10.5061/dryad.3bk3j9kdn
title: Data from: Redirection of ambient light improves predator detection in a diurnal fish

description: Cases where animals use controlled illumination to improve vision are rare
 and thus far limited to chemiluminescence, which only functions in
 darkness. This constraint was recently relaxed by studies on Tripterygion
 delaisi, a small triplefin that redirects sunlight instead. By reflecting
 light sideways with its iris, it has been suggested to induce and detect
 eyeshine in nearby microprey. Here, we test whether "diurnal active
 photolocation" also improves T. delaisi's ability to detect a
 cryptobenthic sit-and-wait predator Scorpaena porcus, a scorpionfish with
 strong daytime retroreflective eyeshine. Three independent experiments
 revealed that triplefins in which light redirection was artificially
 suppressed approached scorpionfish significantly closer than two control
 treatments before moving away to a safer distance. Visual modelling
 confirmed that ocular light redirection by a triplefin is sufficiently
 strong to generate a luminance increase in scorpionfish eyeshine that can
 be perceived by the triplefin over 6-8 cm under average conditions. These
 distances coincide well with the closest approaches observed. We conclude
 that light redirection by small, diurnal fish significantly contributes to
 their ability to visually detect cryptic predators, strongly widening the
 conditions under which active sensing with light is feasible. We discuss
 the consequences for fish eye evolution.
DOI: 10.5061/dryad.jh9w0vt6k
title: Polygenic and major-locus contributions to sexual maturation timing in Atlantic salmon

description: Sexual maturation timing is a life-history trait central to the balance
 between mortality and reproduction. Maturation may be triggered when an
 underlying compound trait, called liability, exceeds a threshold. In many
 different species and especially fishes, this liability is approximated by
 growth and body condition. However, environmental vs. genetic
 contributions either directly or via growth and body condition to
 maturation timing remain unclear. Uncertainty exists also because the
 maturation process can reverse this causality and itself affect growth and
 body condition. In addition, disentangling the contributions of polygenic
 and major loci can be important. In many fishes, males mature before
 females, enabling the study of associations between male maturation and
 maturation-unbiased female liability traits. Using 40 Atlantic salmon
 families, longitudinal common-garden experimentation, and quantitative
 genetic analyses, we disentangled environmental from polygenic and major
 locus (vgll3) effects on male maturation, and sex-specific growth and
 condition. We detected polygenic heritabilities for maturation, growth,
 and body condition, and vgll3 effects on maturation and body condition but
 not on growth. Longitudinal patterns for sex-specific phenotypic
 liability, and for genetic variances and correlations between sexes
 suggested that early growth and condition indeed positively affected
 maturation initiation. However, towards spawning time, causality appeared
 reversed for males whereby maturation affected growth negatively and
 condition positively via both the environmental and genetic effects.
 Altogether, the results indicate that growth and condition are useful
 traits to study liability for maturation initiation, but only until
 maturation alters their expression, and that vgll3 contributes to
 maturation initiation via condition.
description: See manuscript.
description: See manuscript.
DOI: 10.5061/dryad.7m0cfxppz
title: In-plate toxicometabolomics of single zebrafish embryos

description: Toxicometabolomic studies involving zebrafish embryos have become
 increasingly popular for linking apical endpoints to biochemical
 perturbations as part of adverse outcome pathway determination. These
 experiments involve pooling embryos to generate sufficient biomass for
 metabolomic measurement, which adds both time and cost. To address this
 limitation, we developed a high-throughput toxicometabolomic assay
 involving single zebrafish embryos. Incubation, microscopy, embryo
 extraction, and instrumental metabolomic analysis were all performed in
 the same 96-well plate, following acquisition of conventional
 toxicological endpoints. The total time for the assay (including testing
 of 6 doses/n = 12 embryos per dose plus positive and negative
 controls, assessing conventional endpoints, instrumental analysis, data
 processing and multivariate statistics) is &lt;14 days. Metabolomic
 perturbations at low dose were linked statistically to those observed at
 high dose and in the presence of an adverse effect, thereby
 contextualizing omic data amongst apical endpoints. Overall, this assay
 enables collection of high resolution metabolomic data in a high
 throughput manner, suitable for mode of action hypothesis generation in
 the context of pharmaceutical or toxicological screening.
description: A high-throughput toxicometabolomic assay involving single
 zebrafish embryos was developed which links apical endpoints to
 biochemical perturbations.
DOI: 10.5061/dryad.fj6q573q2
title: Geography, seasonality, and host‐associated population structure influence the fecal microbiome of a genetically depauparate Arctic mammal

description: The Canadian Arctic is an extreme environment with low floral and faunal
 diversity characterized by major seasonal shifts in temperature, moisture
 and daylight. Muskoxen (Ovibos moschatus) are one of few large herbivores
 able to survive this harsh environment. Microbiome research of the
 gastrointestinal tract may hold clues as to how muskoxen exist in the
 Arctic, but also how this species may respond to rapid environmental
 changes. In this study, we investigated the effects of season
 (spring/summer/winter), year (2007-2016), and host genetic structure on
 population-level microbiome variation in muskoxen from the Canadian
 Arctic. We utilized 16S rRNA gene sequencing to characterize the fecal
 microbial communities of 78 male muskoxen encompassing two population
 genetic clusters. These clusters are defined by Arctic Mainland and Island
 populations, including; 1) two mainland sampling locations of the
 Northwest Territories and Nunavut; and 2) four locations of Victoria
 Island. Between these geographic populations, we found that differences in
 the microbiome reflected host-associated genetic cluster with evidence of
 migration. Within populations, seasonality influenced bacterial diversity
 with no significant differences between years of sampling. We found
 evidence of pathogenic bacteria, with significantly higher presence in
 mainland samples. Our findings demonstrate the effects of seasonality and
 the role of host population-level structure in driving fecal microbiome
 differences in a large Arctic mammal.
description: DNA from fecal samples were extracted using the Qiagen Power
 Fecal DNA extraction kit. The Illumina 16S metagenomic library protocol
 was followed.
description: Raw fastq files for two different runs are uploaded. The same
 samples were sequenced in both runs, and were used to evaluate possible
 batch effects.
DOI: 10.5061/dryad.1zcrjdfnc
title: Sex differences in IV thrombolysis treatment for stroke: a systematic review and meta-analysis

description: Objective: A prior meta-analysis of reports published between 2000 and
 2008 found that women were 30% less likely to receive IV rt-PA treatment
 for stroke than men; we updated this meta-analysis to determine if this
 sex difference still persisted. Methods: We identified studies that
 reported sex-specific IV rt-PA treatment rates for acute ischemic stroke
 published between 2008 and 2018. Eligible studies included representative
 populations of ischemic stroke patients from hospital-based,
 registry-based, or administrative data. Random effects odds ratios (OR)
 were generated to quantify sex differences. Results: Twenty-four eligible
 studies were identified during this 10-year period. The summary unadjusted
 OR based on 17 studies with data on all ischemic stroke patients was 0.87
 (95% confidence interval [CI]=0.82-0.93), indicating that women had 13%
 lower odds of receiving IV rt-PA treatment than men. However, substantial
 between-study variability existed. Lower treatment odds in women were also
 observed in 7 studies that provided data on the subgroup of patients
 eligible for IV rt-PA treatment, although the summary OR of 0.95 (95% CI =
 0.88-1.02) was not statistically significant. Examination of time trends
 across 33 studies published between 2000 and 2018 found evidence that the
 sex difference had narrowed in more recent years. Conclusions: Although
 there is considerable variability in the findings of individual studies,
 pooled data from recent studies shows that women with acute stroke are
 still less likely to be treated with IV thrombolysis compared with men.
 However, the size of this difference has narrowed compared to studies
 published before 2008.
description: Supplemental Figures and Tables, Study Exclusions and
 References
DOI: 10.13012/b2idb-8141497_v1
title: Data for egg hyperspectral image

description: 1228 egg hyperspectral images, the wavelength from 400 nm to 900 nm.
DOI: 10.5061/dryad.6q573n5vb
title: Palatal myoclonus, abnormal eye movements and olivary hypertrophy in GAD65-related disorder

description: We report a patient with GAD65-Abs with relapsing diplopia, cerebellar
 syndrome, and palatal myoclonus with hypertrophy of the inferior olivary
 nuclei (ION) seen on 1.5T MRI and a dentato-rubro-olivary pathway lesion
 on 7T MRI.
DOI: 10.5061/dryad.ksn02v706
title: The ganglioside, GD2, as a circulating tumor biomarker for neuroblastoma

description: Background: GD2 is a ganglioside that is ubiquitously expressed in the
 plasma membrane of neuroblastoma and is shed into the circulation.
 Procedure: GD2 was measured with a high-pressure liquid
 chromatography/tandem mass spectrometry assay in serum or plasma from 40
 children without cancer (controls) and in biobanked samples from 128 (73
 high-risk) children with neuroblastic tumors at diagnosis, 56 children
 with relapsed neuroblastoma, 14 children with high-risk neuroblastoma
 after treatment, and 8 to 12 children each with 10 other common childhood
 cancers at diagnosis. Results: The C18 (18 carbon fatty acid) lipoform was
 the predominant circulating form of GD2 in controls and in patients with
 neuroblastoma. The median concentration of GD2 in children with high-risk
 neuroblastoma at diagnosis was 167 nM (range, 16.1-1060 nM), which was
 30-fold higher than the median concentration (5.6 nM) in controls. GD2 was
 not elevated in serum from children with the differentiated neuroblastic
 tumors, ganglioneuroma (n = 10) and ganglioneuroblastoma-intermixed
 subtype (n = 12), and in children with 10 other childhood cancers. GD2
 concentrations were significantly higher in serum from children with
 MYCN-amplified tumors (P = 0.0088), high-risk tumors (P &lt; 0.00001),
 International Neuroblastoma Staging System (INSS) stage 4 tumors (P
 &lt; 0.00001), and in children who died (P = 0.034). Conclusions:
 Circulating GD2 appears to be a specific and sensitive tumor biomarker for
 highrisk/ high-stage neuroblastoma and may prove to be clinically useful
 as a diagnostic or prognostic circulating tumor biomarker. GD2 will be
 measured prospectively and longitudinally in children enrolled on a
 high-risk neuroblastoma treatment trial to assess its ability to measure
 response to treatment and predict survival.
description: This was a retrospective analysis. Serum samples were obtained
 from several biorepositories. The C<sub>18</sub> and
 C<sub>20</sub> lipoforms of G<sub>D2</sub> were
 measured in the serum samples using a validated HPLC/MS/MS assay
DOI: 10.5061/dryad.q2bvq83f6
title: Data From: Analysing social media forums to discover potential causes of phasic shifts in cryptocurrency price series

description: The recent extreme volatility in cryptocurrency prices occurred in the
 setting of popular social media forums devoted to the discussion of
 cryptocurrencies. We develop a framework that discovers potential
 causes of phasic shifts in the price movement captured by social media
 discussions. This draws on principles developed in healthcare
 epidemiology where, similarly, only observational data are
 available. Such causes may have a major, one-off effect or
 recurring effects on the trend in the price series. We find a
 one-off effect of regulatory bans on bitcoin, the repeated effects of
 rival innovations on ether and the influence of technical
 traders, captured through discussion of market price, on both
 cryptocurrencies. The results for Bitcoin differ from Ethereum,
 which is consistent with the observed differences in the timing of the
 highest price and the price phases. This framework could
 be applied to a wide range of cryptocurrency price series where there
 exists a relevant social media text source. Identified causes
 with a recurring effect may have value in predictive
 modelling, whilst one-off causes may provide insight into
 unpredictable black swan events that can have a major impact on a system.
DOI: 10.25349/d9p88j
title: Fungal infection alters the selection, dispersal, and drift processes structuring the amphibian skin microbiome

description: Symbiotic microbial communities are important for host health, but the
 processes shaping these communities are poorly understood. Understanding
 how community assembly processes jointly affect microbial community
 composition is limited because inflexible community models rely on
 rejecting dispersal and drift before considering selection. We developed a
 flexible community assembly model based on neutral theory to ask: How do
 dispersal, drift, and selection concurrently affect the microbiome across
 environmental gradients? We applied this approach to examine how a fungal
 pathogen affected the assembly processes structuring the amphibian skin
 microbiome. We found that the rejection of neutrality for the amphibian
 microbiome across a fungal gradient was not strictly due to selection
 processes, but was also a result of species-specific changes in dispersal
 and drift. Our modeling framework brings the qualitative recognition that
 niche and neutral processes jointly structure microbiomes into
 quantitative focus, allowing for improved predictions of microbial
 community turnover across environmental gradients.
DOI: 10.5061/dryad.5qfttdz12
title: Gut microbiota in reintroduction of Giant Panda

description: Reintroduction is a key approach in the conservation of endangered
 species. In recent decades, many reintroduction projects have been
 conducted for conservation purposes, but the rate of success has been low.
 Given the important role of gut microbiota in health and diseases, we
 questioned whether gut microbiota would play a crucial role in giant
 panda's wild‐training process. The wild procedure is when
 captive‐born babies live with their mothers in a wilderness enclosure and
 learn wilderness survival skills from their mothers. During the
 wild‐training process, the baby pandas undergo wilderness survival tests
 and regular physical examinations. Based on their performance through
 these tests, the top subjects (age 2–3 years old) are released
 into the wild while the others are translocated to captivity. After
 release, we tracked one released panda (Zhangxiang) and collected its
 fecal samples for 5 months (January 16, 2013 to March 29 2014).
 Here, we analyzed the Illumina HiSeq sequencing data (V4 region of 16S
 rRNA gene) from captive pandas (n = 24), wild‐training
 baby pandas (n = 8) of which 6 were released and 2 were
 unreleased, wild‐training mother pandas (n = 8), one
 released panda (Zhangxiang), and wild giant pandas
 (n = 18). Our results showed that the gut microbiota of
 wild‐training pandas is significantly different from that of wild pandas
 but similar to that of captive ones. The gut microbiota of the released
 panda Zhangxiang gradually changed to become similar to those of wild
 pandas after release. In addition, we identified several bacteria that
 were enriched in the released baby pandas before release, compared with
 the unreleased baby pandas. These bacteria include several known
 gut‐health related beneficial taxa such
 as Roseburia, Coprococcus, Sutterella,
 Dorea, and Ruminococcus. Therefore, our results suggest
 that certain members of the gut microbiota may be important in panda
 reintroduction.
DOI: 10.5061/dryad.mcvdncjw9
title: Data from: Paradoxical aortic stiffening and subsequent cardiac dysfunction in Hutchinson–Gilford progeria syndrome

description: Hutchinson–Gilford progeria syndrome (HGPS) is an ultra-rare disorder with
 devastating sequelae resulting in early death, presently thought to stem
 primarily from cardiovascular events. We analyse novel longitudinal
 cardiovascular data from a mouse model of HGPS (LmnaG609G/G609G) using
 allometric scaling, biomechanical phenotyping, and advanced computational
 modelling and show that late-stage diastolic dysfunction, with preserved
 systolic function, emerges with an increase in the pulse wave velocity and
 an associated loss of aortic function, independent of sex. Specifically,
 there is a dramatic late-stage loss of smooth muscle function and cells
 and an excessive accumulation of proteoglycans along the aorta, which
 result in a loss of biomechanical function (contractility and elastic
 energy storage) and a marked structural stiffening despite a distinctly
 low intrinsic material stiffness that is consistent with the lack of
 functional lamin A. Importantly, the vascular function appears to arise
 normally from the low-stress environment of development, only to succumb
 progressively to pressure-related effects of the lamin A mutation and
 become extreme in the peri-morbid period. Because the dramatic
 life-threatening aortic phenotype manifests during the last third of life
 there may be a therapeutic window in maturity that could alleviate
 concerns with therapies administered during early periods of arterial
 development.