cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7272/q60000bj
title: Supplementary Methods: Multiple imputation of CVRF trajectories in detail

description: Background: Cardiovascular risk factors (CVRFs) are associated with
 increased risk of cognitive decline, but little is known about how early
 adult CVRFs and those across the life course might influence late-life
 cognition. To test the hypothesis that CVRFs across the adult life course
 are associated with late-life cognitive changes, we pooled data from four
 prospective cohorts(n=15,001, ages 18-95). Methods: We imputed
 trajectories of body mass index (BMI), fasting glucose (FG), systolic
 blood pressure (SBP), and total cholesterol (TC) for older adults. We used
 linear mixed models to determine the association of early adult, mid-life,
 and late-life CVRFs with late-life decline on global cognition (Modified
 Mini-Mental State Exam (3MS)) and processing speed (Digit Symbol
 Substitution Test (DSST)), adjusting for demographics, education, and
 cohort. Results: Elevated BMI, FG, and SBP (but not TC) at each time
 period were associated with greater late-life decline. Early life CVRFs
 were associated with the greatest change, an approximate doubling of mean
 10-year decline (an additional 3-4 points for 3MS or DSST). Late-life
 CVRFs were associated with declines in early late-life (&lt;80 years)
 but with gains in very late-life (≥80 years). After adjusting for CVRF
 exposures at all time periods, the associations for early adult and
 late-life CVRFs persisted. Conclusions: We found that imputed CVRFs across
 the life course, especially in early adulthood, were associated with
 greater late-life cognitive decline. Our results suggest that CVRF
 treatment in early adulthood could benefit late-life cognition, but that
 treatment in very late-life may not be as helpful for these outcomes.
description: The supplement describes the methods used to impute trajectories
 of cardiovascular risk factors in epidemiological cohort
 studies.
DOI: 10.5061/dryad.2rbnzs7mr
title: Primary hybrid zone formation in Tephroseris helenitis (Asteraceae), following postglacial range expansion along the central Northern Alps

description: Secondary vs. primary hybrid zone formation remains a challenging task as
 the time window in which these historical (vicariant) vs. contemporary
 (environmental-selective) processes are distinguishable may be relatively
 narrow. To examine the origin and structure of a transition zone between
 two subspecies of Tephroseris helenitis along the central Northern Alps,
 molecular (AFLP) and morphological (achene type) data as well as
 ecological niche models (ENMs) were used. Samples were collected over a c.
 350 km-long transect, largely covered by ice during the Last Glacial
 Maximum (LGM). Genetically non-admixed individuals of subspp. helenitis
 vs. salisburgensis dominated the westernmost vs. eastern transect areas,
 with admixed individuals occurring in between. Cline for achene morphology
 was steep, largely non-coincidental, and displaced to the east of the
 cline centre for neutral AFLPs. During the LGM, ssp. helenitis should have
 been able to persist in a refugium southwest of the transect, while
 suitable habitat for ssp. salisburgensis was apparently absent at this
 time. Patterns of genetic and clinal variation in combination with our ENM
 data are suggestive of a primary hybrid zone that originated after the
 species’ postglacial, eastward expansion.  
description: File: Teph_456loci_plus_achenetype.csv The
 file contains an AFLP data matrix of 30 <i>T. helenitis</i>
 populations (<i>n</i> = 233 individuals; column labeled
 ‘Pop.’) with a total of 456 unambiguous fragments (columns labeled
 ‘Locus1’ - ‘Locus456’). Values describe fragments are present (1) or
 absent (0) in an individual. The data matrix also contains present (1) or
 absent (0) information on achene type (‘glabrous’, ‘sparsely hairy’,
 ‘pubescent’) as known for 216 of the 233 genotyped individuals. NA
 indicates when no information is available.
DOI: 10.5061/dryad.1rn8pk0sk
title: What evolutionary processes maintain MHCIIβ diversity within and among populations of stickleback?

description: Major Histocompatibility Complex (MHC) genes encode for proteins that
 recognize foreign protein antigens to initiate T-cell mediated adaptive
 immune responses. They are often the most polymorphic genes in vertebrate
 genomes. How evolution maintains this diversity is still an unsettled
 issue. Three main hypotheses seek to explain the maintenance of MHC
 diversity by invoking pathogen-mediated selection: heterozygote advantage,
 frequency-dependent selection, and fluctuating selection across landscapes
 or through time. Here, we use a large-scale field parasite survey in a
 stickleback metapopulation to test predictions derived from each of these
 hypotheses. We identify over a thousand MHCIIβ variants (alleles spanning
 paralogous genes) and find that many of them covary positively or
 negatively with parasite load, suggesting that these genes contribute to
 resistance or susceptibility. However, despite our large sample-size, we
 find no evidence for the widely-cited stabilizing selection on MHC
 heterozygosity, in which individuals with an intermediate number of MHC
 variants have the lowest parasite burden. Nor do we observe a rare-variant
 advantage, or widespread fluctuating selection across populations. In
 contrast, we find that MHC diversity is best predicted by neutral
 genome-wide heterozygosity and between-population genomic divergence,
 suggesting neutral processes are important in shaping the pattern of
 metapopulation MHC diversity. Thus, although MHCIIβ is highly diverse and
 relevant to the type and intensity of macroparasite infection in these
 populations of stickleback, the main models of MHC evolution still provide
 little explanatory power in this system.
DOI: 10.5061/dryad.12jm63xxc
title: Data from: New forms of structure in ecosystems revealed with the Kuramoto model

description: This is the general Mathematica code for the article, "New forms of
 structure in ecosystems revealed with the Kuramoto model" by
 Vandermeer, Hajian-Forooshani, Medina and Perfecto. All results presented
 in the article can be obtained by running the code with appropriate
 parameter settings.
description: This is the code written in the standard Matlab package.
description: To run the code to reproduce the figures all parameters need to
 be set as described in the article.
DOI: 10.5061/dryad.m37pvmd1j
title: Data from: Creating virtual species to test species distribution models: The importance of landscape structure, dispersal and population processes

description: The use of virtual species to test species distribution models is
 important for understanding how aspects of the model development process
 influence model performance. Typically, virtual species are simulated by
 defining its niche as a function of environmental variables and simulate
 occurrence probabilistically via Bernoulli trials. This approach ignores
 endogenous processes known to drive species distribution like dispersal
 and population dynamics. To understand whether these processes are
 important for simulating virtual species we compared the probabilistic
 simulation approach to those incorporating endogenous processes. This
 comparison was done by evaluating changes in the relationship between
 species occurrence and habitat suitability over a number of landscapes
 with varying spatial structure. We found that the combined effects of
 population dynamics and dispersal meant the probability of occurrence of a
 single cell was not only dependent on habitat suitability, but also the
 number of occupied cells nearby. This resulted in a dependence on the size
 of clusters of high suitability cells (analogous to patch size) to
 maintain populations, increased residual spatial autocorrelation and
 nonstationarity of the species response between landscapes. These data
 characteristics are attributes of real species distribution data and are
 not present in probabilistic simulations. Researchers using virtual
 species should consider the importance of these characteristics to their
 study objectives to decide whether the inclusion of endogenous processes
 is necessary.
description: This contains data which is the output of simulations and are
 formatted for direct use in analysis in 10.1111/ecog.05555
DOI: 10.5061/dryad.0vt4b8gxt
title: Natalizumab, fingolimod and dimethyl fumarate use and pregnancy-related relapse and disability in women with multiple sclerosis

description: Objective: To investigate pregnancy-related disease activity in a
 contemporary multiple sclerosis (MS) cohort. Methods: Using data from the
 MSBase Registry, we included pregnancies conceived after 31 Dec 2010 from
 women with relapsing-remitting MS or clinically isolated syndrome.
 Predictors of intrapartum relapse, and postpartum relapse and disability
 progression were determined by clustered logistic regression or Cox
 regression analyses. Results: We included 1998 pregnancies from 1619 women
 with MS. Preconception annualized relapse rate (ARR) was 0.29 (95% CI
 0.27-0.32), fell to 0.19 (0.14-0.24) in third trimester, and increased to
 0.59 (0.51-0.67) in early postpartum. Among women who used fingolimod or
 natalizumab, ARR before pregnancy was 0.37 (0.28-0.49) and 0.29
 (0.22-0.37), respectively, and increased during pregnancy. Intrapartum ARR
 decreased with preconception dimethyl fumarate use. ARR spiked after
 delivery across all DMT groups. Natalizumab continuation into pregnancy
 reduced the odds of relapse during pregnancy (OR 0.76 per month
 [0.60-0.95], p=0.017). DMT re-initiation with natalizumab protected
 against postpartum relapse (HR 0.11 [0.04-0.32], p&lt;0.0001).
 Breastfeeding women were less likely to relapse (HR 0.61 [0.41-0.91],
 p=0.016). 5.6% of pregnancies were followed by confirmed disability
 progression, predicted by higher relapse activity in pregnancy and
 postpartum. Conclusion: Women with MS prescribed natalizumab or fingolimod
 preconception had higher rates of intrapartum and postpartum relapse. In
 women considered to be at high relapse risk, use of natalizumab before
 pregnancy and continued up to 34 weeks gestation, with early re-initiation
 after delivery is an effective option to minimize relapse risks.
 Strategies of DMT use have to be balanced against potential fetal/neonatal
 complications.
DOI: 10.5061/dryad.4xgxd2589
title: Data from: Ultra-slow oscillations in fMRI and resting-state connectivity: Neuronal and vascular contributions and technical confounds

description: Ultra-slow, ~0.1-Hz variations in the oxygenation level of brain blood are
 widely used as an fMRI-based surrogate of ‘‘resting-state’’ neuronal
 activity. The temporal correlations among these fluctuations across the
 brain are interpreted as ‘‘functional connections’’ for maps and
 neurological diagnostics. Ultra-slow variations in oxygenation follow a
 cascade. First, they closely track changes in arteriole diameter. Second,
 interpretable functional connections arise when the ultra-slow changes in
 amplitude of g-band neuronal oscillations, which are shared across even
 far-flung but synaptically connected brain regions, entrain the ~0.1-Hz
 vasomotor oscillation in diameter of local arterioles. Significant
 confounds to estimates of functional connectivity arise from residual
 vasomotor activity as well as arteriole dynamics driven by self-generated
 movements and subcortical common modulatory inputs. Last, methodological
 limitations of fMRI can lead to spurious functional connections. The
 neuronal generator of ultra-slow variations in gamma-band amplitude,
 including that associated with self-generated movements, remains an open
 issue.
description: https://github.com/KL-Turner/Drew_Mateo_Turner_Yu_Kleinfeld_Neuron2020
DOI: 10.5061/dryad.8sf7m0cmc
title: Differences in dietary composition and preference maintained despite gene flow across a woodrat hybrid zone

description: 1. Hybridization can homogenize the gene pools of species that come into
 secondary contact. Alternatively, species differentiation can persist
 despite hybridization and interspecific gene flow. When hybridization
 occurs across sharp environmental transitions (i.e. ecotones), spatial
 variation in selection may reduce interspecific gene flow through pre- and
 post-zygotic isolating mechanisms. Ecotones, characterized by adjacent yet
 distinct biotic communities, provide natural laboratories in which to
 investigate how environmental selection influences the ecology and
 evolution of organisms. For wild herbivores, differential plant
 availability across sharp ecotones may be an important source of
 dietary-based selection. 2. We studied small herbivore diet composition
 across a sharp ecotone where two species of woodrat, Neotoma bryanti and
 N. lepida, come into secondary contact with one another and hybridize. We
 quantified woodrat dietary preference through trnL metabarcoding of
 field-collected fecal pellets and experimental choice trials. Despite gene
 flow, parental N. bryanti and N. lepida maintain distinct diets across
 this fine spatial scale, and across temporal scales that span both wet and
 dry conditions. 3. Neotoma bryanti maintained a more diverse diet, with
 Frangula californica (California coffeeberry) making up a large portion of
 its diet. Neotoma lepida maintains a less diverse diet, with Prunus
 fasciculata (desert almond) comprising more than half of its diet. Both F.
 californica and P. fasciculata are known to produce potentially toxic
 plant secondary compounds (PSCs), which should deter herbivory, yet these
 plants have relatively high nutritional value as measured by crude protein
 content. 4. Neotoma bryanti and N. lepida consumed F. californica and P.
 fasciculata, respectively, in greater abundance than these plants are
 available on the landscape – indicating dietary selection. Finally,
 experimental preference trials revealed that N. bryanti exhibited a
 preference for F. californica, while N. lepida exhibited a relatively
 stronger preference for P. fasciculata. We find that N. bryanti exhibit a
 generalist herbivore strategy relative to N. lepida, which exhibit a more
 specialized feeding strategy in this study system. 5. Our results suggest
 that woodrats respond to fine-scale environmental differences in plant
 availability that may require different metabolic strategies in order to
 balance nutrient acquisition while minimizing exposure to potentially
 toxic PSCs.
DOI: 10.5061/dryad.cc2fqz65h
title: A heterothermic spectrum in hummingbirds

description: Many small endotherms use torpor, saving energy by a controlled reduction
 of their body temperature and metabolic rate. Some species (e.g. arctic
 ground squirrels, hummingbirds) enter deep torpor, dropping their body
 temperatures by 23-37 &[deg]C, while others can only enter shallow
 torpor (e.g., pigeons, 3-10 &[deg]C reductions). However, deep
 torpor in mammals can increase predation risk (unless animals are in
 burrows or caves), inhibit immune function, and result in sleep
 deprivation, so even for species that can enter deep torpor, facultative
 shallow torpor might help balance energy savings with these potential
 costs. Deep torpor occurs in three avian orders. Although the literature
 hints that some bird species can use both shallow and deep torpor, little
 empirical evidence of such an avian torpor spectrum exists. We infrared
 imaged three hummingbird species that are known to use deep torpor, under
 natural temperature and light cycles, to test if they were also capable of
 shallow torpor. All three species used both deep and shallow torpor, often
 on the same night. Depending on the species, they used shallow torpor for
 5-35% of the night. The presence of a bird torpor spectrum indicates a
 capacity for fine-scale physiological and genetic regulation of avian
 torpid metabolism.
description: Thermal imaging data collected from wild-caught hummingbirds
 using a FLIR SC6701 thermal video camera. We studied males of three
 hummingbird species at the Southwestern Research Station (SWRS) in the
 Chiracahua mountains of Arizona (Lat: 31.9, Long: -109.2): the
 blue-throated mountain-gem (<i>Lampornis clemenciae; </i>8.4g,
 n = 14), Rivoli’s hummingbird (<i>Eugenes fulgens</i>; 7.6g, n
 =12) and the black-chinned hummingbird (<i>Archilocus
 alexandri</i>; 2.9g, n = 7). We collected data between June 10 – 19,
 2017 and May 20 – June 7, 2018. All protocols associated with hummingbird
 care and experimentation were approved by the Stony Brook University
 Institutional Animal Care and Use Committee (IRBNet number: 282617-6).
 Field protocols were approved by US Fish and Wildlife in Arizona (USFWS
 MB75714A-0).
description: See metadata for details and code on github
 (https://github.com/nushiamme/TorporShallowDeep).
DOI: 10.5061/dryad.2jm63xsnt
title: Genomic vulnerability of a dominant seaweed points to future-proofing pathways for Australia’s underwater forests

description: Globally, critical habitats are in decline, threatening ecological,
 economic and social values and prompting calls for “future proofing”
 efforts that enhance resilience to climate change. Such efforts rely on
 predicting how neutral and adaptive genomic patterns across a species’
 distribution will change under future climate scenarios, but data is scant
 for most species of conservation concern. Here, we use seascape genomics
 to characterize genetic diversity, structure and gene-environmental
 associations in a dominant forest-forming seaweed, Phyllospora comosa,
 along its entire latitudinal (12o latitude), and thermal  (~14oC)
 range. Phyllospora showed high connectivity throughout its central range,
 with evidence of genetic structure and potential selection associated with
 sea surface temperatures at its rear and leading edges. Rear and
 leading-edge populations harboured only half the genetic diversity of
 central populations. By modelling genetic turnover as a function of sea
 surface temperature, we assessed the genomic vulnerability across
 Phyllospora’s distributional range under climate change scenarios. Despite
 low diversity, range-edge populations were predicted to harbour beneficial
 adaptations to marginal conditions and overall adaptability of the species
 may be compromised by their loss. Assisted gene flow from range edge
 populations may be required to enhance adaptation and increase resilience
 of central and leading-edge populations under warming oceans.
  Understanding genomic vulnerability can inform proactive
 restoration and future-proofing strategies for underwater forests and
 ensure their persistence in changing oceans.
description: Please see associated paper Wood, G., Marzinelli, E.M., Campbell,
 A.H., Steinberg, P.D., Vergés, A. and Coleman, M.A. (2021), Genomic
 vulnerability of a dominant seaweed points to future‐proofing pathways for
 Australia’s underwater forests. Glob Change Biol. Accepted Author
 Manuscript. https://doi.org/10.1111/gcb.15534
description: Missing values are coded at NA. Use readme file.
DOI: 10.5061/dryad.05qfttf29
title: Effects of gravel size and content on the mechanical properties of conglomerate

description: Stress-strain curves and fracture distribution characteristics indicate
 that gravel content influences the mechanical properties of rocks. In this
 study, uniaxial compression tests were conducted on the conglomerate
 containing gravels having diameters between 2–26 mm. In these tests, we
 found that many micro fractures were generated around evenly distributed
 gravels. Additionally, we found that as the gravel content increased, the
 uniaxial compressive strength and elastic modulus of conglomerate
 decreased; however, the plasticity characteristics of conglomerate
 increased. The results of our analysis imply that when the gravel content
 is less than  (14.61–31.72 %), the macro mechanical properties
 are mainly influenced by the cementing material, and between  and
  (78.50 %), failure is determined by the local Orowan additional
 stress, which is related to the mechanical properties of the cement and
 the cementing strength,and higher than fch, failure is determined by the
 mutual Hertz stress among the gravels.
description: The samples in our study are from Mahu 1, which is located in the
 middle of the Mahu depression, with a sampling depth of 3242–3587 m.
 Limited by the size of bottomhole coring tools, samples of size Φ
 50<b> × </b>100 mm were drilled and polished on both ends
 until the parallelism error was less than 0.05 mm. To get the distribution
 of gravel contained in samples, gravel images were extracted from the
 outer cylinder images of the samples. Then, the ImageJ software was used
 to calculate the content and particle size of gravels having diameters
 larger than 1 mm. In the six samples, the area percentages of gravel
 larger than 1 mm in diameter were found to be 0.03 %, 2.46 %, 7.27 %,
 14.61 %, 31.72 %, and 68.47 %, and the maximum particle sizes of gravel
 were 2.50, 3.50, 5.49, 16.67, 21.30, and 26.13 mm, respectively. The
 gravel is mainly garnet, amphibole, potassium feldspar, and albite; the
 former two minerals belong to igneous rocks. Small minerals are mainly
 quartz, potassium feldspar, albite, and calcite. The rocks are cemented by
 calcite, with uniform cementation. An
 RTR-1500 [Geotechnical Consulting & Test Systems (GCTS), USA],
 which is a high temperature and high pressure triaxial rock testing
 system, was used in this experiment. The system, which is controlled by an
 electro-hydraulic closed-loop digital servo, can provide 1500 kN axial
 pressure. The rigidity of the loading frame is 10000 kN/mm. The confining
 pressure is provided by the silicon-oil injected into the chamber and can
 reach 70 MPa, with a precision of 0.01 MPa. The strain data acquisition
 was realized using two axial sensors and one radial sensor. Through the
 LVDT (linear variable differential transformer) operation, the radial
 sensor uses a non-extendable chain to precisely measure the mean diameter
 change caused by radial strain, which is more accurate than the
 point-based strain gauge method because the local deformation caused by
 gravel varies in different parts of conglomerate.
DOI: 10.15468/dl.9ss83t
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Heteroconium chaetospira"
 ]
}

 The dataset includes 39 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002762-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.