cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zgmsbcc6g
title: Sex-driven modifiers of Alzheimer’s risk: a multi-modality brain imaging study

description: Objective: To investigate sex differences in late-onset Alzheimer’s
 disease (AD) risks by means of multi-modality brain biomarkers [β-amyloid
 load via 11C-PiB PET, and neurodegeneration via 18F-FDG PET and structural
 MRI]. Methods: We examined 121 cognitively normal participants [85 women
 and 36 men] ages 40-65, with clinical, laboratory, neuropsychological,
 lifestyle exams, and MRI, FDG- and PiB-PET exams. Several clinical (e.g.
 age, education, APOE status, family history), medical (e.g., depression,
 diabetes, hyperlipidemia), hormonal (e.g. thyroid disease, menopause), and
 lifestyle AD risk factors (e.g., smoking, diet, exercise, intellectual
 activity) were assessed. Statistical parametric mapping and LASSO
 regressions were used to compare AD-biomarkers between men and women, and
 to identify the risk factors associated with sex-related differences.
 Results: Groups were comparable on clinical and cognitive measures.
 Adjusting for each modality-specific confounders, the female group showed
 higher PiB β-amyloid deposition, lower FDG glucose metabolism, and lower
 MRI gray and white matter volumes compared to the male group
 (p&lt;0.05, FWE-corrected for multiple comparisons). The male group
 did not show biomarker abnormalities compared to the female group. Results
 were independent of age and remained significant using age-matched groups.
 Second to female sex, menopausal status was the predictor most
 consistently and strongly associated with the observed brain biomarker
 differences, followed by hormone therapy, hysterectomy status, and thyroid
 disease. Conclusion: Hormonal risk factors, in particular menopause,
 predict AD-endophenotype in middle-aged women. These findings
 suggest that the window of opportunity for AD-preventative
 interventions in women is early in the endocrine aging process.
DOI: 10.5061/dryad.2rbnzs7hw
title: Parental breeding age effects on descendants’ longevity interact over two generations in matrilines and patrilines

description: Individuals within populations vary enormously in mortality risk and
 longevity, but the causes of this variation remain poorly understood. A
 potentially important and phylogenetically widespread source of such
 variation is maternal age at breeding, which typically has negative
 effects on offspring longevity. Here, we show that paternal age can affect
 offspring longevity as strongly as maternal age does, and that breeding
 age effects can interact over two generations in both matrilines and
 patrilines. We manipulated maternal and paternal ages at breeding over two
 generations in the neriid fly Telostylinus angusticollis. To determine
 whether breeding age effects can be modulated by the environment, we also
 manipulated larval diet and male competitive environment in the first
 generation. We found separate and interactive effects of parental and
 grandparental ages at breeding on descendants’ mortality rate and lifespan
 in both matrilines and patrilines. These breeding age effects were not
 modulated by grandparental larval diet quality or competitive environment.
 Our findings suggest that variation in maternal and paternal ages at
 breeding could contribute substantially to intra-population variation in
 mortality and longevity.
description: This experiment was conducted using the neriid fly,
 <em>Telostylinus angusticollis</em>. We reared individuals of
 the grandparental (F1) generation on either a high-nutrient or
 low-nutrient larval diet and then allowed adult females and males from
 these larval diet treatments to breed at 15 and 35 days of age. Neriid
 males fight other males for access to territories and females, and such
 male-male interactions could affect male ageing. We therefore investigated
 the potential for male-male interactions to affect paternal age effects by
 manipulating F1 male competitive environment. Female and male offspring
 (F2) were reared on a standard larval diet (with a nutrient concentration
 intermediate between the high-nutrient and low-nutrient diets) and then
 allowed to breed at 15-day age intervals between ages 15 and 60 days. We
 quantified the adult longevity of grand-offspring (F3) and used these data
 to test for effects of grandparental ages at breeding, grandparental
 environment, and parental ages at breeding on grand-offspring lifespan,
 mortality rate, and actuarial ageing rate. The data was
 processed using linear mixed effects modelling and BaSTA (Bayesian
 Survival Trajectory Analysis) to examine patterns of lifespan and
 mortality.
description: Analysis was conducted using R 3.3.2, the packages
 "lme4", "lmerTest","car", and
 "BaSTA."
DOI: 10.5061/dryad.m63xsj3xj
title: Analysing and optimizing the electrolysis efficiency of a lithium cell based on the electrochemical and multiphase model

description: Based on an electrochemical multiphysical simulation, a method for
 analysing electrolysis efficiency has been presented that considers the
 energy consumption required to produce a single kilogram of lithium and
 for the production of lithium, rather than the voltage in various parts.
 By adopting them as the criteria for analysing electrolysis efficiency in
 the lithium cell, several structural parameters have been optimised, such
 as the anode radius, anode-cathode distance (ACD). These parameters
 strongly affect the cell voltage and the velocity field distribution,
 which has a significant impact on the concentration distribution. By
 integrating the concentration distribution, the lithium production and
 energy consumption per kilogram lithium is computed. By appointing the
 minimum of the chlorine and lithium concentration as the secondary
 reaction intensity, it is clear where the secondary reaction intensity is
 strong in the cell. The structure of a lithium electrolysis cell has been
 optimised by applying an orthogonal design approach, with the energy
 consumption notably decreasing from 35.0 kWh (kg Li)-1 to 28.3 kWh and the
 lithium production successfully increasing by 0.17 mol.
DOI: 10.5061/dryad.xsj3tx99k
title: Winter damage is more important than summer temperature for maintaining the krummholz growth form above alpine treeline

description: 1. Understanding the processes that control alpine treelines, the
 elevational limits of tree growth forms, has been a central question in
 ecology and is growing in importance with concern over climate change.
 Cool summer air temperatures are currently thought to be the ultimate
 limiter of upright tree growth at alpine treelines globally. However,
 winter damage has long been recognized as a shaping force near alpine
 treelines. Low-growing krummholz growth forms provide an opportunity to
 test hypotheses about the controls of upright growth in environments above
 current treelines. 2. To distinguish between effects of growing season
 temperature, winter damage and their interaction on preventing upright
 growth in krummholz, we conducted a field experiment on krummholz growth
 forms of Pinus albicaulis over the summer and winter of
 2015-2016 at 10 mountain top sites in the Tobacco Root Mountains, Montana,
 USA. We experimentally manipulated four factors using a fully crossed
 design: shoot position (natural low position in the krummholz mat vs.
 propped up above the krummholz mat), summer warming (warming chamber vs.
 ambient), winter exposure (shelter cage vs. exposed), and elevation
 position (local high vs. low krummholz limits). We also conducted an
 observational study of the climatic conditions associated with recent
 natural emergent stem establishment from krummholz.  3.
 Experimentally propped shoots that were exposed in winter experienced the
 highest mortality (10-50%), while propped shoots in shelter cages and
 shoots located within the krummholz mat, whether caged or not, had low
 mortality (0-10%). Summer warming had little influence on shoot mortality.
 Surviving mat shoots had marginally higher growth rates than surviving
 propped shoots during the early growing season after treatments were
 established. Natural emergent stem establishment was associated with
 warmer than average summer temperatures, but also warmer winter
 temperatures, lower winter wind speeds, and lower snowpack.
 4. Synthesis. Our results suggest winter damage plays a more
 important role than does growing season temperature in maintaining the
 krummholz growth form. While warming may increase opportunities for
 emergent shoot establishment above krummholz mats, establishment of
 upright trees in the krummholz zone will also require climatic change that
 reduces wind and snow transport which cause winter damage.
DOI: 10.5061/dryad.3bk3j9kdv
title: Synaptic organization of cortico-cortical communication in primates

description: In cortical circuitry synaptic communication across areas is based on two
 types of axon terminals, small and large, with modulatory and driving
 roles, respectively. In contrast, it is not known whether similar synaptic
 specializations exist for intra-areal projections. Using anterograde
 tracing and three-dimensional reconstruction by electron microscopy
 (3D-EM) we asked if large boutons form synapses in the circuit of
 somatosensory cortical areas 3b and 1. In contrast to observations in
 macaque visual cortex, light microscopy showed both small and large
 boutons not only in inter-areal pathways, but also in long-distance
 intrinsic connections. 3D-EM showed that correlation of surface and volume
 provides a powerful tool for classifying cortical endings. Principal
 component analysis supported this observation and highlighted the
 significance of the size of mitochondria as a distinguishing feature of
 bouton type. The larger mitochondrion and higher degree of perforated
 postsynaptic density associated with large rather than to small boutons
 support the driver-like function of large boutons. In contrast to bouton
 size and complexity, the size of the postsynaptic density appeared
 invariant across the bouton types. Comparative studies in human supported
 that size is a major distinguishing factor of bouton type in the cerebral
 cortex. In conclusion, the driver-like function of the large endings could
 facilitate fast dissemination of tactile information within the intrinsic
 and inter-areal circuitry of areas 3b and 1.
description: The dataset contains two types of data: txt files for the light
 microscopic  (LM) maps made by Neurolucida (e.g. Area1 ij_infra_M:
 injection was made into area 1 and the dataset contains only the
 infragranular layers). "Areal and granular distribution of large
 boutons" excel file includes the distribution of large boutons
 according to LM observations. The other main part of
 the dataset is electronmicroscopic data (EM). The txt files
 (e.g. VB3_A1_p3, ID of an individual bouton) were created by Reconstruct
 software and they contain tracing information by boutons with full series
 separately. "Bouton.data_full.series.selected" excel file
 contains all of the ultrastructural futures, which was extracted from
 Reconstruct and derived and measured data used for our analyses.
description: Row data of a few boutons are missing in the dataset. The reason
 is those tracing work made in the past at my previous institution in my
 previouis computer, which was broken in the last year.
DOI: 10.5061/dryad.pg4f4qrj8
title: Impact of short- and long-term exposure to elevated seawater pCO2 on metabolic rate and hypoxia tolerance in Octopus rubescens

description: Much of the CO2 released by human activity into the atmosphere is
 dissolving into the oceans making them more acidic. In this study we
 provide the first data on the short- and long-term impacts of ocean
 acidification on octopuses. We measured routine metabolic rate (RMR) and
 critical oxygen pressure (Pcrit) of Octopus rubescens at elevated CO2
 pressure (pCO2) with no prior acclimation, one, and five weeks
 acclimation. Octopuses showed significantly higher RMRs in 1500 μatm pCO2
 environments with no prior acclimation than octopuses in 700 μatm or 360
 μatm environments. However, both one and five weeks of acclimation showed
 no significant difference in RMRs between octopuses at differing pCO2,
 indicating that octopuses acclimated rapidly to elevated pCO2. In
 octopuses acclimated for five weeks at 1500 μatm pCO2 we observed impaired
 hypoxia tolerance as demonstrated by a significantly higher critical
 oxygen pressure than those acclimated to 700 μatm pCO2. Our findings
 suggest that O. rubescens experiences short-term stress in elevated pCO2,
 but is able to acclimate over time. However, while this species may be
 able to acclimate to near-term ocean acidification, compounding
 environmental effects of acidification and hypoxia may present a
 physiological challenge for this species.
description: This data provides the analysis and datasets to replicate the
 statistical analyses and figures that appear in the paper "Impact of
 short- and long-term exposure to elevated seawater pCO2 on metabolic rate
 and hypoxia tolerance in Octopus rubescens", as well as some
 additional figures that more fully explain analyses such as semivariograms
 and test statistic distributions.  To run critical oxygen pressure
 measurements analyses you will need the raw data contained in
 "Pcrit_data.zip" and the code contained in
 "Pcrit_Analysis.pdf".  This will write a .csv file of Pcrit
 values that will be used the further analysis.  For the remainder of the
 analyses, you will need the code contained in
 "Octopus_hydpercapnia.pdf" or alternatively in
 "Octopus_hypercapnia.Rmd", and you will need the data contained
 in "GPS_waypoints.zip", "Seawater_ph_2015.csv",
 "treatment_carbonate2014.csv",
 "Short_Term_RMR_2014.csv", "Long_Term_RMR_2014.csv",
 and "Pcrit_2014.csv".
DOI: 10.5061/dryad.gmsbcc2hs
title: Symbiotic lifestyle triggers drastic changes in the gene expression of the algal endosymbiont Breviolum minutum (Symbiodiniaceae)

description: Coral-dinoflagellate symbiosis underpins the evolutionary success of
 corals reefs. Successful exchange of molecules between the cnidarian host
 and the Symbiodiniaceae algae enables the mutualistic partnership. The
 algae translocate photosynthate to their host in exchange for nutrients
 and shelter. The photosynthate must traverse multiple membranes, most
 likely facilitated by transporters. Here, we compared gene expression
 profiles of free-living cultured and freshly isolated Breviolum minutum,
 the homologous symbiont of the coral model, the sea anemone Exaiptasia
 pallida. Additionally, we assessed expression levels of a select a list of
 candidate host transporters-of-interest in anemones with and without
 symbionts. Our transcriptome analyses highlight the distinctive nature of
 the two algal life stages, with many gene expression level changes
 correlating to the different morphologies, cell cycles, and metabolisms
 adopted in hospite versus free-living. Morphogenesis-related genes that
 likely underpin the metamorphosis process observed when symbionts enter a
 host cell were up-regulated. Conversely, many down-regulated genes appear
 to be indicative of the protective and confined nature of the symbiosome.
 Our results emphasize the significance of transmembrane transport to the
 symbiosis, and in particular of ammonium and sugar transport. Further, we
 pinpoint and characterize candidate transporters—localized variously to
 the algal plasma membrane, the host plasma membrane, and the symbiosome
 membrane— that likely serve pivotal roles in the interchange of material
 during symbiosis. Our study provides new insights that expand our
 understanding of the molecular exchanges that enable symbiotic
 relationship.
DOI: 10.5061/dryad.jdfn2z372
title: Data from: Fine-scale appendage structure of the Cambrian trilobitomorph Naraoia spinosa and its ontogenetic and ecological implications

description: Trilobitomorphs are a species-rich Palaeozoic arthropod assemblage that
 unites trilobites with several other lineages that share
 similar appendage structure. Post-embryonic development
 of the exoskeleton is well documented for some trilobitomorphs, especially
 trilobites, but little is known of the ontogeny of their soft parts,
 limiting understanding of their autecology. Here we
 document appendage structure of
 the Cambrian naraoiid trilobitomorph Naraoia spinosa by computed microtomography, resulting in three-dimensional reconstructions of appendages at both juvenile and adult stages. The adult has dense, strong spines on the protopods of post-antennal appendages, implying a predatory/scavenging behavior. Absence of such gnathobasic structures but instead tiny protopodal bristles and a number of endopodal setae suggests a detritus-feeding strategy for the juvenile. Our data add strong morphological evidence for ecological-niche shifting by Cambrian arthropods during their life cycles. A conserved number of appendages across the sampled developmental stages demonstrates that Naraoia ceased budding off new appendages by the mid-juvenile stage.    
description: The specimens, which are presented as mud-stone slabs, were
 scanned with a GE Phoenix Nanotom m scanner, resulting in a set of tiff
 images for each scan. Slabs a and b of YKLP 11408 are each represented by
 400 tiff images. YKLP 11409 is represented by 2200 tiff images. These tiff
 images can be further processed with 3D reconstruction software such as
 Drishti, Mimics and Dragonfly, to visualize the fossil
 structures.
description: These are the micro-CT data that support the paper
 "Fine-scale appendage structure of the Cambrian trilobitomorph
 <i>Naraoia spinosa</i> and its ontogenetic and ecological
 implications", which has been accepted for publications in
 Proceedings B. The data for the two specimens (YKLP 11408 and YKLP 11409)
 described in that paper are presented here. The specimens were scanned
 with a GE Phoenix Nanotom m scanner. For more technical details please see
 Zhai et al. (2019, Proceedings B). Anyone who is going
 to use these data for publication should contact Yu Liu
 (yu.liu@ynu.edu.cn) or Dayou Zhai (dyzhai@ynu.edu.cn). Please cite Zhai et
 al. (2019, Proceedings B,
 doi: http://dx.doi.org/10.1098/rspb.2019.2371).
DOI: 10.71964/126
title: Data Supporting the Manuscript "Clumped at the Waterhole: Density Estimate Biases and Methods of Correction"

description: Transect surveys and distance sampling are widely used to estimate wildlife population densities, but these methods can be biased when animals aggregate near features such as waterholes that occur along survey routes. Using empirical data from the NamibRand Nature Reserve in Namibia, we developed spatial simulations to examine how clumping of oryx (Oryx gazella) near water sources affects density and population estimates. We simulated a 50-km survey transect and varied the proportion of the population concentrated at waterholes (5–20%). Our results show that such aggregation can cause substantial positive bias, with population estimates inflated by 67% to 967% relative to known population size. We evaluated two correction approaches: censoring observations and transect segments near waterholes and redistributing animals from waterholes across the landscape. Both methods reduced bias, but censoring was simpler and consistently produced more accurate estimates. These findings demonstrate that non-random animal distributions near linear survey features can severely compromise distance sampling assumptions. Accounting for such biases is essential for producing reliable population estimates, particularly in arid and semi-arid systems where wildlife strongly congregates around limited water sources.
DOI: 10.5061/dryad.r7sqv9s7j
title: Differential expression of olfactory genes in Atlantic salmon (Salmo salar) during the parr-smolt transformation

description: The anadromous salmon life-cycle includes two migratory events, downstream
 smolt migration and adult homing migration, during which they must
 navigate with high precision. During homing migration, olfactory cues are
 used for navigation in coastal and freshwater areas, and studies have
 suggested that the parr-smolt transformation has a sensitive period for
 imprinting. Accordingly, we hypothesized that there would be significant
 changes in gene expression in the olfactory epithelium specifically
 related to smoltification and sampled olfactory rosettes from
 hatchery-reared upper growth modal juvenile Atlantic salmon at three-week
 intervals from January to June, using lower growth modal non-smolting
 siblings as controls. A suite of olfactory receptors and receptor-specific
 proteins involved in functional aspects of olfaction and peripheral odor
 memorization was analyzed by qPCR. Gene expression in juveniles was
 compared with mature adult salmon of the same genetic strain caught in the
 river Gudenaa. All mRNAs displayed significant variation over time in both
 modal groups. Furthermore, 5 receptor genes (olfc13.1, olfc15.1, sorb,
 ora2, asor1) and four olfactory-specific genes (soig, ependymin, gst,
 omp2) were differentially regulated between modal groups, suggesting
 altered olfactory function during smoltification. Several genes were
 differentially regulated in mature salmon compared to juveniles,
 suggesting that homing and odor recollection involves a different set of
 genes than during imprinting. Thyroid hormone receptors thrα and thrβ
 mRNAs were elevated during smolting suggesting increased sensitivity to
 thyroid hormones. Treatment of pre-smolts with triiodothyronine in vivo
 and ex vivo had, however, only subtle effects on the investigated
 olfactory targets, questioning the hypothesis that thyroid hormones
 directly regulate gene expression in the olfactory epithelium.
description: Olfactory epithelium from upper/lower mode salmon sampled during
 smoltification from January to June. RNA extracted and converted into
 cDNA. qPCR on olfactory receptors.
description: Missing values noted as N/A
DOI: 10.5061/dryad.w0vt4b8m8
title: Changing environments and genetic variation: natural variation in inbreeding does not compromise short-term physiological responses

description: Selfing plant lineages are surprisingly widespread and successful in a
 broad range of environments, despite showing reduced genetic diversity,
 which is predicted to reduce long-term evolutionary potential. However,
 appropriate short-term plastic responses to new environmental conditions
 might not require high levels of standing genetic variation. In this
 study, we tested whether mating system variation among populations, and
 associated changes in genetic variability, affected short-term responses
 to environmental challenges. We compared relative fitness and metabolome
 profiles of naturally outbreeding (genetically diverse) and inbreeding
 (genetically depauperate) populations of a perennial plant, Arabidopsis
 lyrata, under constant growth chamber conditions and an outdoor common
 garden environment outside its native range. We found no effect of
 inbreeding on survival, flowering phenology or short-term physiological
 responses. Specifically, naturally occurring inbreeding had no significant
 effects on the plasticity of metabolome profiles, using either
 multivariate approaches or analysis of variation in individual
 metabolites, with inbreeding populations showing similar physiological
 responses to outbreeding populations over time in both growing
 environments. We conclude that low genetic diversity in naturally inbred
 populations may not always compromise fitness or short-term physiological
 capacity to respond to environmental change, which could help to explain
 the global success of selfing mating strategies.