cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rm74c6b
title: Data from: Autopolyploidy alters nodule-level interactions in the legume-rhizobium mutualism

description: Premise of the study: Polyploidy is a major genetic driver of ecological
 and evolutionary processes in plants, yet its effects on plant
 interactions with mutualistic microbes remain unresolved. The
 legume-rhizobium symbiosis regulates global nutrient cycles and plays a
 role in the diversification of legume taxa. In this mutualism, rhizobia
 bacteria fix nitrogen in exchange for carbon provided by legume hosts.
 This exchange occurs inside root nodules, which house bacterial cells and
 represent the interface of legume-rhizobial interactions. Although
 polyploidy may directly impact the legume-rhizobium mutualism, no studies
 have explored how it alters the internal structure of nodules. Methods: We
 created synthetic autotetraploids using Medicago sativa subsp. caerulea.
 Neotetraploid plants and their diploid progenitors were singly inoculated
 with two strains of rhizobia, Sinorhizobium meliloti and S. medicae.
 Confocal microscopy was used to quantify internal traits of nodules
 produced by diploid and neotetraploid plants. Key Results: Autotetraploid
 plants produced larger nodules with larger nitrogen fixation zones than
 diploids across both strains of rhizobia, although significance of this
 difference was limited by power. Neotetraploid M. sativa subsp. caerulea
 plants also produced symbiosomes that were significantly larger, nearly
 twice the size, than those present in diploids. Conclusions: This study
 sheds light on how polyploidy directly affects a plant-bacterial mutualism
 and uncovers novel mechanisms. Changes in plant-microbe interactions that
 directly result from polyploidy likely contribute to the increased ability
 of polyploid legumes to establish in diverse environments.
description: Data from diploid,
 revertant diploid, and neotetraploid Medicago sativa subsp. caerulea root
 nodulesPlants were grown in a
 controlled, growth room experiment at the University of Pittsburgh. Mature
 root nodules from plants inoculated with Sinorhizobium meliloti and S.
 medicae were processed using confocal microscopy. Data was collected on
 nodule number per plant and internal histologic traits of nodules,
 including total nodule area, area of the nitrogen-fixation zone, and
 symbiosome area. Additional details are provided in the Metadata tab of
 the data sheet.DE_Data.xlsxR Code used to analyze nodule traits of diploid and autotetraploid Medicago sativa subsp. caeruleaData on nodule traits of diploid and neotetraploid Medicago sativa subsp. caerulea was analyzed using MANOVA, ANOVAs, and power analyses in R.RCode_Autopolyploidy.R
DOI: 10.5061/dryad.kp8c5j3
title: Data from: Haemoglobin and anaemia in relation to dementia risk and accompanying changes on brain MRI

description: Objective: To determine the long-term association of haemoglobin levels
 and anaemia with risk of dementia, and explore underlying substrates on
 brain MRI in the general population. Methods: Serum haemoglobin was
 measured in 12,305 non-demented participants of the population-based
 Rotterdam Study (mean age 64.6 years, 57.7% women). We determined risk of
 dementia and Alzheimer’s disease (until 2016) in relation to haemoglobin
 and anaemia. Among 5,267 non-demented participants with brain MRI, we
 assessed haemoglobin in relation to vascular brain disease, structural
 connectivity, and global cerebral perfusion. Results: During a mean
 follow-up of 12.1 years, 1,520 individuals developed dementia, of whom
 1,194 had Alzheimer’s disease. We observed a U-shaped association between
 haemoglobin levels and dementia (P=0.005), such that both low and high
 haemoglobin levels were associated with increased dementia risk (hazard
 ratio [95% confidence interval]– lowest versus middle quintile 1.29
 [1.09-1.52]; highest versus middle quintile 1.20 [1.00-1.44]). Overall
 prevalence of anaemia was 6.1%, and anaemia was associated with a 34%
 increased risk of dementia (95%CI: 11-62%) and 41% (15-74%) for
 Alzheimer’s disease. Among non-demented individuals with brain MRI,
 similar U-shaped associations were seen of haemoglobin with white matter
 hyperintensity volume (P=0.03), and structural connectivity (for mean
 diffusivity, P&lt;0.0001), but not with presence of cortical and
 lacunar infarcts. Cerebral microbleeds were more common with anaemia.
 Haemoglobin levels inversely correlated to cerebral perfusion
 (P&lt;0.0001). Conclusion: Low and high levels of haemoglobin are
 associated with an increased risk of dementia, including Alzheimer’s
 disease, which may relate to differences in white matter integrity and
 cerebral perfusion.nn
description: Haemoglobin and anaemia
 in relation to dementia risk and accompanying changes on brain MRI
 (2019)Supplementary material
 to Haemoglobin and anaemia in relation to dementia risk and accompanying
 changes on brain MRI (2019), including two figures and five tables with
 the results from additional analyses referred to in the main published
 manuscript.Supplementary
 material.docx
DOI: 10.5061/dryad.ts53383
title: Transitions in paternal social status predict patterns of offspring growth and metabolic transcription

description: Parental effects occur when changes in the parental phenotype or
 environment cause changes to offspring phenotype. While some parental
 effects are triggered in response to an environmental cue in a time-locked
 fashion, other parental effects persist even after the cue has been
 removed, suggesting multiple timescales of action. For parental effects to
 serve as reliable signals of current environmental conditions, they should
 be reversible, such that when the cue changes, offspring phenotypes change
 in accordance. Social hierarchy is a prevalent feature of the environment,
 and current parental social status could signal the environment in which
 offspring will be born. Here, we sought to address parental effects of
 social status and their timescale of action in mice. We show that
 competition in seminatural environments affects offspring growth rate.
 Although dominant males are not heavier than nondominant or control males,
 they produce faster growing offspring, particularly sons. The timing,
 effect-size, and sex-specificity of this association are modulated by
 maternal social experience. We show that a change in paternal social
 status is sufficient to modulate offspring weight: from one breeding cycle
 to the next, status-ascending males produce heavier sons than before, and
 status-descending males produce lighter sons than before. Current paternal
 status is also highly predictive of liver transcription in sons, including
 molecular pathways controlling oxidative phosphorylation and iron
 metabolism. These results are consistent with a parental effect of social
 experience, although alternative explanations are considered. In summary,
 changes in paternal social status are associated with changes in offspring
 growth and metabolism.
description: Wild-derived mouse body
 mass measurements and other factors"offspringID"
 is a unique identifying number for one experimental offspring.
 "offspringAge" is that offspring's age in weeks,
 "offspringMassGrams" is the body mass of that offspring at that
 age. Column headers should be of sufficient description, but please
 contact corresponding author if clarifications are
 needed.Experment1and2_offspringTables.xlsxtwo RNA analyses of six week old mouse son livers with different paternal social historiesThis excel file contains the TPM data that was used to for the “birth status” and “social rank (losses)" analyses, as well as the model output (results) for the two associated models.RNAdata_Abundances-Results_birthStatus-paternalRank.xlsx
DOI: 10.5061/dryad.4j07c14
title: Data from: Early molecular oxidative stress biomarkers of ischemic penumbra in acute stroke

description: Objectives: To assess whether plasma biomarkers of oxidative stress
 predict diffusion-perfusion mismatch in acute ischemic stroke (AIS)
 patients. Methods: We measured plasma levels of oxidative stress
 biomarkers such as F2-isoprostanes (F2-isoP), total and perchloric acid
 Oxygen Absorbance Capacity (ORACTOT and ORACPCA), urinary levels of
 8-oxo-7,8-dihydro-2’-deoxyguoanosine, and inflammatory and tissue-damage
 biomarkers (high-sensitivity CRP, matrix metalloproteinase 2 and 9), in a
 prospective study of AIS patients presenting within 9 hours of symptom
 onset. Diffusion- (DWI) and perfusion-weighted (PWI) MRI sequences were
 analyzed using a semi-automated volumetric method. Mismatch was defined as
 baseline mean transit time volume minus DWI volume. A percent mismatch
 cut-off of &gt;20% was considered clinically significant. A stricter
 definition of mismatch was also used. Mismatch salvage was the region free
 of overlap by final infarction. Results: Mismatch &gt;20% was present
 in 153/216 (70.8%) patients (69.2±14.3 years; 41.2% women). Patients with
 mismatch &gt;20% were more likely to have higher baseline plasma
 levels of ORACPCA (P=0.020) and F2-isoP (P=0.145). Multivariate binary
 logistic regression demonstrated that lnF2-isoP (OR 2.44 95% CI 1.19-4.98;
 P=0.014) and lnORACPCA (OR 4.18, 95% CI 1.41-12.41; P=0.010) were
 independent predictors of &gt;20% PWI-DWI mismatch and the stricter
 mismatch definition, respectively. lnORACTOT, significantly predicted
 mismatch salvage volume (&gt;20% mismatch: P=0.010; stricter mismatch
 definition: P=0.003). Conclusions: Elevated hyperacute plasma levels of
 F2-isoP and ORAC are associated with radiographic evidence of mismatch and
 mismatch salvage in AIS subjects. If validated, these findings may add to
 our understanding of the role of oxidative stress in cerebral tissue fate
 during acute ischemia.
description: Lorenzano-S et al_EARLY
 BIOMARKERS OF ISCHEMIC PENUMBRA_Supplemental MaterialSupplemental
 Material
DOI: 10.5061/dryad.499c4j2
title: Data from: A Bayesian approach for inferring the impact of a discrete character on rates of continuous-character evolution in the presence of background-rate variation

description: Understanding how and why rates of character evolution vary across the
 Tree of Life is central to many evolutionary questions; e.g., does the
 trophic apparatus (a set of continuous characters) evolve at a higher rate
 in fish lineages that dwell in reef versus non-reef habitats (a discrete
 character)? Existing approaches for inferring the relationship between a
 discrete character and rates of continuous-character evolution rely on
 comparing a null model (in which rates of continuous-character evolution
 are constant across lineages) to an alternative model (in which rates of
 continuous-character evolution depend on the state of the discrete
 character under consideration). However, these approaches are susceptible
 to a "straw-man" effect: the influence of the discrete character
 is inflated because the null model is extremely unrealistic. Here, we
 describe MuSSCRat, a Bayesian approach for inferring the impact of a
 discrete trait on rates of continuous-character evolution in the presence
 of alternative sources of rate variation ("background-rate
 variation"). We demonstrate by simulation that our method is able to
 reliably infer the degree of state-dependent rate variation, and show that
 ignoring background-rate variation leads to biased inferences regarding
 the degree of state-dependent rate variation in grunts (the fish group
 Haemulidae).
description: musscrat_dryadSupplemental data and scripts.
DOI: 10.5281/zenodo.18392978
title: РЕСПУБЛИКАМИЗ ҲУДУДЛАРИДА САБЗИ ПУШТАСИНИНГ ШАКЛИ ВА ЎЛЧАМЛАРИНИ ЎРГАНИШ НАТИЖАЛАРИ ВА УСЛУБЛАРИ

description: Ушбу мақолада илдиз меваларни ковлашнинг ҳозирги ҳолати, Тошкент вилояти Янги йўл туманининг тупроқ шароитлари ҳамда сабзи пушталари ўрганилиб, сабзининг пушталарда жойлашувига оид маълумот келтирилган.
DOI: 10.5281/zenodo.18392977
title: РЕСПУБЛИКАМИЗ ҲУДУДЛАРИДА САБЗИ ПУШТАСИНИНГ ШАКЛИ ВА ЎЛЧАМЛАРИНИ ЎРГАНИШ НАТИЖАЛАРИ ВА УСЛУБЛАРИ

description: Ушбу мақолада илдиз меваларни ковлашнинг ҳозирги ҳолати, Тошкент вилояти Янги йўл туманининг тупроқ шароитлари ҳамда сабзи пушталари ўрганилиб, сабзининг пушталарда жойлашувига оид маълумот келтирилган.
DOI: 10.5061/dryad.04df893
title: Data from: Cumulative Gadodiamide administration leads to brain Gadolinium deposition in early MS

description: Objective: Frequent administration of gadolinium-based contrast agents in
 multiple sclerosis (MS) may increase signal intensity (SI) unenhanced
 T1-WI MRI throughout the brain. We evaluated the association between
 lifetime cumulative doses of gadodiamide administration and increased SI
 within the dentate nucleus (DN), globus pallidus (GP) and thalamus in
 patients with early MS. Methods: 203 (107 with baseline and follow-up MRI
 assessments) MS patients, and 262 age- and sex-matched controls were
 included in this retrospective, longitudinal, 3T MRI-reader-blinded study.
 MS patients had disease duration &lt;2 years at baseline and received
 exclusively gadodiamide at all MRI time points. SI ratio (SIR) to pons and
 cerebrospinal fluid of lateral ventricle volume (CSF-LVV) were assessed.
 Analysis of covariance and correlation analyses, adjusted for age, sex and
 region of interest volume, were used. Results: The mean follow-up time was
 55.4 months, and the mean number of GBCA administrations was 9.2. At
 follow-up, 49.3% MS patients and no controls showed DN T1 hyperintensity
 (p&lt;0.001). The mean SIR of DN (p&lt;0.001) and of GP (p=0.005)
 to pons and the mean SIR of DN, GP and thalamus to CSF-LVV were higher in
 MS patients compared to controls (p&lt;0.001). SIR of DN to pons was
 associated with number of gadodiamide doses (p&lt;0.001). No
 associations between SIR of DN, GP and thalamus, and clinical and MRI
 outcomes of disease severity were detected over the follow-up.
 Conclusions: DN, GP and thalamus gadolinium deposition in early MS is
 associated with lifetime cumulative gadodiamide administration without
 clinical or radiological correlates of more aggressive disease.
description: Supplement Figure
 1Supplement Figure
 2Supplement Table
 1Supplement Table
 2
DOI: 10.5061/dryad.37qt6nm
title: Data from: Sex-specific effects of fisheries and climate on the demography of sexually dimorphic seabirds

description: 1. Many animal taxa exhibit sex-specific variation in ecological traits,
 such as foraging and distribution. These differences could result in
 sex-specific responses to change, but such demographic effects are poorly
 understood. 2. Here we test for sex-specific differences in the demography
 of northern (NGP, Macronectes halli) and southern (SGP, M. giganteus)
 giant petrels - strongly sexually size-dimorphic birds that breed
 sympatrically at South Georgia, South Atlantic Ocean. Both species feed at
 sea or on carrion on land, but larger males (30% heavier) are more reliant
 on terrestrial foraging than the more pelagic females. Using multi-event
 mark-recapture models we examine the impacts of long-term changes in
 environmental conditions and commercial fishing on annual adult survival
 and use two-sex matrix population models to forecast future trends. 3. As
 expected, survival of male NGP was positively affected by carrion
 availability, but negatively affected by zonal winds. Female survival was
 positively affected by meridional winds and El Niño Southern Oscillation
 (ENSO), and negatively affected by sea ice concentration and pelagic
 longline effort. Survival of SGPs did not differ between sexes; however,
 survival of males only was positively correlated with the Southern Annular
 Mode (SAM). 4. Two-sex population projections indicate that future
 environmental conditions are likely to benefit giant petrels. However, any
 potential increase in pelagic longline fisheries could reduce female
 survival and population growth. 5. Our study reveals that sex-specific
 ecological differences can lead to divergent responses to environmental
 drivers (i.e. climate and fisheries). Moreover, because such effects may
 not be apparent when all individuals are considered together, ignoring sex
 differences could underestimate the relative influence of a changing
 environment on demography.
description: Northern giant petrels
 encounter historiesThe files contain the
 individual capture-mark-recapture encounter histories of northern giant
 petrels breeding at Bird Island (South Georgia), from 2000 to 2014
 breeding seasons, where “0” denotes not encountered, “1” encountered as a
 successful breeder and “2” encountered as a failed breeder. The 16th and
 17th columns indicate if a bird is a male or a female,
 respectively..NGP_encounter_histories.txtSouthern giant petrels encounter historiesThe files contain the individual capture-mark-recapture encounter histories of southern giant petrels breeding at Bird Island (South Georgia), from 2000 to 2014 breeding seasons, where “0” denotes not encountered, “1” encountered as a successful breeder and “2” encountered as a failed breeder. The 16th and 17th columns indicate if a bird is a male or a female, respectively..SGP_encounter_histories.txt
DOI: 10.5061/dryad.sb5844c
title: Data from: Biotic and abiotic factors driving the diversification dynamics of Crocodylia

description: Species diversity patterns are governed by complex interactions
 among biotic and abiotic factors over time and space, but are essentially
 the result of the diversification dynamics (differential speciation and
 extinction rates) over the long-term evolutionary history of a clade.
 Previous studies have suggested that temporal variation in global
 temperature drove long-term diversity changes in Crocodylia, a
 monophyletic group of large ectothermic organisms. We use a large database
 of crocodylian fossil occurrences (192 spp.) and body mass estimations,
 under a taxic approach, to characterize the global diversification
 dynamics of crocodylians since the Cretaceous, and their correlation with
 multiple biotic and abiotic factors in a Bayesian framework. The
 diversification dynamic of crocodylians, which appears to have originated
 in the Turonian (c. 92.5 Ma), is characterized by several phases with high
 extinction and speciation rates within a predominantly low long-term mean
 rate. Our results reveal long-term diversification dynamics of Crocodylia
 to be a highly complex process driven by a combination of biotic and
 abiotic factors which influenced the speciation and extinction rates in
 dissimilar ways. Higher crocodylian extinction rates are related to low
 body mass disparity, indicating selective extinctions of taxa at both ends
 of the body mass spectrum. Speciation rate slowdowns are noted when the
 diversity of the clade is high and the warm temperate climatic belt is
 reduced. Our finding supports the idea that temporal variations of body
 mass disparity, self-diversity, and the warm climate belt size provided
 more direct mechanistic explanations for crocodylian diversification than
 do proxies of global temperature.
description: Database_Solorzano_et_al._2019 Data for fossil ocurrences employed in our work   Electronic supplementary material_Solorzano_et_al._2019 Electronic suplemenrary materials, includes: Body size calculations (ESM_1), and diversification results and body size as time continuous variable (ESM_2).
DOI: 10.5061/dryad.33g0b1r
title: Genetic consequences of plant edaphic specialisation to solfatara fields; phylogenetic and population genetic analysis of Carex angustisquama (Cyperaceae)

description: Edaphic specialisation is one of the main drivers of plant diversification
 and has multifaceted effects on population dynamics. Carex angustisquama
 is a sedge plant growing only on heavily acidified soil in solfatara
 fields, where only extremophytes can survive. Because of the lack of
 closely related species in similar habitats and its disjunct distribution,
 the species offers ideal settings to investigate the effects of adaptation
 to solfatara fields and historical biogeography on genetic consequences of
 plant edaphic specialisation to solfatara fields. Here, genome-wide
 single-nucleotide polymorphisms were used to reveal the phylogenetic
 origin of C. angustisquama, and 16 expressed sequence tag–simple sequence
 repeat markers were employed to infer population demography of C.
 angustisquama. Molecular phylogenetic analysis strongly indicated that C.
 angustisquama formed a monophyletic clade with C. doenitzii, a species
 growing on non-acidified soil in sympatric sub-alpine zone. The result of
 population genetic analysis showed that C. angustisquama possesses much
 lower genetic diversity than the sister species, and notably, all 16 loci
 were completely homozygous in most individuals of C. angustisquama.
 Approximate Bayesian computation analysis supported the model that assumed
 hierarchical declines of population size through its evolutionary
 sequence. We propose that the edaphic specialist in solfatara fields has
 newly attained the adaptation to solfatara fields in the process of
 speciation. Furthermore, we found evidence of a drastic reduction in
 genetic diversity in C. angustisquama, suggesting that the repeated
 founder effects associated with edaphic specialisation and subsequent
 population demography bring the loss of genetic diversity to the
 extremophyte in solfatara fields.
description: GenALex_Dryad_SubmitGenotypic data obtained by 16 EST-SSR markers was submitted in GenALex format.
DOI: 10.5061/dryad.dj5g9v3
title: Data from: A lattice Boltzmann model for the open channel flows described by the Saint-Venant equations

description: A new lattice Boltzmann method to simulate open channel flows with complex
 geometry described by a conservative form of Saint-Venant equations
 (LBCSVE) is developed. The Saint–Venant equations include an original
 treatment of the momentum equation source term. Concrete hydrostatic
 pressure thrust expressions are provided for rectangular, trapezoidal and
 irregular cross-section shapes. A D1Q3 lattice arrangement is adopted.
 External forces, such as bed friction and the static term, are discretised
 with a centred scheme. Bounce back and imposed boundary conditions are
 considered. To verify the LBCSVE model, four cases are carried out: tidal
 flow over a regular bed in a rectangular cross section, steady flow in a
 channel with horizontal and vertical contractions, steady flow over a bump
 in a trapezoidal channel and steady flow in a non-prismatic channel with
 friction. Results indicate that the proposed scheme is simple and can
 provide accurate predictions for open channel flows.
description: velocity data of section
 4.1Data for the figure
 5(b)water level data of
 section 4.1data for the figure
 5(a)water level data of
 section 4.2data for figure
 7(a)velocity data of section
 4.2data for figure
 7(b)water level data of
 section 4.3data for figure
 9(a)wetted area data of
 section 4.3data for figure
 9(b)water level data of
 section 4.4data for figure
 12fortran
 codefortran code for the
 LBCSVE model