Find research datasets worth reusing

Raising offspring increases ageing: Differences in senescence among three populations of a long-lived seabird, the Atlantic puffin

1. Actuarial senescence, the decline of survival with age, is well documented in the wild. Rates of senescence vary widely between taxa, to some extent also between sexes, with the fastest life histories showing the highest rates of senescence. Few studies have investigated differences in senescence among populations of the same species, although such variation is expected from population-level differences in environmental conditions, leading to differences in vital rates and thus life histories. 2. We predict that, within species, populations differing in productivity (suggesting different paces of life) should experience different rates of senescence, but with little or no sexual difference in senescence within populations of monogamous, monomorphic species where the sexes share breeding duties. 3. We compared rates of actuarial senescence among three contrasting populations of the Atlantic puffin Fratercula arctica. The data set comprised 31 years (1990–2020) of parallel capture-mark-recapture data from three breeding colonies, Isle of May (North Sea), Røst (Norwegian Sea) and Hornøya (Barents Sea), showing contrasting productivities (i.e. annual breeding success) and population trends. We used time elapsed since first capture (TFC) as a proxy for bird age, and productivity and the winter North Atlantic Oscillation Index (wNAO) as proxies for the environmental conditions experienced by the populations within and outside the breeding season, respectively. 4. In accordance with our predictions, we found that senescence rates differed among the study populations, with no evidence for sexual differences. There was no evidence for an effect of wNAO, but the population with the lowest productivity, Røst, showed the lowest rate of senescence. As a consequence, the negative effect of senescence on the population growth rate (λ) was up to 3–5 times smaller on Røst (Δλ = -0.009) than on the two other colonies. 5. Our findings suggest that environmentally induced differences in senescence rates among populations of a species should be accounted for when predicting effects of climate variation and change on species persistence. There is thus a need for more detailed information on how both actuarial and reproductive senescence influence vital rates of populations of the same species, calling for large-scale comparative studies.

Sex-specific paternal age effects on offspring quality in Drosophila melanogaster

Advanced paternal age has been repeatedly shown to modulate offspring quality via male- and/or female-driven processes, and there are theoretical reasons to expect that some of these effects can be sex-specific. For example, sex allocation theory predicts that, when mated with low-condition males, mothers should invest more in their daughters compared to their sons. This is because male fitness is generally more condition-dependent and more variable than female fitness, which makes it less risky to invest in female offspring. Here, we explore whether paternal age can affect the quality and quantity of offspring in a sex-specific way using Drosophila melanogaster as model organism. In order to understand the contribution of male-driven processes on paternal age effects, we also measured the seminal vesicle size of young and older males and explored its relationship with reproductive success and offspring quality. Older males had lower competitive reproductive success, as expected, but there was no difference between the offspring sex ratio of young and older males. However, we found that paternal age caused an increase in offspring quality (i.e., offspring weight), and that this increase was more marked in daughters than sons. We discuss different male- and female-driven processes that may explain such sex-specific paternal age effects.

Age-dependent genetic variation in aggression

Understanding the extent to which behavioural variance is underlain by genotypic, environmental and genotype-by-environment effects is important for predicting how behavioural traits might respond to selection and evolve. How behaviour varies both within and among individuals can change across ontogeny, leading to differences in the relative contribution of genetic and environmental effects to phenotypic variation across ages. We investigated among-individual and among-genotype variation in aggression across ontogeny by measuring, twice as juveniles and twice as adults, both approaches and attacks against a three-dimensional-printed model opponent in eight individuals from each of eight genotypes ( N = 64). Aggression was only significantly repeatable and heritable in juveniles. Additionally, how aggression changed between juvenile and adult life-history stages varied significantly among individuals and genotypes. These results suggest that juvenile aggression is likely to evolve more rapidly via natural selection than adult aggression and that the trajectory of behavioural change across the lifespan has the potential to evolve. Determining when genetic variation explains (or does not explain) behavioural variation can further our understanding of key life-history stages during which selection might drive the strongest or swiftest evolutionary response.

Data from: Validation of Quality-of-Life assessment tool for Ethiopian old age people

Background: Reliable quality of life assessment is critical for identifying health issues, evaluating health interventions, and establishing the best health policies and care packages. The World Health Organization Quality of Life-Old Module is a tool for assessing the subjective quality of life in old age people. It's validated and available in more than 20 languages, except Amharic. Hence, this study was intended to translate it into Amharic language and validate it among old age people in Ethiopia. Methods: A cross-sectional study was conducted among 180 community-dwelling old age people in Ethiopia, from January 16 to March 13, 2021. Psychometric validation was achieved through Cronbach's alpha of the internal consistency reliability test, and construct validity from confirmatory factor analysis. Results: The study participants aged from 60 to 90 years old with a mean age of 69.44. Females made up 61.7% of the population, and 40% of them could not read and write. The results showed a relatively low level of quality of life, with the total transformed score of 58.58 ± 23.15. The Amharic version of the World Health Organization Quality of Life-Old Module showed a Cronbach's Alpha value of 0.96 and corrected item-total correlations of more than 0.74. Confirmatory factor analysis confirmed the six-factor model with a chi-square (X2) of 341.98 with a p-value less than 0.001. The comparative fit index (CFI) was 0.98, Tucker-Lewis's index (TCL) was 0.97, and the root mean square error of approximation (RMSEA) was 0.046. Conclusion: The Amharic version of the World Health Organization Quality of Life-Old Module indicated good internal consistency reliability and construct validity. The tool can be utilized to provide care to Ethiopian community-dwelling old age people.

opencc-by-4.0Feb 2023View details →

Fig. 2 in Deep time extinction of largest insular ant predators and the first fossil Neoponera (Formicidae: Ponerinae) from Miocene age Dominican amber

Fig. 2 Artistic reconstruction of Neoponera vejestoria sp. nov. Artist: Minsoo Dong

opencc-zeroFeb 2023View details →

Data from: Aging and memory are altered by genetically manipulating lactate dehydrogenase in the neurons or glia of flies

The astrocyte-neuron lactate shuttle hypothesis posits that glial-generated lactate is transported to neurons to fuel metabolic processes required for long-term memory. Although studies in vertebrates have revealed that lactate shuttling is important for cognitive function, it is uncertain if this form of metabolic coupling is conserved in invertebrates or is influenced by age. Lactate dehydrogenase (Ldh) is a rate-limiting enzyme that interconverts lactate and pyruvate. Here we genetically manipulated expression of Drosophila melanogaster lactate dehydrogenase (dLdh) in neurons or glia to assess the impact of altered lactate metabolism on invertebrate aging and long-term courtship memory at different ages. We also assessed survival, negative geotaxis, brain-neutral lipids (the core component of lipid droplets), and whole head metabolites. Both upregulation and downregulation of dLdh in neurons resulted in decreased survival and memory impairment with age. Glial downregulation of dLdh expression caused age-related memory impairment without altering survival, while upregulated glial dLdh expression lowered survival without disrupting memory. Both neuronal and glial dLdh upregulation increased neutral lipid accumulation. We provide evidence that altered lactate metabolism with age affects the tricarboxylic acid (TCA) cycle, 2-hydroxyglutarate (2HG), and neutral lipid accumulation. Collectively, our findings indicate that the direct alteration of lactate metabolism in either glia or neurons affects memory and survival but only in an age-dependent manner.

opencc-by-4.0Feb 2023View details →

Aerogel Spring-Back Correlates with Strain Recovery: Effect of Silica Concentration and Aging - Dataset

Dataset corresponding to the scientific publication: Sivaraman, Deeptanshu, Shanyu Zhao, Subramaniam Iswar, Marco Lattuada, and Wim J. Malfait. "Aerogel Spring‐Back Correlates with Strain Recovery: Effect of Silica Concentration and Aging." Advanced Engineering Materials 23, no. 10 (2021): 2100376. <a href="https://doi.org/10.1002/adem.202100376">https://doi.org/10.1002/adem.202100376</a> This project was funded by the Swiss National Science Foundation through grant 200021_179000 (W.J.M). S.I. acknowledges the Flemish agency “Agentschap Innoveren en Ondernemen” (VLAIO) for providing financial support of this research through subvention IWT 130668.

Nowhere to escape: The cross-age avian haemosporidian exposure of migrants in Northeast China

Pathogen infection has been progressively recognized as a potential driver of animal migration, and the infection pattern in a certain host may be related to its migration status. Nestling viability can be a crucial life stage in the evolution of the migration cycle but has been irregularly studied to date. In this study, we tested the 'migratory exposure' hypothesis by comparing the prevalence and diversity of avian haemosporidian parasites in the breeding area between two dominant species including adults and nestlings: yellow-rumped flycatcher (Ficedula zanthopygia), which is a summer migratory species, and Japanese tit (Parus minor), which is a local resident species. The yellow-rumped flycatcher harboured more diverse parasite lineages than the Japanese tit, which is in line with the expectation of the 'migratory exposure' hypothesis, while nestlings present a similar but more applicable pattern. Among the 40 unique identified parasite lineages, only one was shared between host species and three between age classes. Nestlings suffered a high parasite diversity with plenty of age-specific lineages in the breeding area, mainly Leucocytozoon, which may suggest an extraordinary selection pressure in the life-stages not just for adults during migration. However, the most common lineages in adults were not detected in nestlings, and the prevalence of infection is significantly lower in nestlings than in adults. Our results suggest that migratory birds may have suffered from more frequent parasite infections during migration, but escaped from more virulent lineages at the same time. The difference in susceptibility and parasite assembly between adults and nestlings in migrants may result from an intricate interaction along the evolution of life history. Our investigations have revealed the significance of avian haemosporidian parasite infection patterns in nestlings in breeding areas, and provide a novel insight into the driving forces of migration.

opencc-by-4.0Mar 2023View details →

Three dimensional reconstruction of an existing age-old wooden shingle roof

This dataset provides a complete and thorough three-dimensional reconstruction of an age-old shingled roof located in Rossinière, Switzerland (<a href="https://www.google.com/maps/dir//46.468247,7.059739/@46.4670828,7.012801,12z/data=!4m2!4m1!3e0">46.46837286488975, 7.059749511857417</a>), which provides reliable documentation to archive this valuable type of architecture. This dataset was obtained using a 3D Farco Focus scanner and the point clouds were processed using FaroScene software. This research was funded by the National Centres of Competence in Research (<a href="https://www.snf.ch/en/FJBJ8XGQ1tjG8J8w/funding/programmes/national-centres-of-competence-in-research-nccr">NCCRs</a>) and EPFL.

Genetic insights into the age-specific biological mechanisms governing human ovarian ageing

There is currently little evidence that the genetic basis of human phenotype varies significantly across the lifespan. However, time-to-event phenotypes are understudied and can be thought of as reflecting an underlying hazard, which is unlikely to be constant through life when values take a broad range. Here, we find that 74% of 245 genome-wide significant genetic associations with age at natural menopause (ANM) in the UK Biobank show a form of age-specific effect. Nineteen of these replicated discoveries are identified only by our modelling framework, which determines the time-dependency of DNA variant-age-at-onset associations, without a significant multiple-testing burden. Across the range of early to late menopause, we find evidence for significantly different underlying biological pathways, changes in the sign of genetic correlations of ANM to health indicators and outcomes, and differences in inferred causal relationships. We find that DNA damage response processes only act to shape ovarian reserve and depletion for women of early ANM. Genetically mediated delays in ANM were associated with increased relative risk of breast cancer and leiomyoma at all ages, and with high cholesterol and heart failure for late-ANM women. These findings suggest that a better understanding of the age-dependency of genetic risk factor relationships among health indicators and outcomes is achievable through appropriate statistical modelling of large-scale biobank data.

Age estimation based on blood DNA methylation levels in brown bears

Age is an essential trait for understanding the ecology and management of wildlife. A conventional method of estimating age in wild animals is counting annuli formed in the cementum of teeth. This method has been used in bears despite some disadvantages, such as high invasiveness and the requirement for experienced observers. In this study, we established a novel age estimation method based on DNA methylation levels using blood collected from 49 brown bears of known ages living in both captivity and the wild. We performed bisulfite pyrosequencing and obtained methylation levels at 39 cytosine-phosphate-guanine (CpG) sites adjacent to 12 genes. The methylation levels of CpGs adjacent to four genes showed a significant correlation with age. The best model was based on DNA methylation levels at just four CpG sites adjacent to a single gene, SLC12A5, and it had high accuracy with a mean absolute error of 1.3 years and median absolute error of 1.0 year after leave-one-out cross-validation. This model represents the first epigenetic method of age estimation in brown bears, which provides benefits over tooth-based methods, including high accuracy, less invasiveness, and a simple procedure. Our model has the potential for application to other bear species, which will greatly improve ecological research, conservation, and management.

Data from: Mitochondrial function declines with age within individuals but is not linked to the pattern of growth or mortality risk in zebra finch

Mitochondrial dysfunction is considered a highly conserved hallmark of ageing. However, most studies in both model and non-model organisms are cross-sectional in design; therefore, little is known, at the individual level, on how mitochondrial function changes with age, its link to early developmental conditions or its relationship with survival. Here we manipulated the postnatal growth in zebra finches (Taeniopygia guttata) via dietary modification that induced accelerated growth without changing adult body size. In the same individuals, we examined blood cells mitochondrial functioning (mainly erythrocytes) when they were young (ca 36 weeks) and again in mid-aged (ca 91 weeks) adulthood. Mitochondrial function was strongly influenced by age but not by postnatal growth conditions. Across all groups, within individual ROUTINE respiration, OXPHOS and OXPHOS coupling efficiency significantly declined with age, while LEAK respiration increased. However, we found no link between mitochondrial function and the probability of survival into relatively old age (ca 4 years). Our results suggests that the association between accelerated growth and reduced longevity, evident in this as in other species, is not attributable to age-related changes in any of the measured mitochondrial function traits.

opencc-zeroApr 2023View details →

Ancient bears provide insights into Pleistocene ice age refugia in Southeast Alaska

During the Late Pleistocene, major parts of North America were periodically covered by ice sheets. However, there are still questions about whether ice-free refugia were present in the Alexander Archipelago along the Southeast (SE) Alaska coast during the Last Glacial Maximum (LGM). Numerous subfossils have been recovered from caves in SE Alaska, including American black (Ursus americanus) and brown (U. arctos) bears, which today are found in the Alexander Archipelago but are genetically distinct from mainland bear populations. Hence, these bear species offer an ideal system to investigate long-term occupation, potential refugial survival, and lineage turnover. Here we present genetic analyses based on 99 new complete mitochondrial genomes from ancient and modern brown and black bears spanning the last ~45,000 years. Black bears form two SE Alaskan subclades that diverged >100,00 years ago, one preglacial and one postglacial. All postglacial ancient brown bears are closely related to modern brown bears in the archipelago, while a single preglacial brown bear is found in a distantly related clade. A hiatus in the bear subfossil record around the LGM and the deep split of their pre- and post-glacial subclades fail to support a hypothesis of continuous occupancy in SE Alaska throughout the LGM for either species. Our results are consistent with an absence of refugia along the SE Alaska coast but indicate that vegetation quickly expanded after deglaciation, allowing bears to recolonize the area after a short-lived LGM peak.

opencc-by-4.0Mar 2023View details →

Impact of monthly age model on coral paleothermometer fidelity: Insights from the northern South China Sea

The repository includes an Excel file and text file that was embedded in the submitted manuscript of  'Impact of monthly age model on coral paleothermometer fidelity: Insights from the northern South China Sea'. The Excel file includes two raw coral sr/ca records that has been published (https://doi.org/10.1177/0959683609337355;  https://doi.org/10.1029/2020PA004173);  The txt file includes python code for the manuscript.

opencc-by-4.0Apr 2023View details →

Dataset for " 4D nanoimaging of early age cement hydration " Nature Communications paper

Abstract of the Nature Communications paper (doi: <a href="https://doi.org/10.1038/s41467-023-38380-1" target="_blank" rel="noopener">https://doi.org/10.1038/s41467-023-38380-1</a>) from this dataset is: "Despite a century of research, our understanding of cement dissolution and precipitation processes at early ages is very limited. This is due to the lack of methods that can image these processes with enough spatial resolution, contrast and field of view. Here, we adapt near-field ptychographic nanotomography to in situ visualise the hydration of commercial Portland cement in a record-thick capillary. At 19h, porous C-S-H gel shell, thickness of 500 nm, covers every alite grain enclosing a water gap. The spatial dissolution rate of small alite grains in the acceleration period, &sim;100 nm/h, is approximately four times faster than that of large alite grains in the deceleration stage, &sim;25 nm/h. Etch-pit development has also been mapped out. This work is complemented by laboratory and synchrotron microtomographies, allowing to measure the particle size distributions with time. 4D nanoimaging will allow mechanistically study dissolution-precipitation processes including the roles of accelerators and superplasticizers. "

opencc-zeroMay 2023View details →

Data from: Compensatory growth is accompanied by changes in insulin-like growth factor-1 but not markers of cellular aging in a long-lived seabird

Developing organisms often plastically modify growth in response to environmental circumstances, which may be adaptive, but is expected to entail long-term costs. However, the mechanisms that mediate these growth adjustments and any associated costs are less well understood. In vertebrates, one mechanism that may be important in this context is the highly conserved signaling factor insulin-like growth factor-1 (IGF-1), which is often positively related to post-natal growth and negatively related to longevity. To test this idea, we exposed captive Franklin's gulls (Leucophaeus pipixcan) to a physiologically relevant nutritional stressor by restricting food availability during post-natal development and examined the effects on growth, IGF-1, and two potential biomarkers of cellular and organismal aging (oxidative stress, and telomeres). During food restriction, experimental chicks gained body mass more slowly and had lower IGF-1 levels than controls. Following the food restriction, experimental chicks underwent compensatory growth, which was accompanied by an increase in IGF-1 levels. Interestingly however, there were no significant effects of the experimental treatment or of variation in IGF-1 levels on oxidative stress or telomeres. These findings suggest that IGF-1 is responsive to changes in resource availability but is not associated with increased markers of cellular aging during development in this relatively long-lived species.

opencc-zeroMay 2023View details →

Fire severity as a key determinant of aboveground and belowground biological community recovery in managed even-aged boreal forests

Changes in fire regime of boreal forests in response to climate warming are expected to impact post-fire recovery. However, quantitative data on how managed forests sustain and recover from recent fire disturbance are limited. Two years after a large wildfire in managed even-aged boreal forests in Sweden, we investigated how recovery of aboveground and belowground communities, i.e., understory vegetation and soil microbial and faunal communities, responded to variation in the severity of soil (i.e., consumption of soil organic matter) and canopy fires (i.e., tree mortality). While fire overall enhanced diversity of understory vegetation through colonization of fire adapted plant species, it reduced the abundance and diversity of soil biota. We observed contrasting effects of tree- and soil-related fire severity on survival and recovery of understory vegetation and soil biological communities. Severe fires that killed overstory Pinus sylvestris promoted a successional stage dominated by the mosses Ceratodon purpureus and Polytrichum juniperum, but reduced regeneration of tree seedlings and disfavoured the ericaceous dwarf-shrub Vaccinium vitis-idaea and the grass Deschampsia flexuosa. Moreover, high tree mortality from fire reduced fungal biomass and changed fungal community composition, in particular that of ectomycorrhizal fungi, and reduced the fungivorous soil Oribatida. In contrast, soil-related fire severity had little impact on vegetation composition, fungal communities and soil animals. Bacterial communities responded to both tree- and soil-related fire severity. Synthesis: Our results two years post-fire suggest that a change in fire regime from a historically low-severity ground-fire regime, with fires that mainly burns into the soil organic layer, to a stand-replacing fire regime with a high degree of tree mortality, as may be expected with climate change, is likely to impact the short-term recovery of stand structure and above- and belowground species composition of even-aged P. sylvestris boreal forests.

opencc-by-4.0Dec 2022View details →

Edited Abalone Age dataset

Categorical data has been one-hot encoded which makes it ready for running experiments with e.g. KNN.

opencc-by-4.0May 2023View details →

Tailored machine learning for evaluating the long-term diabetes risk in older individuals: Findings from The Irish Longitudinal Study on Ageing (TILDA)

The original data for "Tailored machine learning for evaluating the long-term diabetes risk in older individuals: Findings from The Irish Longitudinal Study on Ageing (TILDA)" that published in BMJ Open.