Find research datasets worth reusing

opencc-zeroSep 2012View details →

FIG. 3 in Hypsodont Myomiminae (Gliridae, Rodentia) from five new localities in the Lower Miocene Tudela Formation (Bardenas Reales, Ebro Basin, Spain) and their bearing on the age of the Agenian-Ramblian boundary

FIG. 3. — Distribution chart of the Myomiminae species studied in this paper and in Daams (1990). The succession of the localities from Daams (1990) is, though in stratigraphical order, not calibrated.

CLaMS results used for age of air analysis in the report of assessment of the ESA Earth Explorer candidate mission CAIRT

Results of the Chemical Lagrangian Model of the Stratosphere (CLaMS) used for age of air analysis in the report of assessment of the ESA Earth Explorer candidate mission CAIRT. Days of results: 2011-01-01, 2011-04-01, 2011-07-01, 2011-10-01 and 2019-09-23. Included trace gases: SF6, CFC-11, CFC-12, HCFC-22, N2O and CH4. The results also include the clock tracer BA, which can be converted into the precise mean age of or air of the model environment with the attached python script 'AOA2age_years.py'.

Data from: Methylation-based markers for the estimation of age in African Cheetah, Acinonyx jubatus

This is a dataset for methylation analyses in cheetah done by EpiTYPER mass array.

Sex and Age Impact CD4+ T Cell Susceptibility to HIV In Vitro Through Cell Activation Dynamics

Cellular composition and the responsiveness of the immune system evolve upon aging and are influenced by biological sex. CD4+ T cells from women living with HIV exhibit a decreased viral replication ex vivo compared to men's. We, thus, hypothesized that these findings could be recapitulated in vitro and infected primary CD4+ T cells with HIV-based vectors pseudotyped with VSV-G or HIV envelopes. We used cells isolated from twenty donors to interrogate the effect of sex and age on permissiveness over a six-day activation kinetics. Our data identified an increased permissiveness to HIV between 24 and 72 h post-stimulation. Sex- and age-based analyses at these time points showed an increased susceptibility to HIV of the cells isolated from males and from donors over 50 years of age, respectively. A parallel assessment of surface markers' expression revealed higher frequencies of activation marker CD69 and of immune checkpoint inhibitors (PD-1 and CTLA-4) in the cells from highly permissive donors. Furthermore, positive correlations were identified between the expression kinetics of CD69, PD-1 and CTLA-4 and HIV expression kinetics. The cell population heterogeneity was assessed using a single-cell RNA-Seq analysis and no cell subtype enrichment was identified according to sex. Finally, transcriptomic analyses further highlighted the role of activation in those differences with enriched activation and cell cycle gene sets in male and older female cells. Altogether, this study brought further evidence about the individual features affecting HIV replication at the cellular level and should be considered in latency reactivation studies for an HIV cure.

opencc-zeroNov 2023View details →

Age estimation of captive Asian elephants (Elephas maximus) based on DNA methylation: An exploratory analysis using methylation-sensitive high-resolution melting (MS-HRM)

Age is an important parameter for bettering the understanding of biodemographic trends-development, survival, reproduction and environmental effects-critical for conservation. However, current age estimation methods are challenging to apply to many species, and no standardised technique has been adopted yet. This study examined the potential use of methylation-sensitive high-resolution melting (MS-HRM), a labour, time, and cost-effective method to estimate chronological age from DNA methylation in Asian elephants (Elephas maximus). The objective of this study was to investigate the accuracy and validation of MS-HRM use for age determination in long-lived species, such as Asian elephants. The average lifespan of Asian elephants is between 50-70 years but some have been known to survive for more than 80 years. DNA was extracted from 53 blood samples of captive Asian elephants across 11 zoos in Japan, with known ages ranging from a few months to 65 years. Methylation rates of two candidate age-related epigenetic genes, RALYL and TET2, were significantly correlated with chronological age. Finally, we established a linear, unisex age estimation model with a mean absolute error (MAE) of 7.36 years. This exploratory study suggests an avenue to further explore MS-HRM as an alternative method to estimate the chronological age of Asian elephants.

Underlying dataset for battery pack degradation - Understanding aging in parallel-connected lithium-ion batteries under thermal gradients

This record constitutes the raw data underlying the paper "Battery pack degradation - Understanding aging in parallel-connected lithium-ion batteries under thermal gradients" (<a href="https://www.researchsquare.com/article/rs-2535223/v1">preprint link</a>)The dataset contains all raw data, processed data and analysis codes used to generate figures in the publication. Abstract is as follows:<blockquote>Practical lithium-ion battery systems require parallelisation of tens to hundreds of cells, however understanding of how pack-level thermal gradients influence lifetime performance  remains a research gap. Here we present an experimental study of surface cooled parallel-string battery packs (temperature range 20-45 °C), and identify two main operational modes; convergent degradation with homogeneous temperatures, and (the more detrimental) divergent degradation driven by thermal gradients. We attribute the divergent case to the, often overlooked, cathode impedance growth. This was negatively correlated with temperature and can cause positive feedback where the impedance of cells in parallel diverge over time; increasing heterogeneous current and state-of-charge distributions. These conclusions are supported by current distribution measurements, decoupled impedance measurements and degradation mode analysis. From this, mechanistic explanations are proposed, alongside a publicly available aging dataset, which highlights the critical role of capturing cathode degradation in parallel-connected batteries; a key insight for battery pack developers.</blockquote>

opencc-by-4.0Dec 2023View details →

Brinell-Hardness (HBW 2.5/62.5) of Al-alloy EN AW-2618A after different aging times and temperatures

The dataset contains data from Brinell hardness measurements of Al-alloy EN AW-2618A after aging for different times and temperatures. Aging was either load free or with applied tensile load (creep). The investigated material and the applied methods were described in detail in two publications. Version 2.0 has been extended with additional data for further ageing temperatures. Further information is provided in the file content.pdf.

opencc-by-4.0Dec 2023View details →

Philosophy in the Age of AI: Is Synthetic Philosophy Feasible?

Talk at the <a href="https://www.digital-philosophy.org/" target="_blank" rel="noopener">Philosophy [in:of:for:and] Digital Knowledge Infrastructures</a> online workshop 2023 (28/09/2023).

opencc-zeroJan 2024View details →

Data from: A cost-effective blood DNA methylation-based age estimation method in domestic cats, Tsushima leopard cats (Prionailurus bengalensis euptilurus), and Panthera species, using targeted bisulfite sequencing and machine learning models

Knowledge of individual age can help both in-situ and ex-situ conservation programs to design more efficient and suitable management plans for targeted wildlife species. DNA methylation is one of the epigenetic aging markers that has emerged as a promising tool that can estimate age with high accuracy using only a tiny amount of biological material, which can be collected in a minimally invasive way. Here, we sequenced five targeted genetic regions and used 8–23 selected CpG sites to build age estimation models with machine learning methods with about only $3–7 per sample, using blood samples of seven Felidae species—ranging from small to big, and domestic to endangered species: domestic cats (Felis catus, 139 samples), Tsushima leopard cats (Prionailurus bengalensis euptilurus, 84 samples), and five Panthera species (96 samples). The models built achieved satisfactory accuracy—the mean absolute error of the best models was 1.966, 1.348, and 1.552 years in domestic cats, Tsushima leopard cats, and Panthera spp., respectively. Our models in domestic cats and Tsushima leopard cats were applicable to individuals regardless of health conditions, indicating the high applicability of our models to samples collected from diverse situations, e.g., rescued individuals in the context of conservation. We also showed the possibility of developing universal age estimation models for the five Panthera spp. using two of the five genetic regions, suggesting an even lower cost to use our models for future applications.

opencc-by-4.0May 2023View details →

Fig. 1 in The Original Published Description Of An Embryonic Apparatus From The Orbitolinidae (Foraminifera) (Lower Cretaceous Of Borneo) With A Brief Commentary On The Age Of Orbitolinid Occurrences In Borneo

Fig. 1 Palorbitolina lenticularis (Blumenbach) from the Lower Cretaceous of Borneo (a-b) and south-eastern France (c-e). a-b transverse section of megalospheric embryo (from Martin, 1890, pl. XXV, fig. 18; b modified: light red = protoconch; light orange = periembryonic ring or zone). c transverse section of the megalospheric embryo (from Schroeder, 1963, pl. 24, fig. 4). d view of cone base, e view of cone surface, f Side view (from Blumenbach, 1805, pl. 80, figs. 5-6, 2, without scale).

opencc-zeroJan 2024View details →

Epigenetic aging of Māui and Hector's dolphins

The age of an individual is an essential demographic parameter but is difficult to estimate without long-term monitoring or invasive sampling. Epigenetic approaches are increasingly used to age organisms, including non-model organisms such as cetaceans. Māui dolphins (Cephalorhynchus hectori maui) are a critically endangered subspecies endemic to Aotearoa New Zealand, and the age structure of this population is important for informing conservation. Here we present an epigenetic clock for aging Māui and Hector's dolphins (C. h. hectori) developed from methylation data using DNA from tooth aged individuals (n = 48). Based on this training dataset, the optimal model required only eight methylation sites, provided an age correlation of 0.95, and had a median absolute age error of 1.54 years. A leave-one-out cross-validation analysis with the same parameters resulted in an age correlation of 0.87 and median absolute age error of 2.09 years. To improve age estimate, we included previously published beluga whale (Delphinapterus leucas) data to develop a joint beluga/dolphin clock, resulting in a clock with comparable performance and improved estimation of older individuals. Application of the models to DNA from skin biopsy samples of living Māui dolphins revealed a shift in the median age of 8–9 years to a younger population aged 7–8 years 10 years later. These models could be applied to other dolphin species and demonstrate the ability to construct a clock even when the number of known age samples is limited, removing this impediment to estimating demographic parameters vital to the conservation of critically endangered species.

opencc-by-4.0Feb 2025View details →

Effect of older age and/or ACL injury on the dose–response relationship between ambulatory load magnitude and immediate load-induced change in serum cartilage oligomeric matrix protein

The data presented here was used in the models in the pulication doi <a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.jshs.2024.100993" target="_blank" rel="noreferrer noopener">https://doi.org/10.1016/j.jshs.2024.100993</a>. The purpose of this study was to assess the influence of age, anterior cruciate ligament (ACL) injury, and sex on resting sCOMP concentration, on the immediate load-induced sCOMP kinetics after a 30-minute treadmill walking stress, and on the dose-response relationship between ambulatory load magnitude and the load-induced sCOMP change. Overall, data of 85 participants in four groups (20–30 years healthy, HEA20–30, n=24; 20–30 years ACL-injured, ACL20–30, n=23; 40–60 years healthy, HEA40–60, n=23; 40–60 years ACL-injured, ACL40–60, n=15) were included in this dataset. ACL injured participants suffered from an ACL injury 2-10 years prior to inclusion. The dateaset includes, patient data and serum cartilage oligomeric matrix protein (sCOMP) concentration measured on three testdays (m1, m2, m3) immediately before (t0) and immediately after 30 minutes of treadmill walking (t1) where the ambulatory loads were 80% bodyweight (BW), 100% BW or 120% BW (block randomized order). This dateset represents a subset of data collected in the parent study. The detailed experimental protocol of the parent study has been described in Herger, S., Vach, W., Nüesch, C., Liphardt, A. M., Egloff, C., & Mündermann, A. (2022). Dose-response relationship of in vivo ambulatory load and mechanosensitive cartilage biomarkers—The role of age, tissue health and inflammation: A study protocol. PLoS One, 17(8), e0272694. <a href="https://doi.org/10.1371/journal.pone.0272694">https://doi.org/10.1371/journal.pone.0272694</a>

opencc-by-4.0Mar 2024View details →

Title: Health-Related Quality of Life and DNA Methylation-Based Aging Biomarkers among Survivors of Childhood Cancer

Abstract Background: Childhood cancer survivors are at high risk for morbidity and mortality and poor patient-reported outcomes, typically health-related-quality-of-life (HRQOL). However, associations between DNA methylation (DNAm)-based aging biomarkers and HRQOL have not been evaluated. Methods: DNAm was generated with Infinium EPIC BeadChip on blood-derived DNA (median[range] for age at blood draw=34.5[18.5-66.6] years) and HRQOL was assessed with age at survey (32.3[18.4-64.5] years) from 2,206 survivors in the St. Jude Lifetime Cohort. DNAm-based aging biomarkers, including epigenetic age using multiple clocks (e.g., GrimAge) and others (e.g., DNAmB2M: beta-2-microglobulin; DNAmADM: adrenomedullin), were derived from the DNAm Age Calculator (https://dnamage.genetics.ucla.edu). HRQOL was assessed using the Medical Outcomes Study 36-Item Short-Form Health Survey to capture eight domains, and physical and mental component summaries (PCS and MCS). General linear models evaluated associations between HRQOL and epigenetic age acceleration (EAA, e.g., EAA_GrimAge) or other age-adjusted DNAm-based biomarkers (e.g., ageadj_DNAmB2M) after adjusting for age at blood draw, sex, cancer treatments, and DNAm-based surrogate for smoking pack-years. All P values were 2-sided. Results: Worse HRQOL was associated with greater EAA_GrimAge (PCS: β[95%CI]=-0.18[-0.251,-0.11] years, P=1.85×10-5; and four individual HRQOL domains), followed by ageadj_DNAmB2M (PCS: -0.08[-0.124,-0.037], P=0.003; and three individual HRQOL domains), and ageadj_DNAmADM (PCS: -0.082[-0.125,-0.039], P=0.002; and two HRQOL domains). EAA_Hannum (Hannum clock) was not associated with any HRQOL. Conclustion: Overall and domain-specific measures of HRQOL are associated with DNAm measures of biological aging. Future longitudinal studies should test biological aging as a potential mechanism.

opencc-zeroMar 2024View details →

Data from: Sleep and subjective age: Protect your sleep if you want to feel young

The current studies examined the impact of insufficient sleep and sleepiness on the subjective experience of age. Study 1, a cross-sectional study of 429 participants (282 females (66%), 144 males, 3 other; age range 18-70) showed that for each additional day of insufficient sleep in the last 30 days, subjective age increased by 0.23 years. Study 2, an experimental crossover sleep restriction study (N = 186; 102 females (55%); 84 males; age range 18-46) showed that two nights of sleep restriction (4h in bed/night) made people feel 4.44 years older compared to sleep saturation (9h in bed/night). Additionally, moving from feeling extremely alert (KSS score of 1) to feeling extremely sleepy (KSS score of 9) was associated with feeling 10 years older in both studies. These findings provide compelling support for insufficient sleep and sleepiness to exert a substantial influence on how old we feel, and that safeguarding sleep is likely a key factor in feeling young.

opencc-by-4.0Mar 2024View details →

DNA methylation in sperm of rats at two ages exposed or not to 2,2',4,4'-tetrabromodiphenyl ether

Introduction This study was designed to determine the potential of environmentally relevant levels of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) to induce age-dependent changes in a rat’s sperm epigenome. The methods used to generate the files are described below.   Experimental design Twelve seven-week-old pregnant Wistar rats were divided into two groups (6 per group) – control and BDE-47 exposed group. Between pregnancy day 8 and postnatal day 21 (PND21), dams in each group were fed from the tip of pipette 0.2 µL/g body weight of the vehicle (tocopherol-stripped corn oil) or the same volume of a 1 mg/mL solution of BDE-47 daily. The BDE-47 group resulted in an exposure level of 0.2 mg/kg body weight of BDE-47 per day. On PND65 and PND120, one male pup randomly selected from each litter was euthanized, and epididymal motile spermatozoa were collected via the swim-up procedure as described in detail elsewhere (Suvorov et al., 2018). Sperm DNA was extracted using the rapid method (Wu et al., 2015). Extracted sperm DNA was subjected to reduced representation bisulfite sequencing (RRBS).   Reduced representation bisulfite sequencing For RRBS, bisulfite-converted libraries were prepared from 100 ng of the sperm DNA using Ovation RRBS Methyl-Seq System and EpiTect Fast DNA Bisulfite Kit (Cat. #59824, Qiagen) following manufacturers’ protocols. Sequencing of libraries was done using the HiSeq 2500 sequencing system (Illumina) in Deep Sequencing Core Facility of the University of Massachusetts Medical School (Schrewsbury, MA) with an average of 18.0 million unique reads per sample.   Bioinformatic analysis Raw reads from the sequence were processed following the recommended protocol for libraries prepared with Ovation RRBS Methyl-Seq System (NuGEN) and then mapped to the rn6 Rattus norvegicus reference genome using Bismark (version 0.16.1) and bowtie-2 (version 2.2.9). PCR duplicates were removed using nudup.py (version 2.2). The resulting SAM files for the control and BDE-47 group for the two ages, PND65 and 120 are uploaded.

opencc-zeroMar 2024View details →

Neglected patterns of variation in transgenerational plasticity: The importance of different sources of environmental variation differs across ages and sexes in a cyprinid fish

Adaptive transgenerational plasticity (TGP) requires individuals to integrate environmental experience across multiple sources. However, few empirical studies have considered that the relative relevance of certain sources might vary across ontogeny and sexes. Here, we address this knowledge gap by studying inducible antipredator defenses, one of the most convincing examples of TGP. We assessed individual and combined effects of perceived high predation risk in mothers, fathers, caring males and personal environments on the morphology of juvenile, adult male and adult female cyprinids Pimephales promelas. Parental rather than personal environmental experience determined morphological defense expression across ages and sexes, likely because parents had a longer sampling period. In juveniles and adult males, egg-mediated environmental experience outweighed sperm-mediated environmental experience in the induction of body shape differences, likely because eggs can transmit information beyond epigenomes. However, in adult females, where body shape responses can be interpreted as life-history plasticity, information from egg and sperm were equally important, likely resulting from different integration mechanisms between morphological and life-history plasticity. The importance of care-mediated relative to gamete-mediated variation changed between juveniles and adult males, likely because they represent short- and long-term environmental experience, respectively. Instead, in adult females, both sources were again equally important, potentially owing to lag-times of life-history plasticity. Parental care intensity only contributed marginally to defense formation. These results highlight age- and sex-specific prioritization of different environmental experiences so as to generate optimal phenotypes.

Figure 4. Alpheus brasileiro Anker, 2012. A in Growth, age at sexual maturity, longevity and natural mortality of Alpheus brasileiro (Caridea: Alpheidae) from the south-eastern coast of Brazil

Figure 4. Alpheus brasileiro Anker, 2012. A, Cohorts identified during sampling describing the growth of each sex. B, Bertalanffy´s equation parameters estimated for males and females. The central line = mean; external lines = prediction intervals (95%).

Figure 5. Alpheus brasileiro Anker, 2012. Logistic curve interpolation where 50 in Growth, age at sexual maturity, longevity and natural mortality of Alpheus brasileiro (Caridea: Alpheidae) from the south-eastern coast of Brazil

Figure 5. Alpheus brasileiro Anker, 2012. Logistic curve interpolation where 50% of females reach functional sexual maturity (CL50).

Figure 3. Alpheus brasileiro Anker, 2012 in Growth, age at sexual maturity, longevity and natural mortality of Alpheus brasileiro (Caridea: Alpheidae) from the south-eastern coast of Brazil

Figure 3. Alpheus brasileiro Anker, 2012. Size–frequency distribution of individuals both sexually immature (2.5 to 4.5 mm CL) and sexually mature (5.5 to 9.5 mm CL). Undifferentiated individuals (white bars), males (black bars) and females (dark grey bars). The values of morphological sexual maturity (4.9 and 4.7 mm CL for males and females respectively) are from the study of population structure and relative growth with the same population (Pescinelli et al., 2018a).

Figure 2. A in Growth, age at sexual maturity, longevity and natural mortality of Alpheus brasileiro (Caridea: Alpheidae) from the south-eastern coast of Brazil

Figure 2. A, Lateral view of an ovigerous female of Alpheus brasileiro Anker, 2012; B, sampling area at the intertidal zone of the estuary of Cananéia, São Paulo, south–eastern Brazil.