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932 results for “Long term data”
Data from: Reconstructing the phylogenetic history of long-term effective population size and life-history traits using patterns of amino acid replacement in mitochondrial genomes of mammals and birds
The nearly neutral theory, which proposes that most mutations are deleterious or close to neutral, predicts that the ratio of nonsynonymous over synonymous substitution rates (dN/dS), and potentially also the ratio of radical over conservative amino acid replacement rates (Kr/Kc), are negatively correlated with effective population size. Previous empirical tests, using life-history traits (LHT) such as body-size or generation-time as proxies for population size, have been consistent with these predictions. This suggests that large-scale phylogenetic reconstructions of dN/dS or Kr/Kc might reveal interesting macroevolutionary patterns in the variation in effective population size among lineages. In this work, we further develop an integrative probabilistic framework for phylogenetic covariance analysis introduced previously, so as to estimate the correlation patterns between dN/dS, Kr/Kc, and three LHT, in mitochondrial genomes of birds and mammals. Kr/Kc displays stronger and more stable correlations with LHT than does dN/dS, which we interpret as a greater robustness of Kr/Kc, compared with dN/dS, the latter being confounded by the high saturation of the synonymous substitution rate in mitochondrial genomes. The correlation of Kr/Kc with LHT was robust when controlling for the potentially confounding effects of nucleotide compositional variation between taxa. The positive correlation of the mitochondrial Kr/Kc with LHT is compatible with previous reports, and with a nearly neutral interpretation, although alternative explanations are also possible. The Kr/Kc model was finally used for reconstructing life-history evolution in birds and mammals. This analysis suggests a fairly large-bodied ancestor in both groups. In birds, life-history evolution seems to have occurred mainly through size reduction in Neoavian birds, whereas in placental mammals, body mass evolution shows disparate trends across subclades. Altogether, our work represents a further step toward a more comprehensive phylogenetic reconstruction of the evolution of life-history and of the population-genetics environment.
Data from: Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli
Large-scale rearrangements may be important in evolution because they can alter chromosome organization and gene expression in ways not possible through point mutations. In a long-term evolution experiment, twelve Escherichia coli populations have been propagated in a glucose-limited environment for over 25 years. We used whole-genome mapping (optical mapping) combined with genome sequencing and PCR analysis to identify the large-scale chromosomal rearrangements in clones from each population after 40,000 generations. A total of 110 rearrangement events were detected, including 82 deletions, 19 inversions, and 9 duplications, with lineages having between 5 and 20 events. In three populations, successive rearrangements impacted particular regions. In five populations, rearrangements affected over a third of the chromosome. Most rearrangements involved recombination between insertion sequence (IS) elements, illustrating their importance in mediating genome plasticity. Two lines of evidence suggest that at least some of these rearrangements conferred higher fitness. First, parallel changes were observed across the independent populations, with ~65% of the rearrangements affecting the same loci in at least two populations. For example, the ribose-utilization operon and the manB-cpsG region were deleted in 12 and 10 populations, respectively, suggesting positive selection, and this inference was previously confirmed for the former case. Second, optical maps from clones sampled over time from one population showed that most rearrangements occurred early in the experiment, when fitness was increasing most rapidly. However, some rearrangements likely occur at high frequency and may have simply hitchhiked to fixation. In any case, large-scale rearrangements clearly influenced genomic evolution in these populations.
Data from: An approach to estimate short-term, long-term, and reaction norm repeatability
Evolutionary ecologists increasingly study reaction norms that are expressed repeatedly within the same individual's lifetime. For example, foragers continuously alter anti-predator vigilance in response to moment-to-moment changes in predation risk. Variation in this form of plasticity occurs both among and within individuals. Among-individual variation in plasticity (individual by environment interaction or I×E) is commonly studied; by contrast, despite increasing interest in its evolution and ecology, within-individual variation in phenotypic plasticity is not. We outline a study design based on repeated measures and a multi-level extension of random regression models that enables quantification of variation in reaction norms at different hierarchical levels (such as among- and within-individuals). The approach enables the calculation of repeatability of reaction norm intercepts (average phenotype) and slopes (level of phenotypic plasticity); these indices are not specific to measurement or scaling and are readily comparable across data sets. The proposed study design also enables calculation of repeatability at different temporal scales (such as short- and long-term repeatability) thereby answering calls for the development of approaches enabling scale-dependent repeatability calculations. We introduce a simulation package in the R statistical language to assess power, imprecision and bias for multi-level random regression that may be utilised for realistic datasets (unequal sample sizes across individuals, missing data, etc). We apply the idea to a worked example to illustrate its utility. We conclude that consideration of multi-level variation in reaction norms deepens our understanding of the hierarchical structuring of labile characters and helps reveal the biology in heterogeneous patterns of within-individual variance that would otherwise remain 'unexplained' residual variance.
Three-Dimensional Geostatistical Inverse Analyses of Transient Head and Temperature Data from a Long-Term Heat Tracer Test
<p>The spreadsheet contains datasets utilized to accomplish the study. </p>
Supplementary Data for Manuscript "Examining the mid to long-term variability in saturated hydraulic conductivity of sandy soils and its influencing factors under constant head test in the laboratory"
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Data of industrial heat source between 2012 and 2021 using long-term Active Fire/Hotspot data in China
<p>Industrial heat sources serve as crucial indicators of energy consumption levels and air pollution. Energy-intensive industries are facing substantial challenges in transforming and upgrading in China. Therefore, accurately identifying industrial heat source locations and monitoring their temporal patterns are becoming utmost importance. In this study, a long-term industrial heat source datasets between 2012 and 2021 in China using long-term Active Fire/Hotspots (ACF) data has been constructed to monitor and analyze large-scale industrial heat sources. Firstly, density segmentation method based on an improved k-means algorithm using long-term ACF data and spatial topological correlation analysis was conducted to build industrial heat sources. Then, 4410 industrial heat sources were obtained between 2012 and 2021 in China, with an identification accuracy of 95.08% by manual verification using high-resolution remote sensing images and point of interest (POI) data. Finally, the trend in the spatio-temporal variation of industrial heat sources was analyzed using long-term series. The results from 2012 to 2021 showed that the spatial distribution of industrial heat sources in China exhibits local aggregation and a gradual shift from east to west.And,the number of industrial heat sources in China has followed a trend of an initial increase from 2012 to 2014, followed by a decrease since 2014, consistent with national energy reform-related policies.The result of this study indicated the temporal variation of industrial heat sources, enhanced the accuracy of fire points category identification, and demonstrated potential for advancing energy efficiency, emission reduction, and sustainable development in China.</p>
raw data - Old Questions, New Answers: Real-World, Long-Term Efficacy of Hymenoptera Venom Immunotherapy: Prevalence of Venom-Induced Anaphylaxis, Risk Factors, Field Sting Reactions
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data - Long-term outcomes of pseudomyxoma peritonei after cytoreductive surgery and hyperthermic intraperitoneal chemotherapy and its relevant risk factors
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Supplementary Data File for Safeguarding China's long-term sustainability against systemic disruptors
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Data for manuscript titled "Long-term orientation and innovation: Influence of CPTPP on R&D investment in Japanese firms"
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Supplementary data for: Long-term Glycemic Variability Predicts Adverse Outcomes in Diabetic Heart Failure with Preserved Ejection Fraction
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Long-term water quality monitoring data of Shenzhen Bay
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Data from: Incubator-independent cell-culture perfusion platform for continuous long-term microelectrode array electrophysiology and time-lapse imaging
Most in vitro electrophysiology studies extract information and draw conclusions from representative, temporally limited snapshot experiments. This approach bears the risk of missing decisive moments that may make a difference in our understanding of physiological events. This feasibility study presents a simple benchtop cell-culture perfusion system adapted to commercial microelectrode arrays (MEAs), multichannel electrophysiology equipment and common inverted microscopy stages for simultaneous and uninterrupted extracellular electrophysiology and time-lapse imaging at ambient CO2 levels. The concept relies on a transparent, replica-casted polydimethylsiloxane perfusion cap, gravity- or syringe-pump-driven perfusion and preconditioning of pH-buffered serum-free cell-culture medium to ambient CO2 levels at physiological temperatures. The low-cost microfluidic in vitro enabling platform, which allows us to image cultures immediately after cell plating, is easy to reproduce and is adaptable to the geometries of different cell-culture containers. It permits the continuous and simultaneous multimodal long-term acquisition or manipulation of optical and electrophysiological parameter sets, thereby considerably widening the range of experimental possibilities. Two exemplary proof-of-concept long-term MEA studies on hippocampal networks illustrate system performance. Continuous extracellular recordings over a period of up to 70 days revealed details on both sudden and gradual neural activity changes in maturing cell ensembles with large intra-day fluctuations. Correlated time-lapse imaging unveiled rather static macroscopic network architectures with previously unreported local morphological oscillations on the timescale of minutes.
Data from: Dynamics of short- and long-term association between a bacterial plant pathogen and its arthropod vector
The dynamics of association between pathogens and vectors can strongly influence epidemiology. It has been proposed that wilt disease epidemics in cucurbit populations are sustained by persistent colonization of beetle vectors (Acalymma vittatum) by the bacterial phytopathogen Erwinia tracheiphila. We developed a qPCR method to quantify E. tracheiphila in whole beetles and frass and used it to assess pathogen acquisition and retention following variable exposure to infected plants. We found that (i) E. tracheiphila is present in frass in as little as three hours after feeding on infected plants and can be transmitted with no incubation period by vectors given brief exposure to infected plants, but also by persistently colonized vectors several weeks following exposure; (ii) duration of exposure influences rates of long-term colonization; (iii) frass infectivity (assessed via inoculation experiments) reflects bacterial levels in frass samples across time; and (iv) vectors rarely clear E. tracheiphila infections, but suffer no apparent loss of fitness. These results describe a pattern conducive to the effective maintenance of E. tracheiphila within cucurbit populations.
Data from: Long-term effects of early nutrition and environmental matching on developmental and personality traits in zebra finches
Developmental plasticity is a key feature of many organisms and individuals can benefit from early programming to optimize their phenotypes for the expected environmental conditions. However, environmental conditions may sometimes change unexpectedly. Mismatches between early and adult life, for example, can have important repercussions for adult phenotypes, potentially leading to better performance under matched than mismatched conditions as predicted by the predictive adaptive response hypothesis. We conducted a long-term experimental manipulation of dietary conditions in a population of zebra finches, Taeniopygia guttata. Broods were exposed to two early nutritional treatments until independence and we used a split-brood design to independently manipulate nutritional conditions after independence to create matched and mismatched nutritional environments in later life. Developmental trajectories of all individuals were followed for more than 5 years and we scored behavioural responses in trials in a special environment and while interacting with a special object three times during adult life. Overall, we found no evidence for early programming affecting morphology. Tarsus and wing length were exclusively influenced by the early nutrition. Body weight showed lasting effects of the early treatment and independent effects of nutritional condition during adulthood, but no effects of environmental matching or mismatching. Special-object trials showed effects of the adult nutritional treatment while environmental matching affected hopping activity in special environments. These behavioural responses showed substantial long-term individual stability over a 3-month period and were only marginally smaller when measured over a period of more than 4 years. Interestingly, survival of individuals from low-quality early nutritional condition was higher compared with high-quality early condition individuals, which became evident only after years of survival monitoring. Beyond the nutritional treatment itself, we found sizable brood identity effects that slowly but steadily declined with age, indicating a significant but decaying effect of natural variation in parental provisioning on adult phenotypes.
Data from: Comparison of infinitesimal and finite locus models for long-term breeding simulations with direct and maternal effects at the example of honeybees
Stochastic simulation studies of animal breeding have mostly relied on either the infinitesimal genetic model or finite polygenic models. In this study, we investigated the long-term effects of the chosen model on honeybee breeding schemes. We implemented the infinitesimal model, as well as finite locus models, with 200 and 400 gene loci and simulated populations of 300 and 1000 colonies per year over the course of 100 years. The selection was of a directly and maternally influenced trait with maternal heritability of h²_m = 0.42, direct heritability of h² d = 0.27, and a negative correlation between the effects of r_md = −0.18. Another set of simulations was run with parameters h²_m = 0.53, h²_d = 0.34, and r_md = −0.53. All models showed similar behavior for the first 20 years. Throughout the study, we observed a higher genetic gain in the direct than in the maternal effects and a smaller gain with a stronger negative covariance. In thelong-term, however, only the infinitesimal model predicted sustainable linear genetic progress, while the finite locus models showed sublinear behavior and, after 100 years, only reached between 58% and 62% of the mean breeding values in the infinitesimal model. While the infinitesimal model suggested a reduction of genetic variance by 33% to 49% after 100 years, the finite locus models saw a more drastic loss of 76% to 92%. When designing sustainable breeding strategies, one should, therefore, not blindly trust the infinitesimal model as the predictions may be overly optimistic. Instead, the more conservative choice of the finite locus model should be favored.
Health care-related economic burden of polycystic ovary syndrome in the United States: Pregnancy-related and long-term health consequences - supplemental data
<p><b>Context: </b>Polycystic ovary syndrome (PCOS) is the most common endocrine disorder of reproductive-aged women, affecting approximately 5-20% of women of reproductive age. A previous estimate noted that the economic burden of PCOS approximates $3.7 billion annually in 2020 USD when considering only the costs of the initial diagnosis and of reproductive endocrine morbidities, not considering the costs of pregnancy-related and long-term morbidities.</p> <p><span><span><span><span><span><span><span><span><b>Objective: </b>To estimate the excess prevalence and economic burden of pregnancy-related and long-term health morbidities attributable to PCOS.</span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><b>Data Sources: </b>PubMed, EmBase and Cochrane Library.</span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><b>Study Selection: </b>Studies in which the diagnosis of PCOS was consistent with the Rotterdam, National Institutes of Health (NIH), or Androgen Excess & PCOS (AE-PCOS) Society criteria, or that used electronic medical record diagnosis codes, or diagnosis based on histopathologic sampling were eligible for inclusion. Studies that included an outcome of interest and a control group of non-PCOS patients who were matched or controlled for body mass index (BMI) were included. </span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><b>Data Extraction: </b>Two investigators working independently extracted data on study characteristics and outcomes. </span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><b>Data Synthesis: </b>Data was pooled using random-effects meta-analysis. The I <sup>2 </sup>statistic was used to assess inter-study heterogeneity. The quality of selected studies was assessed using the Newcastle-Ottawa Scale.</span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><b>Results: </b>The additional total healthcare-related economic burden due to pregnancy-related and long-term morbidities associated with PCOS in the United States is estimated to be $4.3 billion annually in 2020 USD.</span></span></span></span></span></span></span></span></p>
Data set for: Long-term Perfluorooctanesulfonic acid (PFOS) exposure alters anxiety-like behaviour but not boldness in zebrafish (Danio rerio)
<p>Perfluorooctanesulfonic acid (PFOS) is an organic pollutant that is commonly detected in wildlife, humans, and the environment. PFOS can cause a variety of toxic effects in zebrafish, however, the impact on complex behaviours like boldness and anxiety-like behaviour is unknown. To investigate the behavioural effects of PFOS in zebrafish, we exposed adult zebrafish to either 0, 0.1, or 1.0 mg/L PFOS for 40 days. After 20- and 40-days anxiety-like behaviour and boldness were assessed using the novel approach test and novel tank dive test, respectively. After 40- day exposure at a concentration of 1.0 mg/L, PFOS caused a significant increase in time spent in the upper zone and a significant decrease in time spent in the bottom zone of the novel tank dive test, suggesting decreased anxiety-like behaviour compared to controls. Neither 0.1 or 1.0 mg/L had an impact on zebrafish boldness at any time point. Exposure to 1.0 mg/L PFOS significantly decreased locomotion in the novel tank dive test after 20 days, whereas after 40 days there was no impact of PFOS on locomotion at any concentration, indicating potential short-term influences on locomotion. These results suggest chronic PFOS exposure can modulate anxiety-like behaviour, while exploratory activity and locomotion are not altered.</p>
Data from: Tolerability and efficacy of long-term medical therapy in primary aldosteronism
<p>Introduction: Patients with primary aldosteronism (PA) have increased cardiovascular risk and studies have found that medical therapy fails to ameliorate this. This may be due to side effects and limited efficacy of medications at tolerable doses.</p> <p>Methods: We conducted a retrospective study on 201 patients with PA treated with medical therapy (spironolactone, eplerenone or amiloride) for PA from 2000-2020 at two tertiary centres. Patients were assessed for efficacy to achieve clinical and biochemical control, and for side effects.</p> <p>Results: 53.7% of patients achieved blood pressure <140/90mmHg, 44.6% achieved potassium ≥4.3mmol/L, 63.2% achieved renin >1ng/ml/hr, and only 24.6% achieved all three. Concordance of biochemical control using potassium and renin levels was 49%. 45.3% of patients experienced side effects, with 8.5% switching to another medication, 18.9% decreasing dose, and 10.0% stopping medications altogether. Risk factors for side effects were spironolactone use, dose ≥50mg, duration of treatment ≥1year, male gender and unilateral PA. Patients with unilateral PA, compared to bilateral PA, used higher median doses of spironolactone, 75mg vs 50mg, <i>P</i><0.001, but more had persistent hypokalemia, 20.5% vs 6.4%, <i>P</i>=0.007. 44 patients with unilateral PA underwent surgery after initial medical therapy, which further improved systolic and diastolic BP, from 142 to 134mmHg, <i>P</i><0.001, and from 85 to 79mmHg, <i>P</i><0.001, respectively.</p> <p>Conclusion: Dose-dependent side effects limit the efficacy of medical therapy in PA. Future prospective studies should assess the best monitoring strategy for biochemical control during long-term medical therapy. In patients with unilateral PA, surgery remains a better option compared to life-long medications.</p>
Data from: Substrate composition impacts long-term vegetation development on blue-green roofs: Insights from an experimental roof and greenhouse study
<p>Data from: van der Kolk et al. (2022). Substrate composition impacts long-term vegetation development on blue-green roofs: Insights from an experimental roof and greenhouse study. Ecological Engineering.</p> <p> </p> <p>See the main article on how data was collected.</p> <p> </p> <p>The dataset contains three tables:</p> <p>greenhouse_biomass.csv: The biomass (in g dry weight) harvested from each container in the greenhouse experiment.</p> <p>greenhouse_percentage_share.csv: The estimated percentage that each species contributes to the total harvested biomass in the greenhouse experiment.</p> <p>roof_cover.csv: The cover (in %) of all species per plot for all surveys.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.