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Data set for the paper "What are the Effects of History Length and Age on Mining Software Change Impact?"
<p>Data set for the paper What are the Effects of History Length and Age on Mining Software Change Impact?<br> by Leon Moonen, Thomas Rolfsnes, David Binkley and Stefano di Alesio.<br> In Journal of Empirical Software Engineering (EMSE), 2018, Springer. https://doi.org/10.1007/s10664-017-9588-z<br> Available from https://evolveit.bitbucket.io/publications/emse2018/</p> <p>Please cite this work by referring to the corresponding journal publication (a preprint is included in this package).</p> <p>The goal of Software Change Impact Analysis is to identify artifacts (typically source-code files or individual methods therein) potentially affected by a change. Recently, there has been increased interest in <em>mining</em> software change impact based on evolutionary coupling. A particularly promising approach uses association rule mining to uncover potentially affected artifacts from patterns in the system’s change history. Two main considerations when using this approach are the <em>history length</em>, the number of transactions from the change history used to identify the impact of a change, and <em>history age</em>, the number of transactions that have occurred since patterns were last mined from the history. Although history length and age can significantly affect the quality of mining results, few guidelines exist on how to best select appropriate values for these two parameters.</p> <p>In this paper, we empirically investigate the effects of history length and age on the quality of change impact analysis using mined evolutionary coupling. Specifically, we report on a series of systematic experiments using three state-of-the-art mining algorithms that involve the change histories of two large industrial systems and 17 large open source systems. In these experiments, we vary the length and age of the history used to mine software change impact, and assess how this affects precision and applicability. Results from the study are used to derive practical guidelines for choosing history length and age when applying association rule mining to conduct software change impact analysis. </p>
Fig. 1 in Helminths in common eiders (Somateria mollissima): Sex, age, and migration have differential effects on parasite loads
Fig. 1. Distributions of breeding and wintering populations of S. m. borealis, S. m. dresseri, and S. m. sedentaria in North America and Greenland. Populations of S. m. borealis are wintering in two areas in the pictured region; one in Southwest Greenland and one in East Canada (Newfoundland and Labrador). Individuals wintering in Southwest Greenland migrate to breed in West Greenland or Arctic Canada, whereas individuals wintering in East Canada have breeding areas in Arctic Canada (illustrated by the different direction of the red diagonal lines). For S. m. dresseri the breeding and wintering ranges overlap in one area that covers Newfoundland and Labrador as well as the northeastern part of the US, as shown by the grey horizontal lines. The subspecies S. m. sedentaria has its year-round residence in the Hudson Bay area as shown by the blue vertical lines. Dark stars mark the sampling locations of eiders in this study, whereas the white star marks the sampling location of eiders by Tourangeau et al. (2018). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 3 in Helminths in common eiders (Somateria mollissima): Sex, age, and migration have differential effects on parasite loads
Fig. 3. Prevalences of the cestodes Lateriporus sp. (A) and Microsomacanthus spp. (B), and the acanthocephalan Profilicollis sp. (C) in common eiders. Abbreviations: bor, CD = S. m. borealis, Cape Dorset; bor, GRLD = S. m. borealis, Greenland; bor, NFLD = S. m. borealis, Newfoundland; dre, NFLD = S. m. dresseri, Newfoundland; sed, BI = S. m. sedentaria [data published in Tourangeau et al. (2018)]. n-m = non-migratory, po-m = post-migratory, prm = pre-migratory. Letters describe significant differences between groups: if two groups share a letter, there is no significant difference in their prevalences.
Fig. 2 in Helminths in common eiders (Somateria mollissima): Sex, age, and migration have differential effects on parasite loads
Fig. 2. Examples of gastrointestinal parasites retrieved from common eiders in this study. (A) The trematode Notocotylus sp., (B) the cestode Lateriporus sp., (C) the acanthocephalan, Profilicollis sp. (D) microphallid trematodes, and (E) Microsomacanthus spp. cestodes.
Fig. 5 in Helminths in common eiders (Somateria mollissima): Sex, age, and migration have differential effects on parasite loads
Fig. 5. Cumulative percentages of birds infected with (A) Microsomacanthus spp., (B) Microphallus spp. and (C) Gymnophallus spp. from five different locations. Legend denotes the five infection levels: 0, 1s, 10s, 100s, and 1000s of parasite individuals within a single host. Abbreviations: bor, GRLD = S. m. borealis, Greenland; bor, NFLD = S. m. borealis, Newfoundland; dre, NFLD = S. m. dresseri, Newfoundland; bor, CD = S. m. borealis, Cape Dorset; sed, BI = S. m. sedentaria, Belcher Islands [data published in (Tourangeau et al., 2018)]. nm = non-migratory, po-m = post-migratory, pr-m = pre-migratory.
Fig. 1 in Effect of the oviposition period and age of the females of Dalbulus maidis (Hemiptera: Cicadellidae) in the emergence of egg parasitoids
Fig. 1. Average (± SE) number of eggs laid per d by Dalbulus maidis in treatments (Young-3, Young-6, Mature-3, and Mature-6). The circles represent the mature (8-wk-old) leafoppers, whereas the squares represent the young (2-wk-old) leafoppers.
Figure 1 in The effect of photobleaching on bee (Hymenoptera: Apoidea) setae color and its implications for studying aging and behavior
Figure 1. Unstandardized color photographs of the dorsal view of a worker of Bombus huntii Greene. The square box demarcates the lateral distal region of terga 2 and 3 where setal color was sampled for the 'before' and 'after' comparisons in the control and sun-exposed treatments.
Figure 2 in The effect of photobleaching on bee (Hymenoptera: Apoidea) setae color and its implications for studying aging and behavior
Figure 2. Data distributions of 'before' and 'after' measurements of setal color on the lateral distal region of the terga 2 and 3 for the control and sun-exposed treatments. Setal color was measured using the color property hue (H). Letters above each boxplot correspond to a significant difference between treatments of at least 0.05 based on Tukey's adjusted multiple comparison tests.
Figure 3 in The effect of photobleaching on bee (Hymenoptera: Apoidea) setae color and its implications for studying aging and behavior
Figure 3. Correlation (τ) between wing wear (W) and setal color (hue, H) of three bee species: Bombus huntii Greene, Melecta pacifica fulvida Cresson, and Osmia integra Cresson. Larger H values represent increased photobleaching of setae, whereas smaller values of H represent less photobleaching of setae. Larger W represents increased wing wear, whereas smaller W represents decreased wing wear.
Age-specific effects of deletions: Implications for ageing theories
<p><span>Evolution of ageing requires mutations with late-life deleterious effects. Classic theories assume these mutations either have neutral (Mutation Accumulation) or beneficial (Antagonistic Pleiotropy) effects early in life, but it is also possible that they start out as mildly harmful and gradually become more deleterious with age. Despite a wealth of studies on the genetics of ageing, we still have a poor understanding of how common mutations with age-specific effects are and what ageing theory they support. To advance our knowledge on this topic we measure a set of genomic deletions for their heterozygous effects on juvenile performance, fecundity at three ages, and adult survival. Most deletions have age-specific effects, and these are commonly harmful late in life. Many of the deletions assayed here would thus contribute to ageing if present in a population. Taking only age-specific fecundity into account, some deletions support Antagonistic Pleiotropy, but the majority of them better fit a scenario where their negative effects on fecundity become progressively worse with age. Most deletions have a negative effect on juvenile performance, a fact which strengthens the conclusion that deletions primarily contribute to ageing through negative effects that amplify with age.</span></p>
Data for: Effects of parental age on salt stress tolerance in an aquatic plant
<p>Parental age influences components of offspring fitness in many species. The ability to tolerate stress also affects fitness, but less is known regarding changes in offspring stress tolerance with increasing parental age, especially in plants. We examined first and fifth-born clonal offspring (using birth order as a proxy for parental age), and compared their fitness in several sub-lethal concentrations of salt (NaCl), to investigate the interactive effects of birth order and salt stress on the offspring of the aquatic plant <em>Lemna minor </em>L. We found that increasing salt concentration reduced reproduction particularly at early ages, which detrimentally affected fitness, as measured by the intrinsic rate of natural increase. Fifth offspring had greater fitness than first offspring, potentially due to the hump-shaped relationship between offspring fitness and birth order observed in other studies on <em>Lemna</em>, with fifth offspring near the peak of the hump. We found no interactive effect of birth order and salt concentration on offspring fitness; however, there were interactive effects on the time to first reproduction and the size of fronds. Specifically, first offspring exposed to increasing salt concentrations exhibited longer delays to first reproduction and grew to a greater size, while fifth offspring showed little change in either variable with increasing salt concentration. Thus, variation in birth order affected offspring response to salt stress, although not in terms of fitness. These results help illuminate factors impacting the age-specific strength of natural selection and stress responses, and may be environmentally relevant in the context of environmental salinization.</p>
Summary statistics for: Phenome-wide analyses identify an association between the parent-of-origin effects dependent methylome and the rate of aging in humans
<p>Summary statistics of single POE-CpG based and POE-CpG co-methylation module based phenome-wide association analyses for the manuscript "Phenome-wide analyses identify an association between the parent-of-origin effects dependent methylome and the rate of aging in humans"</p>
Effects of brain maintenance and cognitive reserve on age-related decline in three cognitive abilities
<p><strong>Objectives </strong></p> <p>Age-related cognitive changes can be influenced by both brain maintenance (BM), which refers to the relative absence over time of changes in neural resources or neuropathologic changes, and cognitive reserve (CR), which encompasses brain processes that allow for better-than-expected behavioral performance given the degree of life-course related brain changes. This study evaluated the effects of age, BM, and CR on longitudinal changes over two visits, 5 years apart, in three cognitive abilities that capture most of age-related variability.</p> <p><strong>Method </strong></p> <p>Participants included 254 healthy adults aged 20–80 years at recruitment. Potential BM was estimated using whole brain cortical thickness and white matter mean diffusivity at both visits. Education and IQ (estimated with AMNART) were tested as moderating factors for cognitive changes in the three cognitive abilities.</p> <p><strong> Results </strong></p> <p>Consistent with BM—after accounting for age, sex, and baseline performance—individual differences in the preservation of mean diffusivity and cortical thickness were independently associated with relative preservation in the three abilities. Consistent with CR—after accounting for age, sex, baseline performance, and structural brain changes—higher IQ, but not education, was associated with reduced 5-year decline in Reasoning (𝛽=0.387, p=0.002), and education was associated with reduced decline in Speed (𝛽=0.237, p=0.039). <strong> </strong></p> <p><strong>Discussion</strong></p> <p>These results demonstrate that both CR and BM can moderate cognitive changes in healthy aging and that the two mechanisms can make differential contributions to preserved cognition.</p>
On ageing and age-specific effects of spontaneous mutations
<p>Evolutionary theories of ageing assume causal mutations either have beneficial early-life effects which gradually become deleterious with advancing age (antagonistic pleiotropy: AP) or mutations that only have deleterious effects at old age (mutation accumulation: MA). Mechanistically, ageing is predicted to result from damage accumulating in the soma. While this scenario is compatible with AP, it is not immediately obvious how damage would accumulate under MA. In a modified version of the MA theory, it has been suggested that mutations with weakly deleterious effects at young age can also contribute to ageing, if they generate damage that gradually accumulates with age. Mutations with increasing deleterious effects have recently gained support from theoretical work and studies of large-effect mutations. Here we address if spontaneous mutations also have negative effects that increase with age. We accumulate mutations with early-life effects in <em>Drosophila</em> <em>melanogaster</em> across 27 generations and compare their relative effects on fecundity early and late in life. Our mutation accumulation lines on average have substantially lower early-life fecundity compared to controls. These effects were further maintained throughout life, but they did not increase with age. Our results thus suggest that most spontaneous mutations do not contribute to damage accumulation and ageing.</p>
Figure 6 The age-specific predation rate k in Long-term effects of saffron pollen on development, reproduction and predation capacity of Neoseiulus cucumeris (Acari: Phytoseiidae)
Figure 6 The age-specific predation rate k (x), and age-specific net predation rateqx() of Neoseiulus cucumeris when fed on saffron pollen for 10 and 20 generations (G10, G20) then switched toTetrany-
Combined Effects of Rotation and Age Spreads on Extended Main-Sequence Turn Offs - Isochrones and Stellar Tracks
<p>Theoretical isochrones and EEP stellar tracks featured in <a href="https://ui.adsabs.harvard.edu/abs/2019ApJ...887..199G/abstract">Gossage et al. 2019</a> (Combined Effects of Rotation and Age Spreads on Extended Main-Sequence Turn Offs). These 1D stellar evolution models are based on <a href="https://docs.mesastar.org/en/release-r22.11.1/">MESA</a> r7503, and utilize the same physical assumptions as in MIST v1.0 (<a href="https://ui.adsabs.harvard.edu/abs/2016ApJ...823..102C/abstract">Choi et al. 2016</a>).</p> <p>The models are described in <a href="https://ui.adsabs.harvard.edu/abs/2018ApJ...863...67G/abstract">Gossage et al. 2018</a> and <a href="https://ui.adsabs.harvard.edu/abs/2019ApJ...887..199G/abstract">Gossage et al. 2019</a>\(^1\), but salient features include:</p> <ul> <li>Metallicities [Fe/H] = -0.45, -0.30, -0.15, 0.0, 0.15, 0.30, 0.45 (assuming <a href="https://ui.adsabs.harvard.edu/abs/2009ARA%26A..47..481A/abstract">Asplund et al. 2009</a> protosolar abundances \(\rm Z_{\odot}\) = 0.0142).</li> <li>Rotation rates from v/v<sub>crit </sub>= 0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9 (initiated at ZAMS)</li> <li>Masses from 0.1 to 8 solar masses with spacings of: <ul> <li>\(\rm \Delta M = 0.05 M_{\odot}\) for \(\rm M < 1 M_{\odot}\)</li> <li>\(\rm \Delta M = 0.04 M_{\odot}\) for \(\rm 1 M_{\odot} \leq M < 2 M_{\odot}\)</li> <li>\(\rm \Delta M = 0.2 M_{\odot}\) for \(\rm 2 M_{\odot} \leq M \leq 8 M_{\odot}\)</li> </ul> </li> <li>Models are evolved up to the first thermal pulse.</li> </ul> <p><strong>File name convention:</strong> zip files, e.g., \(\texttt{MIST_v1.0_feh_p0.15_rotating_tracks.zip}\), contain theoretical models at a particular metallcity ([Fe/H] = 0.15 in this case), at all rotation rates and masses. The file \(\texttt{MIST_v1.0_feh_m0.15_rotating_tracks.zip}\) contains models at [Fe/H] = -0.15, and so on. \(\texttt{*_tracks.zip}\) contain EEP stellar track files and \(\texttt{*_isochrones.zip}\) files contain theoretical isochrone files, both in the same format as EEP track and theoretical isochrones found on the <a href="https://waps.cfa.harvard.edu/MIST/index.html">MIST website</a>. Zip files labeled, e.g.,\(\texttt{*_isochrones_FILTERSET.zip}\) contain observable isochrones, with synthetic photometry produced for a particular filter set (as on the <a href="https://waps.cfa.harvard.edu/MIST/model_grids.html">MIST packaged grids</a> site, which contains more information on the filter sets), computed without extinction (\(A_V=0\)). At the moment, filter sets for \(\texttt{UBVRIplus}\) (containing Gaia filters), \(\texttt{HST_WFC3}\), \(\texttt{HST_ACSWF}\), \(\texttt{HST_WFPC2}\), and \(\texttt{CFHTugriz}\) are included, but more can be added upon request\(^2\). </p> <p><strong>Notes:</strong></p> <p>\(^1\) These are the same models as featured in <a href="https://ui.adsabs.harvard.edu/abs/2018ApJ...863...67G/abstract">Gossage et al. 2018</a>, but in that work, [Fe/H] = -0.60 and -0.75 were featured as well and only included models up to v/v<sub>crit </sub>= 0.6. We include these models from <a href="https://ui.adsabs.harvard.edu/abs/2018ApJ...863...67G/abstract">Gossage et al. 2018</a> here as well. Models at [Fe/H] = -0.60 have been extended to v/v<sub>crit </sub>= 0.9, while [Fe/H] = -0.75 only includes up to the original v/v<sub>crit </sub>= 0.6.</p> <p>\(^2\) These tracks and isochrones may be converted into observable tracks and isochrones (w/ gravity darkening effects if desired) via Aaron Dotter's <a href="https://github.com/aarondotter/iso">iso code</a>.</p> <p>\(^3\) Although astroseismic \(\nu_{max}\) and \(\Delta \nu\) are included in the included history files, be aware that these are based on scaling relations reliant on solar values, assuming the Coriolis and centrifugal forces do not play a role. While an OK assumption for the Sun, this is less applicable models with rapid rotation and their values should not be trusted in such regimes.</p>
A Study to Test if Fremanezumab is Effective in Preventing Episodic Migraine in Patients 6 to 17 Years of Age
ClinicalTrials.gov study NCT04458857. IPD Sharing: YES. Countries: 9. Publications: 1.
Study to Evaluate the Effectiveness of a High-Dose Quadrivalent Influenza Vaccine (QIV-HD) Compared to a Standard-Dose Quadrivalent Influenza Vaccine (QIV-SD) in Adults 65 Years of Age and Older
ClinicalTrials.gov study NCT04137887. IPD Sharing: YES. Countries: 1. Publications: 2.
A Study to Assess the Effects of Brolucizumab in Adult Patients With Neovascular Age Related Macular Degeneration
ClinicalTrials.gov study NCT04239027. IPD Sharing: YES. Countries: 1. Publications: 1.
Study to Evaluate the Safety and Effectiveness of Intravitreal Injections (IVI) of Brolucizumab in Patients With Neovascular Age-related Macular Degeneration (nAMD)
ClinicalTrials.gov study NCT05269966. IPD Sharing: YES. Countries: 1. Publications: 16.
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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.