Diurnal oscillations of MRI metrics in human brains

Restricted access dataset used for the study "Diurnal oscillations of MRI metrics in human brains". Contains subject-level data within the following files: whole_brain_data.csv - average of each MRI metric across the relevant atlas for each time point. processed_ROI_data.csv - average of each MRI metric within each atlas ROI for each time point. whole_brain_techvar_data.csv - average of each MRI metric across the relevant atlas for each time point and back-to-back replicate. weights_kg.csv - body weight at each time point. actigraphy_3day.csv - steps registered by the FitBit device each minute for the 3 days of observation. actigraphy_sleep.csv - sleep intervals registered by the FitBit device during the 3 days of observation

Diurnal oscillations of MRI metrics in the brains of male participants

Abstract Regulation of biological processes according to a 24-hr rhythm is essential for the normal functioning of an organism. Temporal variation in brain MRI data has often been attributed to circadian or diurnal oscillations; however, it is not clear if such oscillations exist. Here, we provide evidence that diurnal oscillations indeed govern multiple MRI metrics. We recorded cerebral blood flow, diffusion-tensor metrics, T1 relaxation, and cortical structural features every three hours over a 24-hr period in each of 16 adult male controls and eight adult male participants with bipolar disorder. Diurnal oscillations are detected in numerous MRI metrics at the whole-brain level, and regionally. Rhythmicity parameters in the participants with bipolar disorder are similar to the controls for most metrics, except for a larger phase variation in cerebral blood flow. The ubiquitous nature of diurnal oscillations has broad implications for neuroimaging studies and furthers our understanding of the dynamic nature of the human brain

DiscoRhythm: an easy-to-use web application and R package for discovering rhythmicity

MOTIVATION: Biological rhythmicity is fundamental to almost all organisms on Earth and plays a key role in health and disease. Identification of oscillating signals could lead to novel biological insights, yet its investigation is impeded by the extensive computational and statistical knowledge required to perform such analysis. RESULTS: To address this issue, we present DiscoRhythm (Discovering Rhythmicity), a user-friendly application for characterizing rhythmicity in temporal biological data. DiscoRhythm is available as a web application or an R/Bioconductor package for estimating phase, amplitude, and statistical significance using four popular approaches to rhythm detection (Cosinor, JTK Cycle, ARSER, and Lomb-Scargle). We optimized these algorithms for speed, improving their execution times up to 30-fold to enable rapid analysis of -omic-scale datasets in real-time. Informative visualizations, interactive modules for quality control, dimensionality reduction, periodicity profiling, and incorporation of experimental replicates make DiscoRhythm a thorough toolkit for analyzing rhythmicity. AVAILABILITY AND IMPLEMENTATION: The DiscoRhythm R package is available on Bioconductor (https://bioconductor.org/packages/DiscoRhythm), with source code available on GitHub (https://github.com/matthewcarlucci/DiscoRhythm) under a GPL-3 license. The web application is securely deployed over HTTPS (https://disco.camh.ca) and is freely available for use worldwide. Local instances of the DiscoRhythm web application can be created using the R package or by deploying the publicly available Docker container (https://hub.docker.com/r/mcarlucci/discorhythm). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Use of Photography in Geography Teaching

This dissertation is concerned on visual literacy and the usage of photograph. The theoretical part shows different views on photographs. Photograph is described by psychologists, sociologists, journalists and as a picture material and research task. The practical part is based on classification of visual literacy. At first the author judges the literacy on a model example and afterwards he does research based on his own questionary. The questionary is devided into four packs of questions. The first pack introduces the research to the respondents and states their gender, age and education. The other three packs are filled with questions tied with certain photographs. The individual questions are mostly devided into two parts, the first part seeks for a concrete answer and the second part asks the respondents to explain the way they found their answers. The study has the nature of a pilot project that verifies the dependance of visual literacy, or more precisely validity of answers, according to education, age, gender and field of study. Based on the respondents' answers their ways of perception, reading, interpretation and further work with information contained in the photographs are investigated. The addenda contain some examples of exercises that can be used to practice the work with photographs. Powered..

Additional file 7: Figure S4. of Epigenetic assimilation in the aging human brain

Permuted null distribution of mean domain length. The histogram represents the densities of the permuted null distribution from all samples and the red dashed line is the mean domain length in the indicated subset sample of interest (i.e., older individuals (>75 years), EAO cortex, or AD buccal cells). a Mean DNA modification domain length of older individual in the cerebral cortex (permuted p = 0.01). b Mean DNA modification domain length of older individual in the cerebellum (permuted p = 0.13). c Mean domain length of older individual transcriptome in the cerebral cortex (permuted p = 0.01). d Mean domain length of older individual transcriptome in the cerebellum (permuted p = 0.51). e Mean domain length of the EAO cerebral cortex (permuted p = 0.015). f Mean domain length of the AD-affected twin buccal samples (permuted p = 0.04). (PDF 131 kb

Additional file 5: Figure S3. of Epigenetic assimilation in the aging human brain

ICC of DNA modification for the 82 disease-specific differentially modified loci (p < 0.05). The Z-scores are normalized ICC coefficients, where positive Z-scores represent ICC coefficients that are higher than the mean, while negative Z-scores show the opposite. Cumulative Z-scores for normalized ICC coefficients represent the following: 0 % includes none, 50 % includes half, and 100 % includes all Z-scores. a Approximately 90 % of Z-scores are positive in the comparison of the EAO AD cortex samples versus cerebellum (CB) but only ~25 % of Z-scores are positive in the LAO versus cerebellum, indicating a more advanced state of dedifferentiation for EAO AD cortices. LAO versus EAO show an even distribution. b Buccal cell analysis showed that ~75 % AD twins, but only ~50 % of their healthy co-twins, had higher than average similarity as measured by Z-scores of ICC. (PDF 123 kb

Additional file 2: Figure S1. of Epigenetic assimilation in the aging human brain

Examples of data distribution for DNA modification and transcriptome data in older (>75 years) and younger (>75 years) individuals. Violin plots showing representative densities of DNA modification (beta values) and probe signal intensities in transcriptome data for older and younger individuals for a given probe. One-tailed F-test was used to identify cases where older individuals had lower variance than the young (i.e., F-test p < 0.05). a An example of a DNA modification probe where the older individuals had significantly lower variance than the younger individuals. b An example of a DNA modification probe where older individuals did not show significantly smaller variance compared with the younger individuals. c An example of a transcript with smaller variance in older compared with younger individuals. d An example of a transcript with non-significant difference of variance. (PDF 410 kb

Additional file 4: Figure S2. of Epigenetic assimilation in the aging human brain

Permuted null distribution of mean ICC in AD twin samples. ICC densities of the permuted null from all samples compared with the mean ICC in the indicated subset sample of interest (red dashed line). a EAO cortex versus cerebellum using the top 5 % of differentially modified loci (permuted p = 0.014). b EAO cortex versus cerebellum using the bottom 5 % of differentially modified loci (permuted p = 0.51). c EAO cortex versus cerebellum using the nominally significant (p < 0.05) DNA modification loci (permuted p < 10-6). d AD affected versus unaffected co-twin buccal samples using the top 5 % of differentially modified loci (permuted p = 1.4 × 10-3). e AD affected versus unaffected co-twin buccal samples using the bottom 5 % of differentially modified loci (permuted p = 0.43). f AD affected versus unaffected co-twin buccal samples using the nominally significant (p < 0.05) DNA modification loci from the cortex (permuted p = 0.07). (PDF 441 kb