The tidyomics ecosystem: enhancing omic data analyses.

The growth of omic data presents evolving challenges in data manipulation, analysis and integration. Addressing these challenges, Bioconductor provides an extensive community-driven biological data analysis platform. Meanwhile, tidy R programming offers a revolutionary data organization and manipulation standard. Here we present the tidyomics software ecosystem, bridging Bioconductor to the tidy R paradigm. This ecosystem aims to streamline omic analysis, ease learning and encourage cross-disciplinary collaborations. We demonstrate the effectiveness of tidyomics by analyzing 7.5 million peripheral blood mononuclear cells from the Human Cell Atlas, spanning six data frameworks and ten analysis tools.

Mariner: explore the Hi-Cs.

MOTIVATION: 3D chromatin structure plays an important role in regulating gene expression and alterations to this structure can result in developmental abnormalities and disease. While genomic approaches like Hi-C and Micro-C can provide valuable insights in 3D chromatin architecture, the resulting datasets are extremely large and difficult to manipulate. RESULTS: Here, we present mariner, a rapid and memory efficient tool to extract, aggregate, and plot data from Hi-C matrices within the R/Bioconductor environment. Mariner simplifies the process of querying and extracting contacts from multiple Hi-C files using a parallel and block-processing approach. Modular functions allow complete workflow customization for advanced users, yet all-in-one functions are available for running the most common types of analyses. Finally, tight integration with existing Bioconductor infrastructure enables complete analysis and visualization of Hi-C data in R. AVAILABILITY AND IMPLEMENTATION: Available on GitHub at https://github.com/EricSDavis/mariner and on Bioconductor at https://www.bioconductor.org/packages/release/bioc/html/mariner.html.

Anatomical Substrates of Rapid Eye Movement Sleep Rebound in a Rodent Model of Post-sevoflurane Sleep Disruption.

BACKGROUND: Previous research suggests that sevoflurane anesthesia may prevent the brain from accessing rapid eye movement (REM) sleep. If true, then patterns of neural activity observed in REM-on and REM-off neuronal populations during recovery from sevoflurane should resemble those seen after REM sleep deprivation. In this study, the authors hypothesized that, relative to controls, animals exposed to sevoflurane present with a distinct expression pattern of c-Fos, a marker of neuronal activation, in a cluster of nuclei classically associated with REM sleep, and that such expression in sevoflurane-exposed and REM sleep-deprived animals is largely similar. METHODS: Adult rats and Targeted Recombination in Active Populations mice were implanted with electroencephalographic electrodes for sleep-wake recording and randomized to sevoflurane, REM deprivation, or control conditions. Conventional c-Fos immunohistochemistry and genetically tagged c-Fos labeling were used to quantify activated neurons in a group of REM-associated nuclei in the midbrain and basal forebrain. RESULTS: REM sleep duration increased during recovery from sevoflurane anesthesia relative to controls (157.0 ± 24.8 min vs. 124.2 ± 27.8 min; P = 0.003) and temporally correlated with increased c-Fos expression in the sublaterodorsal nucleus, a region active during REM sleep (176.0 ± 36.6 cells vs. 58.8 ± 8.7; P = 0.014), and decreased c-Fos expression in the ventrolateral periaqueductal gray, a region that is inactive during REM sleep (34.8 ± 5.3 cells vs. 136.2 ± 19.6; P = 0.001). Fos changes similar to those seen in sevoflurane-exposed mice were observed in REM-deprived animals relative to controls (sublaterodorsal nucleus: 85.0 ± 15.5 cells vs. 23.0 ± 1.2, P = 0.004; ventrolateral periaqueductal gray: 652.8 ± 71.7 cells vs. 889.3 ± 66.8, P = 0.042). CONCLUSIONS: In rodents recovering from sevoflurane, REM-on and REM-off neuronal activity maps closely resemble those of REM sleep-deprived animals. These findings provide new evidence in support of the idea that sevoflurane does not substitute for endogenous REM sleep.

On the Generalizability of Time-of-Flight Convolutional Neural Networks for Noninvasive Acoustic Measurements.

Bulk wave acoustic time-of-flight (ToF) measurements in pipes and closed containers can be hindered by guided waves with similar arrival times propagating in the container wall, especially when a low excitation frequency is used to mitigate sound attenuation from the material. Convolutional neural networks (CNNs) have emerged as a new paradigm for obtaining accurate ToF in non-destructive evaluation (NDE) and have been demonstrated for such complicated conditions. However, the generalizability of ToF-CNNs has not been investigated. In this work, we analyze the generalizability of the ToF-CNN for broader applications, given limited training data. We first investigate the CNN performance with respect to training dataset size and different training data and test data parameters (container dimensions and material properties). Furthermore, we perform a series of tests to understand the distribution of data parameters that need to be incorporated in training for enhanced model generalizability. This is investigated by training the model on a set of small- and large-container datasets regardless of the test data. We observe that the quantity of data partitioned for training must be of a good representation of the entire sets and sufficient to span through the input space. The result of the network also shows that the learning model with the training data on small containers delivers a sufficiently stable result on different feature interactions compared to the learning model with the training data on large containers. To check the robustness of the model, we tested the trained model to predict the ToF of different sound speed mediums, which shows excellent accuracy. Furthermore, to mimic real experimental scenarios, data are augmented by adding noise. We envision that the proposed approach will extend the applications of CNNs for ToF prediction in a broader range.

Improvement in non-24-h sleep-wake rhythm disorder in a sighted individual treated with a melatonin receptor agonist.

Non-24-hour sleep-wake rhythm disorder (N24SWD) typically presents in patients with visual impairments that disrupt the ability to entrain to the 24 hour solar cycle. We discuss a 43 year old sighted man who presented with periodic daytime hypersomnia and nighttime insomnia, occasionally leading to <3 hours of sleep per day. Previous polysomnography showed an apnea hypopnea index of 6.2 events per hour. A sleep log of 3 months showed irregular time of sleep onset, and an average of 3 hours of sleep per day. Wrist actigraphy confirmed N24SWD. A trial of tasimelteon 20 mg/day resulting in improved daytime hypersomnia (pre-Epworth Sleepiness Scale (ESS) = 21/24, post-ESS = 5/24; a score of > 10/24 is considered sleepy). Follow-up actigraphy showed marked resolution of phase delay with an average of five hours of sleep. The case demonstrates that tasimelteon is a possible treatment for N24SWD in sighted individuals.

Capturing Hydrated Vanadium Ion Dynamics in Ionomer Nanocomposites Used for Redox Flow Batteries.

Herein, we employed high-flux backscattering spectroscopy to capture for the first time the motions of hydrated vanadyl ions in ionomer nanocomposites prepared by both solution-cast and in situ sol-gel condensation methods. Both local and jump diffusion coefficients of the hydrated vanadyl (VO2+) ions as well as the dynamic length scales of ion motions and the fraction of immobile hydrogen atoms were extracted from the scattering spectra. Notably, for solution-cast membranes, the jump and local diffusion coefficients of hydrated VO2+ ions were seen to decrease by over 10- and 4-fold, respectively, with the introduction of 10 mass % silica nanoparticles (SiNPs) compared to their neat counterparts. Further, the VO2+ diffusion coefficients were observed to decrease with thermal annealing, though the impact of annealing was less significant than that seen with the introduction of SiNPs. Finally, in general, thermal annealing and the introduction of SiNPs had no measurable impact on the fraction of immobile hydrogen atoms in both solution-cast and sol-gel ionomer nanocomposites. The data observed in this work, in conjunction with previous structural and chain dynamics studies on hydrated Nafion-SiNP nanocomposites, suggest that a combination of stiffening of the segmental dynamics as well as a decrease in available sulfonic acid groups facilitating transport leads to an overall decrease in mobility of vanadium ions in these ionomer nanocomposites.

Healthy Dietary Patterns with and without Meat Improved Cardiometabolic Disease Risk Factors in Adults: A Randomized Crossover Controlled Feeding Trial.

We assessed the effects of consuming a U.S.-style healthy dietary pattern (HDP) with lean, unprocessed beef (BEEF) compared to a U.S.-style HDP without meat (vegetarian, VEG) on short-term changes in cardiometabolic disease (CMD) risk factors in adults classified as overweight or obese. Forty-one adults (22 females, 19 males; age 39.9 ± 8.0 y; BMI 29.6 ± 3.3 kg/m2; mean ± SD) completed two 5-week controlled feeding periods (randomized, crossover, controlled trial). For the BEEF HDP, two 3-oz (168-g) servings/d of lean, unprocessed beef were predominately substituted for some starchy vegetables and refined grains in the VEG HDP. Baseline and post-intervention measurements were fasting CMD risk factors, with serum low-density lipoprotein (LDL), total cholesterol (TC), and total apolipoprotein B as primary outcomes. VEG reduced LDL, insulin, and glucose compared to BEEF. Reductions did not differ between VEG vs. BEEF for TC, high-density lipoprotein (HDL), apolipoprotein A1, small, dense LDL IV, buoyant HDL2b, TC-to-HDL ratio, and systolic blood pressure. Total apolipoprotein B and all other CMD risk factors measured were not influenced by HDP type nor changed over time. Adopting a U.S.-style HDP that is either vegetarian or omnivorous with beef improved multiple cardiometabolic disease risk factors among adults classified as overweight or obese.

The impact of forced awakening on morning blood pressure surge.

BACKGROUND: Poor sleep quality can cause an increase in morning blood pressure surge (MBPS), an independent risk factor of cardiovascular disease (CVD) events. Awakening induced by external factors such as alarm clocks, may also contribute to increased MBPS. OBJECTIVES: To (1) compare the MBPS and sleep quality parameters between natural and forced awakenings and (2) examine the potential impact of forced awakening on MBPS, independent of sleep quality. METHODS: Thirty-two healthy adults participated in this pilot study, which included one night of natural awakening and one night of forced awakening (i.e., sleep was interrupted by an alarm after five hours). Objective and self-reported sleep quality parameters were measured using a multisensory wristband and sleep diaries, respectively, and beat-to-beat blood pressure variability was assessed using a continuous blood pressure monitor. Analyses included a paired t-test (objective 1) and linear mixed models (objective 2). RESULTS: Participants predominantly consisted of young, healthy, and highly educated Asian adults. During the night of sleep with forced awakening, significantly higher MBPS, lower objective wakefulness after sleep onset, and lower self-reported sleep latency were observed, compared to the night with natural awakening. Forced awakening was significantly associated with increased MBPS after controlling for age, sex, mean arterial pressure, and sleep quality. CONCLUSIONS: Forced awakening may significantly increase MBPS, consequently heightening the risk of CVD events. Study findings should be validated in a larger sample. Further research is also warranted to examine the impact of forced awakening on MBPS in individuals with CVD.

Psychological distress, forced awakening, and morning blood pressure surge.

BACKGROUND: Morning blood pressure surge (MBPS) has been recognized as an independent predictor of cardiovascular disease events. Psychological distress, including anxiety, depression, and perceived stress, and behavioral risk factors, such as poor sleep quality, have been associated with increased MBPS. Elevations in sympathetic activity induced by forced awakening may also contribute to further increases in MBPS. Yet, no examination of the interrelationships among psychological distress, sleep quality, awakening mode (natural vs. forced awakenings), and MBPS has been undertaken. OBJECTIVE: This pilot study aimed: (1) to examine if MBPS differs by awakening mode and (2) to investigate whether psychological distress is associated with MBPS difference between natural and forced awakenings, independent of sleep quality. METHODS: Thirty-two healthy adults were included in this cross-sectional study. Blood pressure was measured using a beat-to-beat blood pressure monitor over two nights, consisting of one night of natural awakening and one night of forced awakening. Psychological distress and sleep quality were assessed using questionnaires. We conducted paired t-tests (aim 1) and multiple linear regressions (aim 2). RESULTS: MBPS was significantly greater during forced awakening compared with natural awakening. In addition, the MBPS difference between natural and forced awakenings was significantly greater in participants with higher anxiety levels, independent of sleep quality. CONCLUSION: We found that augmentation of MBPS by forced awakening was significantly greater in individuals who reported higher anxiety levels. Additional research is needed to examine the potential impacts of forced awakening and anxiety on MBPS in a larger sample of individuals at risk for cardiovascular disease.

Racial/ethnic disparities in availability of volunteer unrelated donors for allogeneic transplantation.

ABSTRACT: Despite the global unrelated donor (URD) registry size, the degree to which URD availability is a transplant barrier is not established. We evaluated the availability of 3,843 URDs requested for 455 diverse adult patients (predominantly with acute leukemia). URDs for non-Europeans were more likely to be domestic and had markedly lower Donor Readiness scores. Of URDs requested for confirmatory HLA-typing (CT) alone (ie, without simultaneous workup), 1,894 of 3,529 (54%) were available. Availability of domestic URDs was 45%. Donor Readiness score was highly predictive of CT availability. More non-European patients (n = 120) than Europeans (n = 335) had >10 URDs requested and <5 available. Of workup requests (after CT or CT-workup), <70% (604/889 [68%]) were available. More non-Europeans had <2 URDs available. URD availability for CT was markedly worse for non-Europeans, with availabilities for African, non-Black Hispanic, and Asian patients being 150/458 (33%), 120/258 (47%), and 119/270 (44%), respectively, with further decrements in URD workup availability. Our data suggest the functional size of the URD pool is much smaller than appreciated, mandating major operational changes for transplant centers and donor registries. Likelihood of donor availability should have a high priority in donor selection. Considering patient ancestry and URD Donor Readiness scores, centers should pursue, and registries permit, simultaneous pursuit of many URDs and abandon futile searches. Patients should be informed about their likelihood of donor availability and alternative options. Finally, although registries should address high URD attrition and speed procurement, use of all HLA-disparate graft types is needed to facilitate timely transplant for all.

The tidyomics ecosystem: Enhancing omic data analyses.

The growth of omic data presents evolving challenges in data manipulation, analysis, and integration. Addressing these challenges, Bioconductor1 provides an extensive community-driven biological data analysis platform. Meanwhile, tidy R programming2 offers a revolutionary standard for data organisation and manipulation. Here, we present the tidyomics software ecosystem, bridging Bioconductor to the tidy R paradigm. This ecosystem aims to streamline omic analysis, ease learning, and encourage cross-disciplinary collaborations. We demonstrate the effectiveness of tidyomics by analysing 7.5 million peripheral blood mononuclear cells from the Human Cell Atlas3, spanning six data frameworks and ten analysis tools.