Biology subjects

Clark, D.

Publications and source records attributed to Clark, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Dose-Dependent Effects of Low-Intensity Focused Ultrasound on Human Deep White Matter Tracts

Background: Low-intensity focused ultrasound (LIFU) is emerging as a method for anatomically specific, noninvasive, and reversible neuromodulation of deep brain structures relevant to psychopathology. A key requirement for clinical translation is evidence of graded target engagement. We examined whether LIFU applied to deep white matter tracts produces dose-dependent functional connectivity changes in healthy adults. Methods: In this preregistered, double-blind, randomized study, 35 healthy adults underwent LIFU targeting (80 s, 10% duty cycle, estimated ISPPA 2.26 W/cm2, 0.5 MHz, in a {theta}-burst pattern) of individually modeled right thalamo-prefrontal white matter tracts under two dose conditions: one and three consecutive sonications. Dose-dependent changes in resting-state functional connectivity were examined during a 30-minute poststimulation period in 31 participants. Results: One sonication acutely increased right thalamic functional connectivity with the left thalamus (28 voxels; Z = 5.48, Cohen's d = 0.61), whereas three sonications decreased connectivity with the right dorsolateral prefrontal cortex (Z = -4.05, Cohen's d = -0.45). Poststimulation time-course analysis revealed a 3-LIFU-specific linear recovery trend in the left cerebellum (Z = 4.14, d = 0.48), reflecting initial suppression followed by progressive recovery across 30 minutes. Stronger thalamo-prefrontal structural connectivity was associated with condition-specific functional connectivity changes (left frontal pole; F = 14.73, {rho}2 = 0.41). Conclusions: These findings provide initial human evidence that LIFU is well tolerated and produces dose-dependent changes in functional connectivity associated with deep white matter tract stimulation, informing parameter selection for future circuit-based mechanistic and clinical studies.

neuroscience↗

bioRxiv2026

Neurodevelopment of Corticostriatal Circuits and Risk for Alcohol Use During the Transition from Adolescence to Adulthood

Adolescence and early adulthood are marked by rapid neurobehavioral development in reward and decision-making processes, coinciding with the initiation and escalation of alcohol use. While adolescent and young adulthood alcohol initiation is not atypical, adult trajectories diverge: some individuals reduce or discontinue use, whereas others escalate to more frequent or problematic patterns leading to substance use disorders. Corticostriatal circuits, including the ventral striatum (nucleus accumbens; NAcc) and dorsal striatum (caudate and putamen), support reward processing, goal-directed behavior, and habit formation, and are thought to contribute to distinct stages of alcohol use. Yet, how the normative maturation of these circuits relates to alcohol initiation and the transition to habitual consumption remains unclear. We used data from the National Consortium on Alcohol and NeuroDevelopment in Adolescence and Adulthood (NCANDA-A) cohort (822 participants, baseline ages 12 - 22 years old, 1 - 9 visits per participant, 4,356 total visits), a large multisite longitudinal neuroimaging sample spanning adolescence to young adulthood. We observed that rsfMRI functional connectivity (FC) patterns varied systematically across striatal subdivisions: NAcc FC followed an inverted U-shaped trajectory, peaking during adolescence; while caudate and putamen FC showed monotonic decreases with age. Adolescent peak NAcc connectivity was associated with alcohol use initiation, while a lack of normative decrease in putamen connectivity was linked to more frequent alcohol use in adulthood. Together, results suggest that the maturation of reward processing circuitry may support alcohol initiation, while a lack of habit system specialization may contribute to continued alcohol use, with potential implications for the timing of interventions aimed at limiting at-risk drinking.

neuroscience↗

bioRxiv2026

Experience-Dependent Gain Modulation Drives Thermosensory Responses in Behavior

Sensory neurons must extract behaviorally relevant features from dynamic environments while maintaining sensitivity across wide stimulus ranges. To understand how sensory encoding adapts to experience during behavior, we combine long-duration calcium imaging in freely moving C. elegans with a temperature-trajectory playback paradigm to determine how the thermosensory neuron AFD extracts behaviorally relevant sensory features during navigation. We observe that AFD functions as a leaky integrator of recently experienced temperature changes, accumulating thermal inputs over a rolling window of tens of seconds, resulting in calcium levels that represent recent temperature dynamics during runs. Importantly, we determine that AFD selectively amplifies responses to temperature changes near its learned preferred temperature. This experience-dependent gain control aligns encoding with the navigational goal, providing a mechanism for representing temperature preference within a derivative-based sensory system. A minimal mathematical model incorporating derivative detection, leaky integration, and temperature-dependent gain captures the calcium dynamics over a range of stimuli, and a simulation based on the mathematical model predicts goal-oriented locomotor strategies across stimulus regimes. Together, these findings show how gain control allows a derivative-based sensory code to represent an absolute goal and guide locomotory strategies during navigation. HighlightsO_LIAFD encodes recent temperature changes over behaviorally relevant timescales. C_LIO_LIAFD amplifies temperature-change responses within a learned temperature-centered gain window. C_LIO_LIGain control provides a mechanism for representing distance to temperature preference within the derivative-based sensory system. C_LIO_LIA mathematical model and simulation of derivative sensing, leaky integration, and gain control predicts AFD calcium responses and goal-oriented locomotory strategies across stimulus regimes. C_LI

neuroscience↗

bioRxiv2026

SWI/SNF nuclear foci scaffold peripheral gene hubs for circadian chromatin control

How dynamic circadian rhythms arise from a relatively static nuclear architecture remains a fundamental open question. Here, we identify the SWI/SNF chromatin-remodeling complex as a critical interface between the circadian clock and nuclear organization. Using endogenously tagged Moira (MOR), a core component of the Drosophila SWI/SNF complex and homolog of human BAF155, we find that MOR assembles into a small number of discrete foci near the nuclear periphery, in stark contrast to the current model of diffuse nuclear distribution for SWI/SNF-family proteins. We demonstrate that this localization is maintained by the inner nuclear envelope LEM-domain protein Otefin, effectively shifting MOR from a global to a localized regulator of chromatin architecture. DNA-FISH reveals that clock-regulated genes cluster into peripheral "hubs" that co-localize with MOR foci throughout the circadian cycle. ATAC-seq analysis shows that while MOR modulates chromatin accessibility genome-wide, it establishes a constitutive restrictive baseline specifically at clock-regulated loci. As a result, MOR depletion abolishes accessibility rhythms at these loci, rendering them constitutively hyper-accessible. This deregulation disrupts rhythmic gene expression and ultimately drives behavioral arrhythmia. Strikingly, oscillations of the core clock proteins PER and TIM remain intact, indicating that MOR loss uncouples the protein oscillator from its genomic output. Together, these results reveal that MOR-containing SWI/SNF foci form a stable perinuclear scaffold that gates chromatin accessibility, enabling the core clock machinery to convert transient protein oscillations into high-amplitude transcriptional rhythms. Significance StatementHow dynamic circadian rhythms emerge from a relatively static nuclear architecture remains a fundamental mystery. Here, we challenge the assumption that clock-target genes are randomly distributed by identifying a precise nuclear organization where these genes cluster into peripheral hubs. These hubs co-localize with stable SWI/SNF (MOR) foci anchored at the nuclear envelope. We demonstrate that this perinuclear scaffold is essential for gating rhythmic chromatin accessibility. Most importantly, loss of this architecture uncouples robustly oscillating clock protein program from its genomic and behavioral outputs. These findings reveal that circadian timekeeping is not merely a biochemical process but a spatially organized one, where nuclear topology licenses the translation of time into circadian rhythms.

cell biology↗

bioRxiv2026

Afterimages drive a shared visual motion reversal illusion in Drosophila

Illusions expose core computations in perception. In one visual apparent-motion illusion, perceptual direction is reversed when phase-shifted gratings are interleaved with uniform frames. Here, we demonstrate that Drosophila exhibits the same direction reversal reported in mammals. Combining behavior, targeted silencing, two-photon imaging, and modeling, we localize the origin of this illusion to elementary motion pathways. Silencing direction-selective T4/T5 neurons abolishes the reversal, and recordings reveal that downstream wide-field neurons invert their directional preference as interleave duration increases. Replacing periodic gratings with random binary patterns preserves the reversal, implicating afterimages rather than spatial periodicity. Imaging neurons upstream of T4/T5 shows signatures of an afterimage, whose emergence depends on interleave luminance. Critically, dark interleaves suppress afterimages and eliminate both the neural and behavioral reversal, whereas light interleaves preserve or enhance it. Thus, afterimages are central to this shared illusion and explain a deficiency of canonical motion-energy accounts. These results link a classic apparent-motion phenomenon to identified circuit elements and reveal a simple stimulus manipulation that switches an illusion on and off.

neuroscience↗

bioRxiv2025

Sequestration of clock proteins into repressive nuclear condensates orchestrates circadian gene repression

Circadian clocks orchestrate [~]24-hour cycles in gene expression, behavior, and physiology across most organisms1. Our recent study has revealed a striking spatial organization in the nucleus during the repression phase: core clock proteins such as Drosophila PERIOD (PER) are organized into distinct nuclear foci close to the inner nuclear envelope of clock neurons, and clock-regulated genes are similarly positioned in the nucleus2. However, the functional relevance of this subnuclear organization is unknown. Here, we investigate how the spatial organization of clock proteins and chromatin regulates circadian gene repression. Given that PER partners with TIMELESS (TIM) to enact transcriptional repression, we first investigated whether TIM is also a component of these nuclear foci. Using CRISPR-Cas9 to endogenously tag TIM with mNeonGreen, we performed high-resolution live imaging in Drosophila clock neurons. We found that TIM forms nuclear foci during the repression phase that co-localize with PER condensates, whereas TIM remains diffuse in the cytoplasm of per01 null mutants. To probe the spatial relationship between these condensates and clock-regulated genes, we combined protein imaging with fluorescence in situ hybridization (FISH) which revealed that PER/TIM condensates were positioned adjacent to, but did not overlap with, clock gene loci during the repression phase. These results suggest that core clock proteins are spatially sequestered into repressive condensates away from chromatin, providing a new framework for understanding how nuclear architecture and phase separation together orchestrate rhythmic gene expression.

cell biology↗

bioRxiv2025

Developmental variation in dopamine neurobiology, neurocognitive functioning, and impulsivity shape substance use trajectories in youth

Theoretical neurodevelopmental models implicate increases in dopamine (DA) function and limitations in neurocognitive control in risk-taking behavior, including substance use, during the transition from adolescence to adulthood. However, developmental relationships between DA, neurocognitive control, and the emergence of substance use are poorly understood. Here, we tested the role of basal ganglia tissue iron, reflecting DA neurophysiology, as well as impulsivity and inhibitory control in longitudinal developmental trajectories of substance use. We leveraged the National Consortium on Alcohol and NeuroDevelopment in Adolescence and Adulthood (NCANDA-A) cohort, a large, multisite longitudinal neuroimaging study of 807 participants (baseline ages 12 - 22 years old, 50% female, 1 - 9 annual visits per participant, 6164 sessions total). Substance use, inhibitory control, and tissue iron increased non-linearly during adolescence into young adulthood, concurrent with decreases in impulsivity. Non-linear Growth Mixture Models identified four common trajectories of substance use: low (no- or low levels of use across visits; 30% of participants), youth peak (peak use in adolescence/young adulthood followed by declines; 26%), adolescent increasing (early, steep linear increases in use from adolescence into adulthood; 17%), and adult increasing (low use in adolescence, followed by late linear increases into adulthood; 26%). We show that increased substance use was associated with a phenotype of high impulsivity, low inhibitory control, and low basal ganglia tissue iron, particularly in early adolescence in individuals who displayed youth peak patterns in substance use trajectories. These findings highlight that early developmental differences in DA-related neurobiology and associated impulsivity and cognitive control shape distinct trajectories of adolescent substance use, underscoring adolescence as a critical window for the early identification and implementation of neurodevelopmentally sensitive interventions for substance use disorders.

neuroscience↗

bioRxiv2025

Regenerative Grazing as a Climate Change Mitigation Strategy: A Systematic Review

Ruminant livestock production is a meaningful contributor to global greenhouse gas (GHG) emissions. Regenerative grazing has been proposed as a climate change mitigation strategy for offsetting livestock GHG emissions by potentially causing additional soil organic carbon (SOC) sequestration. We review the current state of the literature and collect reported and inferred SOC sequestration from regenerative grazing experiments, ranking their study designs by ascending evidentiary strength: observational, cross-sectional and longitudinal. Across 28 studies that compare regenerative to conventional grazing, the reported and inferred SOC sequestration rates in regenerative grazing treatments varied widely, with the highest values reported in lower-strength observational studies. Among higher-strength cross-sectional studies and longitudinal studies, median additional SOC sequestration rates in regenerative grazing treatments were not significantly different than zero, indicating no significant enhancement of SOC across all regenerative grazing interventions. Currently, higher-strength evidence does not support widespread claims of SOC sequestration from regenerative grazing. To clarify its potential for climate mitigation, a greater number of longitudinal studies are needed.

ecology↗

bioRxiv2025

The effects of predator recovery and climate change on the long-term demography of a flagship herbivore

In the western United States, ecosystems are being reshaped from both bottom-up and top-down processes. Widespread carnivore recolonizations after 20th century extirpations have returned top-down pressures to ecosystems, and climate change is reshaping bottom-up forces through shifts in the timing and length of growing seasons, resulting in reduced forage quality and quantity. Large herbivores, such as elk (Cervus canadensis), function as flagship species for conservation and have potential for both top-down and bottom-up forces to shape demography as ecosystems change. To test the roles of top-down (puma density (Puma concolor)) and bottom-up (drought severity and elk density) processes in shaping large herbivore demography, and to tie those effects to population trajectories, we built an integrated population model (IPM) using 36 years of elk data spanning the recolonization of pumas and long-term climate change in eastern Oregon, USA. We tested the effects of top-down and bottom-up forces on elk recruitment, calf survival, and population growth. We also tested effects of bottom-up forces on elk pregnancy rates. Puma recolonization corresponded with declines in mean recruitment from 0.44 to 0.32 calves per female and in calf survival from 0.92 to 0.69, corresponding with a 4% drop in population growth. Drought severity increased over our study period, explaining a decline in mean recruitment from 0.39 to 0.32 calves per female, which corresponds to a 3% reduction in population growth. Drought severity likely acted on recruitment through reduced pregnancy rates. Lactating females showed lower pregnancy rates in drought conditions, while drought from fall breeding periods to the following fall had no effect on recruitment. While both top-down and bottom-up forces explained variation in elk demography over the course of our study, bottom-up forces are likely to be more influential on large herbivores moving forward. Predator populations stabilized following recovery, limiting the top-down contribution to annual variation in vital rates. Climate change-induced drought patterns, however, are accelerating during summer and fall throughout large areas of the interior western U.S. Thus, our results indicate the potential for increasingly strong bottom-up negative effects on herbivores whose performance depends on a narrow period of summer nutrition. Open Research StatementData are not yet provided. Many of the data from Starkey Experimental Forest and Range are already publicly available, and we are currently working to post data for this manuscript on the Forest Service Research Data Archive (FSRDA) linked to the rest of the data from Starkey. Upon acceptance, all data and the relevant code will be archived the FSRDA. Currently, the code for the paper is publicly available on Github at https://github.com/keloonam/starkey_ipm

ecology↗

bioRxiv2025

Spatial and Temporal Patterns of Wolf Occurrences on the Summer Range of the Eastern Migratory Cape Churchill Caribou Population in the Hudson Bay Lowlands of Manitoba

Wolves (Canis lupus) function as a top predator across diverse ecosystems including the sub-arctic, and they have been managed in often controversial ways. Communities and scientists are increasingly supporting minimally invasive research and monitoring, including using trail cameras. We employed a network of 15 Reconyx trail cameras at three monitoring areas aimed at detecting the spatial and temporal aspects of wolf occurrences within the summer range of Eastern Migratory Cape Churchill caribou in Wapusk National Park in the Hudson Bay Lowlands of Manitoba, Canada from 2013-2021. In this first peer-reviewed quantitative study of wolves in the region, we found that wolves detection events were generally consistent across years. Wolf distribution was consistently positively skewed toward the southern part of the caribou summer range in all years. Wolves experienced extreme environmental conditions, with a 60{degrees}C range in temperature, from a low of -32{degrees}C in winter to a high of +28{degrees}C in summer and an annual change in day length of >11 hours between summer and winter. Wolves occurred most commonly in spring and summer and occurred at equal frequency during night and day overall but selected for nighttime in September, October, and November as day length shortened dramatically.

ecology↗

bioRxiv2025

Fly navigational responses to odor motion and gradient cues are tuned to plume statistics

Odor cues guide animals to food and mates. Different environmental conditions can create differently patterned odor plumes, making navigation more challenging. Prior work has shown that animals turn upwind when they detect odor and cast crosswind when they lose it. Animals with bilateral olfactory sensors can also detect directional odor cues, such as odor gradient and odor motion. It remains unknown how animals use these two directional odor cues to guide crosswind navigation in odor plumes with distinct statistics. Here, we investigate this problem theoretically and experimentally. We show that these directional odor cues provide complementary information for navigation in different plume environments. We numerically analyzed real plumes to show that odor gradient cues are more informative about crosswind directions in relatively smooth odor plumes, while odor motion cues are more informative in turbulent or complex plumes. Neural networks trained to optimize crosswind turning converge to distinctive network structures that are tuned to odor gradient cues in smooth plumes and to odor motion cues in complex plumes. These trained networks improve the performance of artificial agents navigating plume environments that match the training environment. By recording Drosophila fruit flies as they navigated different odor plume environments, we verified that flies show the same correspondence between informative cues and plume types. Fly turning in the crosswind direction is correlated with odor gradients in smooth plumes and with odor motion in complex plumes. Overall, these results demonstrate that these directional odor cues are complementary across environments, and that animals exploit this relationship. SignificanceMany animals use smell to find food and mates, often navigating complex odor plumes shaped by environmental conditions. While upwind movement upon odor detection is well established, less is known about how animals steer crosswind to stay in the plume. We show that directional odor cues--gradients and motion--guide crosswind navigation differently depending on plume structure. Gradients carry more information in smooth plumes, while motion dominates in turbulent ones. Neural network trained to optimize crosswind navigation reflect this distinction, developing gradient sensitivity in smooth environments and motion sensitivity in complex ones. Experimentally, fruit flies adjust their turning behavior to prioritize the most informative cue in each context. These findings likely generalize to other animals navigating similarly structured odor plumes.

animal behavior and cognition↗

bioRxiv2024

Variability and correlations among vital rates and their influence on population growth in mule and black-tailed deer

To reverse observed range-wide population declines, managers of mule and black- tailed deer (Odocoileus hemionus) require information on the vital rates and life stages that are most influential to population growth for which to target management actions. We conducted a range-wide literature review and used hierarchical models to provide biological descriptions of mule and black-tailed deer vital rates, their variability, and how they correlate with one another. We then used matrix models and life-stage simulation analysis to determine the individual vital rates that contributed most to lambda, i.e., annual population growth rate. Adult female survival was the vital rate with the greatest ability to predict lambda and explained 62% of the variation in population growth. While annual juvenile survival explained 44% of the variation in lambda, summer and winter juvenile survival by themselves were far less explanatory than adult female survival. Winter fawn:doe ratios, a metric often collected by management agencies, only explained 10% of the variation in lambda. When adult female survival was 0.84, our simulations estimated an equal probability that a population would increase versus decrease, and correspondingly, the estimate of lambda was 1.0 with a 95% credible interval of 0.88-1.14. Simulations suggested that populations with adult survival rates less than 70% would always decline, but as survival increased beyond this value lambda increased linearly and never plateaued. In contrast, the probability of observing a stable lambda plateaued when annual juvenile survival reached approximately 0.5. The mean lambda calculated from all simulated values within the observed range of vital rate values across the species geographical distribution was 0.975, and in 61% of the simulations lambda was < 1. After 20 years, we estimated that this distribution of lambda values would cause populations to decrease in 92% of instances with a mean decrease of 44%. Our results align with the observed declines in mule deer populations throughout their range over recent decades and suggest that these trends will continue until management can improve survival of adult females.

ecology↗

bioRxiv2023

Single-cell Transcriptional Analysis of the Cellular Immune Response in the Oral Mucosa of Mice

Periodontal health is dependent on a symbiotic relationship of the host immune response with the oral microbiota. Pathologic shifts of the microbial plaque elicit an immune response that eventually leads to the recruitment and activation of osteoclasts and matrix metalloproteinases and the eventual tissue destruction that is evident in periodontal disease. Once the microbial stimulus is removed, an active process of inflammatory resolution begins. The goal of this work was to use scRNAseq to demonstrate the unique cellular immune response across three distinct conditions of periodontal health, disease, and resolution using mouse models. Periodontal disease was induced using a ligature model. Resolution was modeled by removing the ligature and allowing the mouse to recover. Immune cells (Cd45+) were isolated from the periodontium and analyzed via scRNAseq. Gene signature shifts across the three conditions were characterized and shown to be largely driven by macrophage and neutrophils during the periodontal disease and resolution conditions. Resolution of periodontal disease was characterized by the differential regulation of unique gene subsets. Clustering analysis characterized multiple cellular subpopulations within B Cells, macrophages, and neutrophils that demonstrated differential expansion and contraction across conditions of periodontal health, disease, and resolution. Interestingly, we identified a transcriptionally distinct macrophage subpopulation that expanded during the resolution condition and demonstrated an immunoregulatory gene signature. We identified a cell surface marker for this resolution-associated macrophage subgroup (Cd74) and validated the expansion of this subgroup during resolution via flow cytometry. This work presents a robust immune cell atlas for study of the immunological changes in the oral mucosa during three distinct conditions of periodontal health, disease, and resolution and it improves our understanding of the cellular and molecular markers that characterize health from disease for the development of future diagnostics and therapies.

immunology↗

bioRxiv2022

Streamlined, cell-specific single-molecule RNA-FISH of core clock mRNAs in clock neurons in whole mount Drosophila brains

Circadian clocks are [~]24-hour timekeepers that control rhythms in almost all aspects of our behavior and physiology. While it is well known that subcellular localization of core clock proteins plays a critical role in circadian regulation, very little is known about the spatiotemporal organization of core clock mRNAs and its role in generating [~]24-hr circadian rhythms. Here we describe a streamlined single molecule Fluorescence In Situ Hybridization (smFISH) protocol and a fully automated analysis pipeline to precisely quantify the number and subcellular location of mRNAs of Clock, a core circadian transcription factor, in individual clock neurons in whole mount Drosophila adult brains. Specifically, we used [~]48 fluorescent oligonucleotide probes that can bind to an individual Clock mRNA molecule, which can then be detected as a diffraction-limited spot. Further, we developed a machine learning-based approach for 3-D cell segmentation, based on a pretrained encoder-decoder convolutional neural network, to automatically identify the cytoplasm and nuclei of clock neurons. We combined our segmentation model with a spot counting algorithm to detect Clock mRNA spots in individual clock neurons. Our results demonstrate that the number of Clock mRNA molecules cycle in large ventral lateral clock neurons (lLNvs) with peak levels at ZT4 (4 hours after lights are turned on) with ~80 molecules/neuron and trough levels at ZT16 with [~]30 molecules/neuron. Our streamlined smFISH protocol and deep learning-based analysis pipeline can be employed to quantify the number and subcellular location of any mRNA in individual clock neurons in Drosophila brains. Further, this method can open mechanistic and functional studies into how spatiotemporal localization of clock mRNAs affect circadian rhythms.

cell biology↗

bioRxiv2021

#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol

We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental methods, which are limited in their ability to interrogate aerosols at the atomic/molecular level and thus ob-scure our understanding of airborne transmission. We demonstrate how our integrated data-driven platform provides a new way of exploring the composition, structure, and dynamics of aerosols and aerosolized viruses, while driving simulation method development along several important axes. We present a series of initial scientific discoveries for the SARS-CoV-2 Delta variant, noting that the full scientific impact of this work has yet to be realized. ACM Reference FormatAbigail Dommer1{dagger}, Lorenzo Casalino1{dagger}, Fiona Kearns1{dagger}, Mia Rosenfeld1, Nicholas Wauer1, Surl-Hee Ahn1, John Russo,2 Sofia Oliveira3, Clare Morris1, AnthonyBogetti4, AndaTrifan5,6, Alexander Brace5,7, TerraSztain1,8, Austin Clyde5,7, Heng Ma5, Chakra Chennubhotla4, Hyungro Lee9, Matteo Turilli9, Syma Khalid10, Teresa Tamayo-Mendoza11, Matthew Welborn11, Anders Christensen11, Daniel G. A. Smith11, Zhuoran Qiao12, Sai Krishna Sirumalla11, Michael OConnor11, Frederick Manby11, Anima Anandkumar12,13, David Hardy6, James Phillips6, Abraham Stern13, Josh Romero13, David Clark13, Mitchell Dorrell14, Tom Maiden14, Lei Huang15, John McCalpin15, Christo- pherWoods3, Alan Gray13, MattWilliams3, Bryan Barker16, HarindaRajapaksha16, Richard Pitts16, Tom Gibbs13, John Stone6, Daniel Zuckerman2*, Adrian Mulholland3*, Thomas MillerIII11,12*, ShantenuJha9*, Arvind Ramanathan5*, Lillian Chong4*, Rommie Amaro1*. 2021. #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy ofDeltaSARS-CoV-2 in a Respiratory Aerosol. In Supercomputing 21: International Conference for High Perfor-mance Computing, Networking, Storage, and Analysis. ACM, New York, NY, USA, 14 pages. https://doi.org/finalDOI

biophysics↗

bioRxiv2021

A Comprehensive Overview of the Physical Health of the Adolescent Brain Cognitive Development Study (ABCD) Cohort at Baseline

Physical health in childhood is crucial for neurobiological as well as overall development, and can shape long-term outcomes into adulthood. The landmark, longitudinal Adolescent Brain Cognitive Development StudySM (ABCD study(R)), was designed to investigate brain development and health in almost 12,000 youth who were recruited when they were 9-10 years old and will be followed through adolescence and early adulthood. The overall goal of this paper is to provide descriptive analyses of physical health measures in the ABCD study at baseline, including but not limited to sleep, physical activity and sports involvement, and body mass index, and how these measures vary across demographic groups. This paper outlines how the physical health of the ABCD sample corresponds with that of the US population and highlights important avenues for health disparity research. This manuscript will provide important information for ABCD users and help guide analyses investigating physical health as it pertains to adolescent and young adult development.

developmental biology↗

bioRxiv2021

Adolescent Binge Drinking is Associated with Accelerated Decline of Gray Matter Volume

The age- and time-dependent effects of binge-drinking on adolescent brain development have not been well characterized even though binge drinking is a health crisis among adolescents. The impact of binge drinking on gray matter volume development was examined using longitudinal data from the National Consortium on Alcohol and NeuroDevelopment in Adolescence (NCANDA). Non-binge drinkers (n=177) were matched to binge drinkers (n=164) on potential confounders. Number of binge drinking episodes in the past year was linked to decreased volumes for total gray matter, frontal, parietal, temporal, and occipital lobes (ps<.001). Interactions of binge drinking episodes and age demonstrated stronger effects in younger subjects for total gray matter, frontal, temporal, and occipital lobes (ps<.001). Subsequent models included binge drinking coded in multiple ways. Models sensitive to number of episodes and temporal proximity to outcomes provided the best fits. Declines in gray matter volume association with binge drinking are potentially related to changes in cognition frequently reported among binge drinking adolescents. Results underscore the potential importance of delaying initiation of binge drinking and provide evidence for a dose-response relationship of binge drinking to gray matter decline. Temporally proximal binge drinking was associated more strongly with gray matter decline, suggesting the potential for recovery.

neuroscience↗

bioRxiv2021

Quantitative dissection of color patterning in the foliar ornamental Coleus reveals underlying features driving aesthetic value

O_LIColeus is a popular ornamental plant that exhibits a diverse array of foliar color patterns. New cultivars are currently hand selected by both amateur and experienced plant breeders. In this study, we reimagine coleus breeding using a quantitative color analysis framework. C_LIO_LIDespite impressive advances in high-throughput data collection and processing, complex color patterns remain challenging to extract from image datasets. Using a new phenotyping approach called "ColourQuant," we extract and analyze pigmentation patterns from one of the largest coleus breeding populations in the world. C_LIO_LIWorking with this massive dataset, we are able to analyze quantitative relationships between maternal plants and their progeny, identify features that underlie breeder-selections, and collect and compare consumer input on trait preferences. C_LIO_LIThis study is one of the most comprehensive explorations into complex color patterning in plant biology and provides new insights and tools for exploring the color pallet of the plant kingdom. C_LI

plant biology↗