Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front.

Antitumoral immunity requires organized, spatially nuanced interactions between components of the immune tumor microenvironment (iTME). Understanding this coordinated behavior in effective versus ineffective tumor control will advance immunotherapies. We re-engineered co-detection by indexing (CODEX) for paraffin-embedded tissue microarrays, enabling simultaneous profiling of 140 tissue regions from 35 advanced-stage colorectal cancer (CRC) patients with 56 protein markers. We identified nine conserved, distinct cellular neighborhoods (CNs)-a collection of components characteristic of the CRC iTME. Enrichment of PD-1+CD4+ T cells only within a granulocyte CN positively correlated with survival in a high-risk patient subset. Coupling of tumor and immune CNs, fragmentation of T cell and macrophage CNs, and disruption of inter-CN communication was associated with inferior outcomes. This study provides a framework for interrogating how complex biological processes, such as antitumoral immunity, occur through concerted actions of cells and spatial domains.

Combined protein and nucleic acid imaging reveals virus-dependent B cell and macrophage immunosuppression of tissue microenvironments.

Understanding the mechanisms of HIV tissue persistence necessitates the ability to visualize tissue microenvironments where infected cells reside; however, technological barriers limit our ability to dissect the cellular components of these HIV reservoirs. Here, we developed protein and nucleic acid in situ imaging (PANINI) to simultaneously quantify DNA, RNA, and protein levels within these tissue compartments. By coupling PANINI with multiplexed ion beam imaging (MIBI), we measured over 30 parameters simultaneously across archival lymphoid tissues from healthy or simian immunodeficiency virus (SIV)-infected nonhuman primates. PANINI enabled the spatial dissection of cellular phenotypes, functional markers, and viral events resulting from infection. SIV infection induced IL-10 expression in lymphoid B cells, which correlated with local macrophage M2 polarization. This highlights a potential viral mechanism for conditioning an immunosuppressive tissue environment for virion production. The spatial multimodal framework here can be extended to decipher tissue responses in other infectious diseases and tumor biology.

Autism-Misregulated eIF4G Microexons Control Synaptic Translation and Higher Order Cognitive Functions.

Microexons represent the most highly conserved class of alternative splicing, yet their functions are poorly understood. Here, we focus on closely related neuronal microexons overlapping prion-like domains in the translation initiation factors, eIF4G1 and eIF4G3, the splicing of which is activity dependent and frequently disrupted in autism. CRISPR-Cas9 deletion of these microexons selectively upregulates synaptic proteins that control neuronal activity and plasticity and further triggers a gene expression program mirroring that of activated neurons. Mice lacking the Eif4g1 microexon display social behavior, learning, and memory deficits, accompanied by altered hippocampal synaptic plasticity. We provide evidence that the eIF4G microexons function as a translational brake by causing ribosome stalling, through their propensity to promote the coalescence of cytoplasmic granule components associated with translation repression, including the fragile X mental retardation protein FMRP. The results thus reveal an autism-disrupted mechanism by which alternative splicing specializes neuronal translation to control higher order cognitive functioning.

Cell4D: a general purpose spatial stochastic simulator for cellular pathways.

BACKGROUND: With the generation of vast compendia of biological datasets, the challenge is how best to interpret 'omics data alongside biochemical and other small-scale experiments to gain meaningful biological insights. Key to this challenge are computational methods that enable domain-users to generate novel hypotheses that can be used to guide future experiments. Of particular interest are flexible modeling platforms, capable of simulating a diverse range of biological systems with low barriers of adoption to those with limited computational expertise. RESULTS: We introduce Cell4D, a spatial-temporal modeling platform combining a robust simulation engine with integrated graphics visualization, a model design editor, and an underlying XML data model capable of capturing a variety of cellular functions. Cell4D provides an interactive visualization mode, allowing intuitive feedback on model behavior and exploration of novel hypotheses, together with a non-graphics mode, compatible with high performance cloud compute solutions, to facilitate generation of statistical data. To demonstrate the flexibility and effectiveness of Cell4D, we investigate the dynamics of CEACAM1 localization in T-cell activation. We confirm the importance of Ca2+ microdomains in activating calmodulin and highlight a key role of activated calmodulin on the surface expression of CEACAM1. We further show how lymphocyte-specific protein tyrosine kinase can help regulate this cell surface expression and exploit spatial modeling features of Cell4D to test the hypothesis that lipid rafts regulate clustering of CEACAM1 to promote trans-binding to neighbouring cells. CONCLUSIONS: Through demonstrating its ability to test and generate hypotheses, Cell4D represents an effective tool to help integrate knowledge across diverse, large and small-scale datasets.

Superlubric Sliding of Graphene Auto-Kirigami with Interfaces Containing Self-Assembled Stripe-Pattern Adsorbates.

Van der Waals heterostructures formed by stacked 2D materials show exceptional electronic, mechanical, and optical properties. Superlubricity, a condition where atomically flat, incommensurate planes of atoms result in ultra-low friction, is a prime example enabling, for example, self-assembly of optically visible graphene nanostructures in air via a sliding auto-kirigami process. Here, it is demonstrated that a subtle but ubiquitous adsorbate stripe structure found on graphene and graphitic surfaces in ambient conditions remains stable within the interface between twisted graphene layers as they slide over each other. Despite this contamination, the interface retains an exceptional superlubricious state with an estimated upper bound frictional shear strength of 10 kPa, indicating that direct atomic incommensurate contact is not required to achieve ambient superlubricity for 2D materials. The results suggest that any phenomena depending on 2D heterostructure interfaces such as exotic electronic behavior may need to consider the presence of stripe adsorbate structures that remain intercalated.

Arabidopsis PROTODERMAL FACTOR2 binds lysophosphatidylcholines and transcriptionally regulates phospholipid metabolism.

Plant homeodomain leucine zipper IV (HD-Zip IV) transcription factors (TFs) contain an evolutionarily conserved steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domain. While the START domain is required for TF activity, its presumed role as a lipid sensor is not clear. Here we used tandem affinity purification from Arabidopsis cell cultures to demonstrate that PROTODERMAL FACTOR2 (PDF2), a representative member that controls epidermal differentiation, recruits lysophosphatidylcholines (LysoPCs) in a START-dependent manner. Microscale thermophoresis assays confirmed that a missense mutation in a predicted ligand contact site reduces lysophospholipid binding. We additionally found that PDF2 acts as a transcriptional regulator of phospholipid- and phosphate (Pi) starvation-related genes and binds to a palindromic octamer with consensus to a Pi response element. Phospholipid homeostasis and elongation growth were altered in pdf2 mutants according to Pi availability. Cycloheximide chase experiments revealed a role for START in maintaining protein levels, and Pi starvation resulted in enhanced protein destabilization, suggesting a mechanism by which lipid binding controls TF activity. We propose that the START domain serves as a molecular sensor for membrane phospholipid status in the epidermis. Our data provide insights toward understanding how the lipid metabolome integrates Pi availability with gene expression.

Lung function changes in children exposed to mine fire smoke in infancy.

BACKGROUND AND OBJECTIVE: Chronic, low-intensity air pollution exposure has been consistently associated with reduced lung function throughout childhood. However, there is limited research regarding the implications of acute, high-intensity air pollution exposure. We aimed to determine whether there were any associations between early life exposure to such an episode and lung growth trajectories. METHODS: We conducted a prospective cohort study of children who lived in the vicinity of the Hazelwood coalmine fire. Lung function was measured using respiratory oscillometry. Z-scores were calculated for resistance (R5 ) and reactance at 5 Hz (X5 ) and area under the reactance curve (AX). Two sets of analyses were conducted: (i) linear regression to assess the cross-sectional relationship between post-natal exposure to mine fire-related particulate matter with an aerodynamic diameter of less than 2.5 micrometres (PM2.5 ) and lung function at the 7-year follow-up and (ii) linear mixed-effects models to determine whether there was any association between exposure and changes in lung function between the 3- and 7-year follow-ups. RESULTS: There were no associations between mine fire-related PM2.5 and any of the lung function measures, 7-years later. There were moderate improvements in X5 (ß: -0.37 [-0.64, -0.10] p = 0.009) and AX (ß: -0.40 [-0.72, -0.08] p = 0.014), between the 3- and 7-year follow-ups that were associated with mean PM2.5 , in the unadjusted and covariance-adjusted models. Similar trends were observed with maximum PM2.5 . CONCLUSION: There was a moderate improvement in lung stiffness of children exposed to PM2.5 from a local coalmine fire in infancy, consistent with an early deficit in lung function at 3-years after the fire that had resolved by 7-years.

Examining the Association between Punishment and Reward Sensitivity and Response Inhibition to Previously-Incentivized Cues across Development.

Processing and learning from affective cues to guide goal-directed behavior may be particularly important during adolescence; yet the factors that promote and/or disrupt the ability to integrate value in order to guide decision making across development remain unclear. The present study (N = 1046) assessed individual difference factors (self-reported punishment and reward sensitivity) related to whether previously-rewarded and previously-punished cues differentially impact goal-directed behavior (response inhibition) in a large developmental sample. Participants were between the ages of 8-21 years (Mage = 14.29, SD = 3.97, 50.38% female). Previously-rewarded cues improved response inhibition among participants age 14 and older. Further, punishment sensitivity predicted overall improved response inhibition among participants aged 10 to 18. The results highlight two main factors that are associated with improvements in the ability to integrate value to guide goal-directed behaviour - cues in the environment (e.g., reward-laden cues) and individual differences in punishment sensitivity. These findings have implications for both educational and social policies aimed at characterizing the ways in which youth integrate value to guide decision making.

Graded Variation in T1w/T2w Ratio during Adolescence: Measurement, Caveats, and Implications for Development of Cortical Myelin.

Adolescence is characterized by the maturation of cortical microstructure and connectivity supporting complex cognition and behavior. Axonal myelination influences brain connectivity during development by enhancing neural signaling speed and inhibiting plasticity. However, the maturational timing of cortical myelination during human adolescence remains poorly understood. Here, we take advantage of recent advances in high-resolution cortical T1w/T2w mapping methods, including principled correction of B1+ transmit field effects, using data from the Human Connectome Project in Development (HCP-D; N = 628, ages 8-21). We characterize microstructural changes relevant to myelination by estimating age-related differences in T1w/T2w throughout the cerebral neocortex from childhood to early adulthood. We apply Bayesian spline models and clustering analysis to demonstrate graded variation in age-dependent cortical T1w/T2w differences that are correlated with the sensorimotor-association (S-A) axis of cortical organization reported by others. In sensorimotor areas, T1w/T2w ratio measures start at high levels at early ages, increase at a fast pace, and decelerate at later ages (18-21). In intermediate multimodal areas along the S-A axis, T1w/T2w starts at intermediate levels and increases linearly at an intermediate pace. In transmodal/paralimbic association areas, T1w/T2w starts at low levels and increases linearly at the slowest pace. These data provide evidence for graded variation of the T1w/T2w ratio along the S-A axis that may reflect cortical myelination changes during adolescence underlying the development of complex information processing and psychological functioning. We discuss the implications of these results as well as caveats in interpreting magnetic resonance imaging (MRI)-based estimates of myelination.SIGNIFICANCE STATEMENT Myelin is a lipid membrane that is essential to healthy brain function. Myelin wraps axons to increase neural signaling speed, enabling complex neuronal functioning underlying learning and cognition. Here, we characterize the developmental timing of myelination across the cerebral cortex during adolescence using a noninvasive proxy measure, T1w/T2w mapping. Our results provide new evidence demonstrating graded variation across the cortex in the timing of T1w/T2w changes during adolescence, with rapid T1w/T2w increases in lower-order sensory areas and gradual T1w/T2w increases in higher-order association areas. This spatial pattern of microstructural brain development closely parallels the sensorimotor-to-association axis of cortical organization and plasticity during ontogeny.

Risk factors for poorer respiratory outcomes in adolescents and young adults born preterm.

RATIONALE: The respiratory outcomes for adult survivors of preterm birth in the postsurfactant era are wide-ranging with prognostic factors, especially those encountered after the neonatal period, poorly understood. OBJECTIVES: To obtain comprehensive 'peak' lung health data from survivors of very preterm birth and identify neonatal and life-course risk factors for poorer respiratory outcomes in adulthood. METHODS: 127 participants born ≤32 weeks gestation (64%, n=81 with bronchopulmonary dysplasia (BPD), initially recruited according to a 2 with-BPD:1 without-BPD strategy), and 41 term-born controls completed a lung health assessment at 16-23 years, including lung function, imaging and symptom review. Risk factors assessed against poor lung health included neonatal treatments, respiratory hospitalisation in childhood, atopy and tobacco smoke exposure. MEASUREMENTS AND MAIN RESULTS: Young adults born prematurely had greater airflow obstruction, gas trapping and ventilation inhomogeneity, in addition to abnormalities in gas transfer and respiratory mechanics, compared with term. Beyond lung function, we observed greater structural abnormalities, respiratory symptoms and inhaled medication use. A previous respiratory admission was associated with airway obstruction; mean forced expiratory volume in 1 s/forced vital capacity z-score was -0.561 lower after neonatal confounders were accounted for (95% CI -0.998 to -0.125; p=0.012). Similarly, respiratory symptom burden was increased in the preterm group with a respiratory admission, as was peribronchial thickening (6% vs 23%, p=0.010) and bronchodilator responsiveness (17% vs 35%, p=0.025). Atopy, maternal asthma and tobacco smoke exposure did not influence lung function or structure at 16-23 years in our preterm cohort. CONCLUSIONS: Even after accounting for the neonatal course, a respiratory admission during childhood remained significantly associated with reduced peak lung function in the preterm-born cohort, with the largest difference seen in those with BPD. A respiratory admission during childhood should, therefore, be considered a risk factor for long-term respiratory morbidity in those born preterm, especially for individuals with BPD.

Factors influencing participation in home, school, and community settings by children and adolescents with neuromuscular disorders: A qualitative descriptive study.

AIM: This study explored how children and adolescents with a neuromuscular disorder (NMD) and their parents experienced barriers and enablers to the child's participation. METHOD: This was a qualitative descriptive design. Fourteen semi-structured interviews were conducted (n = 13 mothers, n = 4 fathers, n = 8 children and adolescents) including one to three family members for each interview according to their preference. Data were analysed by content analysis, using the family of Participation-Related Constructs (fPRC), to characterize the components of participation. RESULTS: Meaningful participation was illustrated in the personal categories of the fPRC including the child's sense of self, preferences, and competence to perform activities. Enablers and barriers related to adaptive equipment and activity modification, social relationships, inclusion, accessibility to venues, social attitudes, and policies. INTERPRETATION: Personal motivators are critical to understanding what participation is meaningful to children and adolescents with NMDs. Social and physical supports within the child's immediate environment as well as accessibility and advocacy more widely in the community enable participation. The fPRC is a useful tool for understanding participation in these children; it informs how to support participation and suggests domains for evaluation in future intervention studies. Advocacy for participation should consider targets in the immediate and broader environments. WHAT THIS PAPER ADDS: The family of Participation-Related Constructs classified the components of participation for children and adolescents with neuromuscular disorders. Meaningful participation involved a complex interaction between personal and environmental factors. Barriers to participation included poor accessibility, lack of equipment, and social exclusion.

Longitudinal effects of prenatal exposure to plastic-derived chemicals and their metabolites on asthma and lung function from childhood into adulthood.

BACKGROUND AND OBJECTIVE: Environmental exposure to phthalates and bisphenol A (BPA), chemicals used in the production of plastics, may increase risk for asthma and allergies. However, little is known about the long-term effects of early life exposure to these compounds. We investigated if prenatal exposure to these compounds was associated with asthma, allergy and lung function outcomes from early childhood into adulthood in a cohort study. METHODS: Maternal serum samples collected from 846 pregnant women in the Raine Study were assayed for BPA and phthalate metabolites. The children of these women were followed up at 5, 13 and 22 years where spirometry and respiratory questionnaires were conducted to determine asthma and allergy status. Lung function trajectories were derived from longitudinal spirometry measurements. Multinomial logistic regression and weighted quantile sum regression was used to test associations of individual and chemical mixtures with asthma phenotypes and lung function trajectories. RESULTS: Effects of prenatal BPA and phthalates on asthma phenotypes were seen in male offspring, where BPA was associated with increased risk for persistent asthma, while mono-iso-butyl phthalate and mono-iso-decyl phthalate was associated with increased risk for adult asthma. Prenatal BPA had no effect on lung function trajectories, but prenatal phthalate exposure was associated with improved lung function. CONCLUSION: Prenatal BPA exposure was associated with increased likelihood of persistent asthma in males, while prenatal phthalate exposure was associated with increased likelihood of adult asthma in males. Results suggest that prenatal exposure to prenatal BPA and phthalates affect asthma risk, particularly in males, however lung function was not adversely affected.

No association between in utero exposure to emissions from a coalmine fire and post-natal lung function.

BACKGROUND AND OBJECTIVE: Studies linking early life exposure to air pollution and subsequent impaired lung health have focused on chronic, low-level exposures in urban settings. We aimed to determine whether in utero exposure to an acute, high-intensity air pollution episode impaired lung function 7-years later. METHOD: We conducted a prospective cohort study of children who lived in the vicinity of a coalmine fire. Respiratory function was measured using the forced oscillation technique (FOT). Z-scores for resistance at 5 Hz (R5), reactance at 5 Hz (X5) and area under the reactance curve (AX) were calculated. Two sets of analyses were conducted to address two separate questions: (1) whether mine fire exposure (a binary indicator; conceived after the mine fire vs in utero exposed) was associated with the respiratory Z-scores; (2) whether there was any dose-response relationship between fire-related PM2.5 exposure and respiratory outcomes among those exposed. RESULTS: Acceptable lung function measurements were obtained from 79 children; 25 unexposed and 54 exposed in utero. Median (interquartile range) for daily average and peak PM2.5 for the exposed children were 4.2 (2.6 - 14.2) and 88 (52-225) µg/m3 respectively. There were no detectable differences in Z-scores between unexposed and exposed children. There were no associations between respiratory Z-scores and in utero exposure to PM2.5 (daily average or peak). CONCLUSION: There was no detectable effect of in utero exposure to PM2.5 from a local coalmine fire on post-natal lung function 7-years later. However, statistical power was limited.

Elevated leukotriene B4 and 8-isoprostane in exhaled breath condensate from preterm-born infants.

BACKGROUND: Inflammation and oxidative stress play a key role in the development of bronchopulmonary dysplasia (BPD), possibly contributing to persistent respiratory morbidity after preterm birth. We aimed to assess if inflammatory markers were elevated in exhaled breath condensate (EBC) of infants born very prematurely (< 32 weeks gestation) at 12-16 corrected months of age, and if increased levels were associated with BPD diagnosis and respiratory morbidity. METHODS: EBC samples and respiratory questionnaires were collected from 15 term-born infants and 33 preterm-born infants, 12 with a neonatal BPD diagnosis. EBC samples were analysed for leukotriene B4 (inflammation) and 8-isoprostane (oxidative stress) concentrations using enzyme-linked immune-assays. Differences between groups were analysed by Kruskal-Wallis Test with post-hoc comparisons, independent samples t-test or Mann-Whitney U test depending on normality of the data. RESULTS: Leukotriene B4 and 8-isoprostane levels were elevated in exhaled breath condensate of preterm-born infants compared to those born at term (mean difference [95% CI]; 1.52 [0.45, 2.59], p = 0.02; 0.77 [0.52, 1.02], p < 0.001, respectively). Leukotriene B4 and 8-isoprostane levels were independent of BPD diagnosis and respiratory morbidity over the first year of life. CONCLUSIONS: Infants born very prematurely exhibit elevated markers of airway neutrophilic inflammation and oxidative stress beyond the first year of life, regardless of a neonatal diagnosis of chronic lung disease or respiratory morbidity during infancy. These findings may have implications for future lung health. TRIAL REGISTRATION: N/A.

Deep Learning Assistance Closes the Accuracy Gap in Fracture Detection Across Clinician Types.

BACKGROUND: Missed fractures are the most common diagnostic errors in musculoskeletal imaging and can result in treatment delays and preventable morbidity. Deep learning, a subfield of artificial intelligence, can be used to accurately detect fractures by training algorithms to emulate the judgments of expert clinicians. Deep learning systems that detect fractures are often limited to specific anatomic regions and require regulatory approval to be used in practice. Once these hurdles are overcome, deep learning systems have the potential to improve clinician diagnostic accuracy and patient care. QUESTIONS/PURPOSES: This study aimed to evaluate whether a Food and Drug Administration-cleared deep learning system that identifies fractures in adult musculoskeletal radiographs would improve diagnostic accuracy for fracture detection across different types of clinicians. Specifically, this study asked: (1) What are the trends in musculoskeletal radiograph interpretation by different clinician types in the publicly available Medicare claims data? (2) Does the deep learning system improve clinician accuracy in diagnosing fractures on radiographs and, if so, is there a greater benefit for clinicians with limited training in musculoskeletal imaging? METHODS: We used the publicly available Medicare Part B Physician/Supplier Procedure Summary data provided by the Centers for Medicare & Medicaid Services to determine the trends in musculoskeletal radiograph interpretation by clinician type. In addition, we conducted a multiple-reader, multiple-case study to assess whether clinician accuracy in diagnosing fractures on radiographs was superior when aided by the deep learning system compared with when unaided. Twenty-four clinicians (radiologists, orthopaedic surgeons, physician assistants, primary care physicians, and emergency medicine physicians) with a median (range) of 16 years (2 to 37) of experience postresidency each assessed 175 unique musculoskeletal radiographic cases under aided and unaided conditions (4200 total case-physician pairs per condition). These cases were comprised of radiographs from 12 different anatomic regions (ankle, clavicle, elbow, femur, forearm, hip, humerus, knee, pelvis, shoulder, tibia and fibula, and wrist) and were randomly selected from 12 hospitals and healthcare centers. The gold standard for fracture diagnosis was the majority opinion of three US board-certified orthopaedic surgeons or radiologists who independently interpreted the case. The clinicians' diagnostic accuracy was determined by the area under the curve (AUC) of the receiver operating characteristic (ROC) curve, sensitivity, and specificity. Secondary analyses evaluated the fracture miss rate (1-sensitivity) by clinicians with and without extensive training in musculoskeletal imaging. RESULTS: Medicare claims data revealed that physician assistants showed the greatest increase in interpretation of musculoskeletal radiographs within the analyzed time period (2012 to 2018), although clinicians with extensive training in imaging (radiologists and orthopaedic surgeons) still interpreted the majority of the musculoskeletal radiographs. Clinicians aided by the deep learning system had higher accuracy diagnosing fractures in radiographs compared with when unaided (unaided AUC: 0.90 [95% CI 0.89 to 0.92]; aided AUC: 0.94 [95% CI 0.93 to 0.95]; difference in least square mean per the Dorfman, Berbaum, Metz model AUC: 0.04 [95% CI 0.01 to 0.07]; p < 0.01). Clinician sensitivity increased when aided compared with when unaided (aided: 90% [95% CI 88% to 92%]; unaided: 82% [95% CI 79% to 84%]), and specificity increased when aided compared with when unaided (aided: 92% [95% CI 91% to 93%]; unaided: 89% [95% CI 88% to 90%]). Clinicians with limited training in musculoskeletal imaging missed a higher percentage of fractures when unaided compared with radiologists (miss rate for clinicians with limited imaging training: 20% [95% CI 17% to 24%]; miss rate for radiologists: 14% [95% CI 9% to 19%]). However, when assisted by the deep learning system, clinicians with limited training in musculoskeletal imaging reduced their fracture miss rate, resulting in a similar miss rate to radiologists (miss rate for clinicians with limited imaging training: 9% [95% CI 7% to 12%]; miss rate for radiologists: 10% [95% CI 6% to 15%]). CONCLUSION: Clinicians were more accurate at diagnosing fractures when aided by the deep learning system, particularly those clinicians with limited training in musculoskeletal image interpretation. Reducing the number of missed fractures may allow for improved patient care and increased patient mobility. LEVEL OF EVIDENCE: Level III, diagnostic study.

Development of structure-function coupling in human brain networks during youth.

The protracted development of structural and functional brain connectivity within distributed association networks coincides with improvements in higher-order cognitive processes such as executive function. However, it remains unclear how white-matter architecture develops during youth to directly support coordinated neural activity. Here, we characterize the development of structure-function coupling using diffusion-weighted imaging and n-back functional MRI data in a sample of 727 individuals (ages 8 to 23 y). We found that spatial variability in structure-function coupling aligned with cortical hierarchies of functional specialization and evolutionary expansion. Furthermore, hierarchy-dependent age effects on structure-function coupling localized to transmodal cortex in both cross-sectional data and a subset of participants with longitudinal data (n = 294). Moreover, structure-function coupling in rostrolateral prefrontal cortex was associated with executive performance and partially mediated age-related improvements in executive function. Together, these findings delineate a critical dimension of adolescent brain development, whereby the coupling between structural and functional connectivity remodels to support functional specialization and cognition.

CellSeg: a robust, pre-trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images.

BACKGROUND: Algorithmic cellular segmentation is an essential step for the quantitative analysis of highly multiplexed tissue images. Current segmentation pipelines often require manual dataset annotation and additional training, significant parameter tuning, or a sophisticated understanding of programming to adapt the software to the researcher's need. Here, we present CellSeg, an open-source, pre-trained nucleus segmentation and signal quantification software based on the Mask region-convolutional neural network (R-CNN) architecture. CellSeg is accessible to users with a wide range of programming skills. RESULTS: CellSeg performs at the level of top segmentation algorithms in the 2018 Kaggle Data Challenge both qualitatively and quantitatively and generalizes well to a diverse set of multiplexed imaged cancer tissues compared to established state-of-the-art segmentation algorithms. Automated segmentation post-processing steps in the CellSeg pipeline improve the resolution of immune cell populations for downstream single-cell analysis. Finally, an application of CellSeg to a highly multiplexed colorectal cancer dataset acquired on the CO-Detection by indEXing (CODEX) platform demonstrates that CellSeg can be integrated into a multiplexed tissue imaging pipeline and lead to accurate identification of validated cell populations. CONCLUSION: CellSeg is a robust cell segmentation software for analyzing highly multiplexed tissue images, accessible to biology researchers of any programming skill level.

Empirical transmit field bias correction of T1w/T2w myelin maps.

T1-weighted divided by T2-weighted (T1w/T2w) myelin maps were initially developed for neuroanatomical analyses such as identifying cortical areas, but they are increasingly used in statistical comparisons across individuals and groups with other variables of interest. Existing T1w/T2w myelin maps contain radiofrequency transmit field (B1+) biases, which may be correlated with these variables of interest, leading to potentially spurious results. Here we propose two empirical methods for correcting these transmit field biases using either explicit measures of the transmit field or alternatively a 'pseudo-transmit' approach that is highly correlated with the transmit field at 3T. We find that the resulting corrected T1w/T2w myelin maps are both better neuroanatomical measures (e.g., for use in cross-species comparisons), and more appropriate for statistical comparisons of relative T1w/T2w differences across individuals and groups (e.g., sex, age, or body-mass-index) within a consistently acquired study at 3T. We recommend that investigators who use the T1w/T2w approach for mapping cortical myelin use these B1+ transmit field corrected myelin maps going forward.

NMDAR-dependent Argonaute 2 phosphorylation regulates miRNA activity and dendritic spine plasticity.

MicroRNAs (miRNAs) repress translation of target mRNAs by associating with Argonaute (Ago) proteins to form the RNA-induced silencing complex (RISC), underpinning a powerful mechanism for fine-tuning protein expression. Specific miRNAs are required for NMDA receptor (NMDAR)-dependent synaptic plasticity by modulating the translation of proteins involved in dendritic spine morphogenesis or synaptic transmission. However, it is unknown how NMDAR stimulation stimulates RISC activity to rapidly repress translation of synaptic proteins. We show that NMDAR stimulation transiently increases Akt-dependent phosphorylation of Ago2 at S387, which causes an increase in binding to GW182 and a rapid increase in translational repression of LIMK1 via miR-134. Furthermore, NMDAR-dependent down-regulation of endogenous LIMK1 translation in dendrites and dendritic spine shrinkage requires phospho-regulation of Ago2 at S387. AMPAR trafficking and hippocampal LTD do not involve S387 phosphorylation, defining this mechanism as a specific pathway for structural plasticity. This work defines a novel mechanism for the rapid transduction of NMDAR stimulation into miRNA-mediated translational repression to control dendritic spine morphology.