ASLPrep: a platform for processing of arterial spin labeled MRI and quantification of regional brain perfusion.

Arterial spin labeled (ASL) magnetic resonance imaging (MRI) is the primary method for noninvasively measuring regional brain perfusion in humans. We introduce ASLPrep, a suite of software pipelines that ensure the reproducible and generalizable processing of ASL MRI data.

Pushing boundaries: mechanisms enabling bacterial pathogens to spread between cells.

For multiple intracellular bacterial pathogens, the ability to spread directly into adjacent epithelial cells is an essential step for disease in humans. For pathogens such as Shigella, Listeria, Rickettsia, and Burkholderia, this intercellular movement frequently requires the pathogens to manipulate the host actin cytoskeleton and deform the plasma membrane into structures known as protrusions, which extend into neighboring cells. The protrusion is then typically resolved into a double-membrane vacuole (DMV) from which the pathogen quickly escapes into the cytosol, where additional rounds of intercellular spread occur. Significant progress over the last few years has begun to define the mechanisms by which intracellular bacterial pathogens spread. This review highlights the interactions of bacterial and host factors that drive mechanisms required for intercellular spread with a focus on how protrusion structures form and resolve.

Diffusion MRI head motion correction methods are highly accurate but impacted by denoising and sampling scheme.

Head motion correction is particularly challenging in diffusion-weighted MRI (dMRI) scans due to the dramatic changes in image contrast at different gradient strengths and directions. Head motion correction is typically performed using a Gaussian Process model implemented in FSL's Eddy. Recently, the 3dSHORE-based SHORELine method was introduced that does not require shell-based acquisitions, but it has not been previously benchmarked. Here we perform a comprehensive evaluation of both methods on realistic simulations of a software fiber phantom that provides known ground-truth head motion. We demonstrate that both methods perform remarkably well, but that performance can be impacted by sampling scheme and the extent of head motion and the denoising strategy applied before head motion correction. Furthermore, we find Eddy benefits from denoising the data first with MP-PCA. In sum, we provide the most extensive known benchmarking of dMRI head motion correction, together with extensive simulation data and a reproducible workflow. PRACTITIONER POINTS: Both Eddy and SHORELine head motion correction methods performed quite well on a large variety of simulated data. Denoising with MP-PCA can improve head motion correction performance when Eddy is used. SHORELine effectively corrects motion in non-shelled diffusion spectrum imaging data.

QSIPrep: an integrative platform for preprocessing and reconstructing diffusion MRI data.

Diffusion-weighted magnetic resonance imaging (dMRI) is the primary method for noninvasively studying the organization of white matter in the human brain. Here we introduce QSIPrep, an integrative software platform for the processing of diffusion images that is compatible with nearly all dMRI sampling schemes. Drawing on a diverse set of software suites to capitalize on their complementary strengths, QSIPrep facilitates the implementation of best practices for processing of diffusion images.

Facilitating Complex Trait Analysis via Reduced Complexity Crosses.

Genetically diverse inbred strains are frequently used in quantitative trait mapping to identify sequence variants underlying trait variation. Poor locus resolution and high genetic complexity impede variant discovery. As a solution, we explore reduced complexity crosses (RCCs) between phenotypically divergent, yet genetically similar, rodent substrains. RCCs accelerate functional variant discovery via decreasing the number of segregating variants by orders of magnitude. The simplified genetic architecture of RCCs often permit immediate identification of causal variants or rapid fine-mapping of broad loci to smaller intervals. Whole-genome sequences of substrains make RCCs possible by supporting the development of array- and targeted sequencing-based genotyping platforms, coupled with rapid genome editing for variant validation. In summary, RCCs enhance discovery-based genetics of complex traits.

Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells.

Genetic screens in mammalian cells commonly focus on loss-of-function approaches. To evaluate the phenotypic consequences of extra gene copies, we used bulk segregant analysis (BSA) of radiation hybrid (RH) cells. We constructed six pools of RH cells, each consisting of ∼2500 independent clones, and placed the pools under selection in media with or without paclitaxel. Low pass sequencing identified 859 growth loci, 38 paclitaxel loci, 62 interaction loci, and three loci for mitochondrial abundance at genome-wide significance. Resolution was measured as ∼30 kb, close to single-gene. Divergent properties were displayed by the RH-BSA growth genes compared to those from loss-of-function screens, refuting the balance hypothesis. In addition, enhanced retention of human centromeres in the RH pools suggests a new approach to functional dissection of these chromosomal elements. Pooled analysis of RH cells showed high power and resolution and should be a useful addition to the mammalian genetic toolkit.

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.

Beyond the Epidermal-Melanin-Unit: The Human Scalp Anagen Hair Bulb Is Home to Multiple Melanocyte Subpopulations of Variable Melanogenic Capacity.

The visual appearance of humans is derived significantly from our skin and hair color. While melanin from epidermal melanocytes protects our skin from the damaging effects of ultraviolet radiation, the biological value of pigmentation in the hair follicle, particularly on the scalp, is less clear. In this study, we explore the heterogeneity of pigment cells in the human scalp anagen hair follicle bulb, a site conventionally viewed to be focused solely on pigment production for transfer to the hair shaft. Using c-KIT/CD117 microbeads, we isolated bulbar c-KIT-positive and c-KIT-negative melanocytes. While both subpopulations expressed MITF, only the c-KIT-positive fraction expressed SOX10. We further localized bulbar melanocyte subpopulations (expressing c-KIT, SOX10, MITF, and DCT) that exhibited distinct/variable expression of downstream differentiation-associated melanosome markers (e.g., gp100 and Melan-A). The localization of a second 'immature' SOX10 negative melanocyte population, which was c-KIT/MITF double-positive, was identified outside of the melanogenic zone in the most peripheral/proximal matrix. This study describes an approach to purifying human scalp anagen hair bulb melanocytes, allowing us to identify unexpected levels of melanocyte heterogeneity. The function of the more immature melanocytes in this part of the hair follicle remains to be elucidated. Could they be in-transit migratory cells ultimately destined to synthesize melanin, or could they contribute to the hair follicle in non-melanogenic ways?

VHL L169P Variant Does Not Alter Cellular Hypoxia Tension in Clear Cell Renal Cell Carcinoma.

In the current era of tumor genome sequencing, single amino acid missense variants in the von Hippel-Lindau (VHL) tumor suppressor gene are frequently identified in clear cell renal carcinoma (ccRCC). Due to the incomplete knowledge of the structural architecture of VHL protein, the functional significance of many missense mutations cannot be assigned. L169P is one such missense mutation identified in the case of aggressive, metastatic ccRCC. Here, we characterized the biochemical activity, transcriptomic hypoxia signature and biological functions of the L169P variant. Lentiviral vector expressing either wildtype (WT) or L169P VHL were used to transduce two VHL-deficient human ccRCC cell lines, 786-O and RCC4. The stability of the VHL protein and the expression level of VHL, HIF1α and HIF2α were analyzed. The impact of restoring L169P or WT VHL on the hypoxia gene expression program in 786-O cells was assessed by mRNA sequencing (RNAseq) and computed hypoxic scores. The impact of restoring VHL expression on the growth of ccRCC models was assessed in cell cultures and in chorioallantoic membrane (CAM) xenografts. In the 786-O cells, the protein stability of L169P VHL was comparable to WT VHL. No obvious difference in the capability of degrading HIF1α and HIF2α was observed between WT and L169P VHL in the 786-O or RCC4 cells. The hypoxic scores were not significantly different in the 786-O cells expressing either wildtype or L169P VHL. From the cellular function perspective, both WT and L169P VHL slowed cell proliferation in vitro and in vivo. The L169P VHL variant is comparable to WT VHL in terms of protein stability, ability to degrade HIF1α factors and ability to regulate hypoxia gene expression, as well as in the suppression of ccRCC tumor cell growth. Taken together, our data indicate that the L169P VHL variant alone is unlikely to drive the oncogenesis of sporadic ccRCC.

Connectivity of Random Geometric Hypergraphs.

We consider a random geometric hypergraph model based on an underlying bipartite graph. Nodes and hyperedges are sampled uniformly in a domain, and a node is assigned to those hyperedges that lie within a certain radius. From a modelling perspective, we explain how the model captures higher-order connections that arise in real data sets. Our main contribution is to study the connectivity properties of the model. In an asymptotic limit where the number of nodes and hyperedges grow in tandem, we give a condition on the radius that guarantees connectivity.

The DNA-Binding High-Mobility Group Box Domain of Sox Family Proteins Directly Interacts with RNA In Vitro.

There is a growing body of evidence that a substantial number of protein domains identified as DNA-binding also interact with RNA to regulate biological processes. Several recent studies have revealed that the Sox2 transcription factor binds RNA through its high-mobility group box (HMGB) domain in vitro and in vivo. A high degree of conservation of this domain among members of the Sox family of transcription factors suggests that RNA-binding activity may be a general feature of these proteins. To address this hypothesis, we examined a subset of HMGB domains from human Sox family of proteins for their ability to bind both DNA and RNA in vitro. We observed selective, high-affinity interactions between Sox family HMGB domains and various model RNA elements, including a four-way junction RNA, a hairpin RNA with an internal bulge, G-quadruplex RNA, and a fragment of long noncoding RNA ES2, which is known to directly interact with Sox2. Importantly, the HMGB domains bind these RNA ligands significantly tighter than nonconsensus dsDNA and in some cases with affinities rivaling those of their consensus dsDNA sequences. These data suggest that RNA binding is a conserved feature of the Sox family of transcription factors with the potential to modulate unappreciated biological functions.

A dynamic graph convolutional neural network framework reveals new insights into connectome dysfunctions in ADHD.

The pathological mechanism of attention deficit hyperactivity disorder (ADHD) is incompletely specified, which leads to difficulty in precise diagnosis. Functional magnetic resonance imaging (fMRI) has emerged as a common neuroimaging technique for studying the brain functional connectome. Most existing methods that have either ignored or simply utilized graph structure, do not fully leverage the potentially important topological information which may be useful in characterizing brain disorders. There is a crucial need for designing novel and efficient approaches which can capture such information. To this end, we propose a new dynamic graph convolutional network (dGCN), which is trained with sparse brain regional connections from dynamically calculated graph features. We also develop a novel convolutional readout layer to improve graph representation. Our extensive experimental analysis demonstrates significantly improved performance of dGCN for ADHD diagnosis compared with existing machine learning and deep learning methods. Visualizations of the salient regions of interest (ROIs) and connectivity based on informative features learned by our model show that the identified functional abnormalities mainly involve brain regions in temporal pole, gyrus rectus, and cerebellar gyri from temporal lobe, frontal lobe, and cerebellum, respectively. A positive correlation was further observed between the identified connectomic abnormalities and ADHD symptom severity. The proposed dGCN model shows great promise in providing a functional network-based precision diagnosis of ADHD and is also broadly applicable to brain connectome-based study of mental disorders.

Structural brain measures linked to clinical phenotypes in major depression replicate across clinical centres.

Abnormalities in brain structural measures, such as cortical thickness and subcortical volumes, are observed in patients with major depressive disorder (MDD) who also often show heterogeneous clinical features. This study seeks to identify the multivariate associations between structural phenotypes and specific clinical symptoms, a novel area of investigation. T1-weighted magnetic resonance imaging measures were obtained using 3 T scanners for 178 unmedicated depressed patients at four academic medical centres. Cortical thickness and subcortical volumes were determined for the depressed patients and patients' clinical presentation was characterized by 213 item-level clinical measures, which were grouped into several large, homogeneous categories by K-means clustering. The multivariate correlations between structural and cluster-level clinical-feature measures were examined using canonical correlation analysis (CCA) and confirmed with both 5-fold and leave-one-site-out cross-validation. Four broad types of clinical measures were detected based on clustering: an anxious misery composite (composed of item-level depression, anxiety, anhedonia, neuroticism and suicidality scores); positive personality traits (extraversion, openness, agreeableness and conscientiousness); reported history of physical/emotional trauma; and a reported history of sexual abuse. Responses on the item-level anxious misery measures were negatively associated with cortical thickness/subcortical volumes in the limbic system and frontal lobe; reported childhood history of physical/emotional trauma and sexual abuse measures were negatively correlated with entorhinal thickness and left hippocampal volume, respectively. In contrast, the positive traits measures were positively associated with hippocampal and amygdala volumes and cortical thickness of the highly-connected precuneus and cingulate cortex. Our findings suggest that structural brain measures may reflect neurobiological mechanisms underlying MDD features.

Extreme phenotypic diversity in operant response to intravenous cocaine or saline infusion in the hybrid mouse diversity panel.

Cocaine self-administration is a complexly determined trait, with a substantial proportion of individual differences being determined by genetic variation. However, the relevant genetic variants that drive heritable differences in cocaine use remain undiscovered. Cocaine intravenous self-administration (IVSA) procedures in laboratory animals provide opportunities to prospectively investigate neurogenetic influences on the acquisition of voluntary cocaine use. Here, we provide information on cocaine (or saline-as a control) IVSA in 84 members of the hybrid mouse diversity panel (HMDP), an array of genetically distinct classical or recombinant inbred strains. We found cocaine IVSA to be substantially heritable in this population, with strain-level intake ranging for near 0 to >25 mg/kg/session. Though saline IVSA was also found to be heritable, a modest genetic correlation between cocaine and saline IVSA indicates that operant responding for the cocaine reinforcer was influenced, at least in part, by unique genetic variants. Genome-wide association studies (GWAS) of infusions earned in cocaine and saline groups revealed significant quantitative trait loci (QTL) on Chromosomes 3 and 14 for cocaine, but not saline, IVSA. Positional candidates were further prioritized through use of bulk RNA sequencing data that revealed genes with cis-eQTL and genetic correlation to number of infusions. Additionally, these data identify reference strains with extreme cocaine IVSA phenotypes, revealing them as polygenic models of risk and resilience to cocaine reinforcement. This work is part of an ongoing effort to characterize genetic variation that moderates cocaine IVSA that may, in turn, provide a more comprehensive understanding of cocaine risk genetics and neurobiology.

Examining associations between social anhedonia and convergent thinking using the Remote Associates Test.

Introduction: Social anhedonia (SocAnh) predicts increased risk of schizophrenia-spectrum disorders, with evidence that these disorders are associated with increased creativity. However, it is still largely unknown whether SocAnh is associated with one central aspect of creative thinking, convergent thinking.Methods: In two studies, college students with either extreme levels of SocAnh (n = 44 and n = 70) or controls with an average level of SocAnh (n = 111 and n = 100) completed a convergent thinking task, the Remote Associates Test, and also completed measures of current affect. In the second study, participants also completed a divergent thinking task.Results: In both studies, the SocAnh group had better performance than controls on the convergent thinking task. Further, this group difference remained after removing shared variance with current affect. In Study 2, groups did not differ on divergent thinking.Conclusions: Overall, consistent with research linking schizophrenia-spectrum disorders and creativity, the current research suggests that SocAnh is associated with increases in some aspects of creativity.

Childhood trauma history is linked to abnormal brain connectivity in major depression.

Patients with major depressive disorder (MDD) present with heterogeneous symptom profiles, while neurobiological mechanisms are still largely unknown. Brain network studies consistently report disruptions of resting-state networks (RSNs) in patients with MDD, including hypoconnectivity in the frontoparietal network (FPN), hyperconnectivity in the default mode network (DMN), and increased connection between the DMN and FPN. Using a large, multisite fMRI dataset (n = 189 patients with MDD, n = 39 controls), we investigated network connectivity differences within and between RSNs in patients with MDD and healthy controls. We found that MDD could be characterized by a network model with the following abnormalities relative to controls: (i) lower within-network connectivity in three task-positive RSNs [FPN, dorsal attention network (DAN), and cingulo-opercular network (CON)], (ii) higher within-network connectivity in two intrinsic networks [DMN and salience network (SAN)], and (iii) higher within-network connectivity in two sensory networks [sensorimotor network (SMN) and visual network (VIS)]. Furthermore, we found significant alterations in connectivity between a number of these networks. Among patients with MDD, a history of childhood trauma and current symptoms quantified by clinical assessments were associated with a multivariate pattern of seven different within- and between-network connectivities involving the DAN, FPN, CON, subcortical regions, ventral attention network (VAN), auditory network (AUD), VIS, and SMN. Overall, our study showed that traumatic childhood experiences and dimensional symptoms are linked to abnormal network architecture in MDD. Our results suggest that RSN connectivity may explain underlying neurobiological mechanisms of MDD symptoms and has the potential to serve as an effective diagnostic biomarker.

Does the osteoarthritic shoulder have altered rotator cuff vectors with increasing glenoid deformity? An in silico analysis.

BACKGROUND: A transverse force couple (TFC) functional imbalance has been demonstrated in osteoarthritic shoulders by recent 3-dimensional (3D) muscle volumetric studies. Altered rotator cuff vectors may be an additional factor contributing to a muscle imbalance and the propagation of glenoid deformity. METHODS: Computed tomography images of 33 Walch type A and 60 Walch type B shoulders were evaluated. The 3D volumes of the entire subscapularis, supraspinatus, and infraspinatus-teres minor (ISP-Tm) and scapula were manually segmented. The volume masks and scapular landmarks were imported into MATLAB to create a coordinate system, enabling calculation of muscle force vectors. The direction of each muscle force vector was described in the transverse and vertical plane, calculated with respect to the glenoid. Each muscle vector was then resolved into compression and shear force across the glenoid face. The relationship between muscle force vectors, glenoid retroversion or inclination, compression/shear forces on the glenoid, and Walch type was determined using linear regression. RESULTS: In the transverse plane with all rotator cuff muscles combined, increasing retroversion was significantly associated with increasing posterior drag (P < .001). Type B glenoids had significantly more posterior drag than type A (P < .001). In the vertical plane for each individual muscle group and in combination, superior drag increases as superior inclination increases (P < .001). Analysis of individual muscle groups showed that the anterior thrust of ISP-Tm and supraspinatus switched to a posterior drag at 8° and 10° of retroversion respectively. The compression force on the glenoid face by ISP-Tm and supraspinatus did not change with increasing retroversion for type A shoulders (P = .592 and P = .715, respectively), but they did for type B shoulders (P < .001 for both). The glenoid shear force ratio in the transverse plane for the ISP-Tm and supraspinatus moved from anterior to posterior shear with increasing glenoid retroversion, crossing zero at 8° and 10° of retroversion, whereas the subscapularis exerted a posterior shear force for every retroversion angle. CONCLUSION: Increased glenoid retroversion is associated with increased posterior shear and decreased compression forces on the glenoid face, explaining some of the pathognomonic bone morphometrics that characterize the osteoarthritic shoulder. Although the subscapularis always maintains a posterior thrust, the ISP-Tm and supraspinatus together showed an inflection at 8° and 10° of retroversion, changing from an anterior thrust to a posterior drag. This finding highlights the importance that in anatomic TSA the rotator cuff functional balance might be better restored by correcting glenoid retroversion to less than 8°.

Metabolic Profile of Reciprocal Supersets in Young, Recreationally Active Women and Men.

ABSTRACT: Realzola, RA, Mang, ZA, Millender, DJ, Beam, JR, Bellovary, BN, Wells, AD, Houck, JM, and Kravitz, L. Metabolic profile of reciprocal supersets in young, recreationally active females and males. J Strength Cond Res 36(10): 2709-2716, 2022-Reciprocal supersets (RSSs) are a time-efficient style of resistance exercise (RE) that consist of performing 2 consecutive exercises with opposing muscle groups while limiting rest times between them. Previous research in men indicates a RSS has an increased physiological response when compared with traditional RE (TRAD). No between-sex comparison of metabolic data for RSSs exists. The purpose of this study was to create a metabolic profile for RSSs in men and women. Eighteen resistance-trained individuals underwent 2 bouts of volume-load equated RE: RSS and TRAD. Reciprocal superset exercises were split into 3 clusters: (a) hexagonal bar deadlift superset with leg press, (b) chest press superset with seated row, and (c) overhead dumbbell press superset with latissimus dorsi pull-downs. The TRAD protocol, doing the same exercises, emulated hypertrophy emphasis training. Oxygen uptake (V̇ o2 ), heart rate (HR), blood lactate ([BLa]), rate of perceived exertion (RPE), and excess post-exercise oxygen consumption (EPOC) were measured. Aerobic and anaerobic energy expenditure were estimated using V̇ o2 and lactate, respectively. The level of significance set for this study was p ≤ 0.05. Regardless of sex, a RSS elicited significantly greater average V̇ o2 , HR, [BLa], RPE, and anaerobic and aerobic energy expenditures, and was completed in a shorter time compared with TRAD ( p ≤ 0.05). When compared with women, men had significantly greater EPOC, average [BLa], and anaerobic and aerobic energy expenditures during RSSs ( p ≤ 0.05). The average [BLa] and aerobic energy expenditure of the men were also significantly greater than the women during TRAD ( p ≤ 0.05). This study suggests that a RSS is a metabolically demanding RE session that may elicit increases in musculoskeletal, cardiorespiratory, and physiological adaptations while decreasing the duration of exercise.

Visible light and human skin pigmentation: The importance of skin phototype.

Melanin is synthesised within melanocytes and transferred to keratinocytes in human skin, thereby regulating skin colour and protecting skin cells against UVR-induced damage. We commonly divide human skin into six phototypes (SPT)-I to -VI (Fitzpatrick scale) according to the skin's tanning response to UVR. In this pilot study, we investigated the impact of UVR (maximum 311nm), blue (peak 450nm) and green visible light (peak 530nm) on melanin production and type in healthy human skin histocultures (SPT-I, -II and -III). UVR, blue and green light stimulated a surface tanning response in SPT-II and -III, but not SPT-I. Using the Warthin-Starry stain for sensitive melanin detection, all three light treatments induced melanogenesis in SPT-II and -III skin. Surprisingly, blue and green light (but not UVR) stimulated melanin synthesis in SPT-I skin. Moreover, melanin synthesis induced by blue and green visible light in SPT-I, SPT-II, and SPT-III skin was not associated with a detectable increase in DNA damage or cell apoptosis. By contrast, both responses were detected after UVR. These data suggest that blue and green visible light can stimulate melanin production in fair-skinned individuals without, at least some of, the harmful consequences of UVR-induced pigmentation. We are currently examining the molecular basis of UVR-independent melanogenesis in fair skin.

Hidradenitis suppurativa: A folliculotropic disease of innate immune barrier dysfunction?

The innate immune system of human skin consists of a multi-layered barrier consisting of cells and soluble effector molecules charged with maintaining homeostasis and responding to insults and infections. It has become increasingly clear that these barrier layers become compromised in skin diseases, especially in disorders of an (auto)inflammatory nature. In the case of hidradenitis suppurativa, great strides have been made in recent years in characterizing the underlying breakdown in homeostatic innate immunity, including an increasing understanding of the central role of the hair follicle in this process. This breakdown appears to occur at multiple levels: the pilosebaceous unit, associated epithelium, the cutaneous microbiome, alteration of immune cell function and local molecular events such as complement activation. This review seeks to summarize, contextualize and analyse critically our current understanding of how these innate immune barriers become dysregulated in the early stage(s) of hidradenitis suppurativa, and to speculate on where potential hidradenitis suppurativa research could be most fruitful.