PARE: A framework for removal of confounding effects from any distance-based dimension reduction method.

Dimension reduction tools preserving similarity and graph structure such as t-SNE and UMAP can capture complex biological patterns in high-dimensional data. However, these tools typically are not designed to separate effects of interest from unwanted effects due to confounders. We introduce the partial embedding (PARE) framework, which enables removal of confounders from any distance-based dimension reduction method. We then develop partial t-SNE and partial UMAP and apply these methods to genomic and neuroimaging data. For lower-dimensional visualization, our results show that the PARE framework can remove batch effects in single-cell sequencing data as well as separate clinical and technical variability in neuroimaging measures. We demonstrate that the PARE framework extends dimension reduction methods to highlight biological patterns of interest while effectively removing confounding effects.

Computer-vision analysis of craniofacial dysmorphology in 22q11.2 deletion syndrome and psychosis spectrum disorders.

BACKGROUND: Minor physical anomalies (MPAs) are congenital morphological abnormalities linked to disruptions of fetal development. MPAs are common in 22q11.2 deletion syndrome (22q11DS) and psychosis spectrum disorders (PS) and likely represent a disruption of early embryologic development that may help identify overlapping mechanisms linked to psychosis in these disorders. METHODS: Here, 2D digital photographs were collected from 22q11DS (n = 150), PS (n = 55), and typically developing (TD; n = 93) individuals. Photographs were analyzed using two computer-vision techniques: (1) DeepGestalt algorithm (Face2Gene (F2G)) technology to identify the presence of genetically mediated facial disorders, and (2) Emotrics-a semi-automated machine learning technique that localizes and measures facial features. RESULTS: F2G reliably identified patients with 22q11DS; faces of PS patients were matched to several genetic conditions including FragileX and 22q11DS. PCA-derived factor loadings of all F2G scores indicated unique and overlapping facial patterns that were related to both 22q11DS and PS. Regional facial measurements of the eyes and nose were smaller in 22q11DS as compared to TD, while PS showed intermediate measurements. CONCLUSIONS: The extent to which craniofacial dysmorphology 22q11DS and PS overlapping and evident before the impairment or distress of sub-psychotic symptoms may allow us to identify at-risk youths more reliably and at an earlier stage of development.

Expanded phenotypic spectrum of neurodevelopmental and neurodegenerative disorder Bryant-Li-Bhoj syndrome with 38 additional individuals.

Bryant-Li-Bhoj syndrome (BLBS), which became OMIM-classified in 2022 (OMIM: 619720, 619721), is caused by germline variants in the two genes that encode histone H3.3 (H3-3A/H3F3A and H3-3B/H3F3B) [1-4]. This syndrome is characterized by developmental delay/intellectual disability, craniofacial anomalies, hyper/hypotonia, and abnormal neuroimaging [1, 5]. BLBS was initially categorized as a progressive neurodegenerative syndrome caused by de novo heterozygous variants in either H3-3A or H3-3B [1-4]. Here, we analyze the data of the 58 previously published individuals along 38 unpublished, unrelated individuals. In this larger cohort of 96 people, we identify causative missense, synonymous, and stop-loss variants. We also expand upon the phenotypic characterization by elaborating on the neurodevelopmental component of BLBS. Notably, phenotypic heterogeneity was present even amongst individuals harboring the same variant. To explore the complex phenotypic variation in this expanded cohort, the relationships between syndromic phenotypes with three variables of interest were interrogated: sex, gene containing the causative variant, and variant location in the H3.3 protein. While specific genotype-phenotype correlations have not been conclusively delineated, the results presented here suggest that the location of the variants within the H3.3 protein and the affected gene (H3-3A or H3-3B) contribute more to the severity of distinct phenotypes than sex. Since these variables do not account for all BLBS phenotypic variability, these findings suggest that additional factors may play a role in modifying the phenotypes of affected individuals. Histones are poised at the interface of genetics and epigenetics, highlighting the potential role for gene-environment interactions and the importance of future research.

Genetic relatedness can alter the strength of plant-soil interactions.

PREMISE: Intraspecific variation may play a key role in shaping the relationships between plants and their interactions with soil microbial communities. The soil microbes of individual plants can generate intraspecific variation in the responsiveness of the plant offspring, yet have been much less studied. To address this need, we explored how the relatedness of seedlings from established clones of Solidago altissima altered the plant-soil interactions of the seedlings. METHODS: Seedlings of known parentage were generated from a series of 24 clones grown in a common garden. Seedlings from these crosses were inoculated with soils from maternal, paternal, or unrelated clones and their performance compared to sterilized control inocula. RESULTS: We found that soil inocula influenced by S. altissima clones had an overall negative effect on seedling biomass. Furthermore, seedlings inoculated with maternal or paternal soils tended to experience larger negative effects than seedlings inoculated with unrelated soils. However, there was much variation among individual crosses, with not all responding to relatedness. CONCLUSIONS: Our data argue that genetic relatedness to the plant from which the soil microbial inoculum was obtained may cause differential impacts on establishing seedlings, encouraging the regeneration of non-kin adjacent to established clones. Such intraspecific variation represents a potentially important source of heterogeneity in plant-soil microbe interactions with implications for maintaining population genetic diversity.

NeuroTri2-VISDOT: An open-access tool to harness the power of second trimester human single cell data to inform models of Mendelian neurodevelopmental disorders.

Whole exome and genome sequencing, coupled with refined bioinformatic pipelines, have enabled improved diagnostic yields for individuals with Mendelian conditions and have led to the rapid identification of novel syndromes. For many Mendelian neurodevelopmental disorders (NDDs), there is a lack of pre-existing model systems for mechanistic work. Thus, it is critical for translational researchers to have an accessible phenotype- and genotype-informed approach for model system selection. Single-cell RNA sequencing data can be informative in such an approach, as it can indicate which cell types express a gene of interest at the highest levels across time. For Mendelian NDDs, such data for the developing human brain is especially useful. A valuable single-cell RNA sequencing dataset of the second trimester developing human brain was produced by Bhaduri et al in 2021, but access to these data can be limited by computing power and the learning curve of single-cell data analysis. To reduce these barriers for translational research on Mendelian NDDs, we have built the web-based tool, Neurodevelopment in Trimester 2 - VIsualization of Single cell Data Online Tool (NeuroTri2-VISDOT), for exploring this single-cell dataset, and we have employed it in several different settings to demonstrate its utility for the translational research community.

Guidelines toward more socially just mental health screening in schools.

Mental health screening is a pivotal practice for promoting the social-emotional-behavioral (SEB) health and well-being of youth in schools. However, some aspects of traditional mental health screening practices may inadvertently perpetuate structural racism and unintentionally facilitate oppression and SEB disparities. We address this issue constructively by presenting an intentional approach to guide school psychologists and related professionals in implementing more socially just mental health screening in schools. Our guidelines are grounded within the four phases of the Participatory Culture-Specific Intervention Modeling (PCSIM) framework: system entry, culture-specific model development, culture-specific program development, and program continuation or extension. We propose that conceptualizing mental health screening within PCSIM methodology promotes more socially just practices by (a) displacing the implicit power of professionals, (b) giving transparent representation to local communities, and (c) employing methods that are recursive, culturally relevant, and intended to build capacity for sustained transformative change. Within each PCSIM phase, we recommend culturally responsive practices for professionals that foster equity in screening and SEB outcomes and discuss ways to resist practices that perpetuate oppression and disparities. We aim to convey a method for mental health screening that is not done to students and schools but rather done in partnership with and for the benefit of students and schools. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

The faculty-to-faculty mentorship experience: a survey on challenges and recommendations for improvements.

Faculty at research institutions play a central role in advancing knowledge and careers, as well as promoting the well-being of students and colleagues in research environments. Mentorship from experienced peers has been touted as critical for enabling these myriad roles to allow faculty development, career progression, and satisfaction. However, there is little information available on who supports faculty and best ways to structure a faculty mentorship programme for early- and mid-career academics. In the interest of advocating for increased and enhanced faculty mentoring and mentoring programmes, we surveyed faculty around the world to gather data on whether and how they receive mentoring. We received responses from 457 early- and mid-career faculty and found that a substantial portion of respondents either reported having no mentor or a lack of a formal mentoring scheme. Qualitative responses on the quality of mentorship revealed that the most common complaints regarding mentorship included lack of mentor availability, unsatisfactory commitment to mentorship, and non-specific or non-actionable advice. On these suggestions, we identify a need for training for faculty mentors as well as strategies for individual mentors, departments, and institutions for funding and design of more intentional and supportive mentorship programmes for early- and mid-career faculty.

Profiles of teachers' classroom management style: Differences in perceived school climate and professional characteristics.

Teachers are tasked with not only delivering high-quality, evidence-based academic instruction, but they are also responsible for managing student behavior within the classroom and school. To manage these behaviors, teachers can use a variety of strategies that result in a range of outcomes on student and school-wide functioning. Although an overreliance on punitive strategies has been shown to worsen behavior problems, positive strategies and social-emotional learning (SEL) techniques are associated with more favorable outcomes for students' global functioning. In a sample of K-12 teachers (N = 111), we examined direct associations between teachers' use of behavior management techniques (i.e., punitive, positive, and SEL) and their self-reports of perceived school climate. Furthermore, latent profile analysis was used to identify teachers' behavior management styles and evaluate whether teachers' characteristics and perceived school climate predicted behavior management style. Findings not only replicate previous research examining direct associations between behavior management techniques and school climate, but also extend the theoretical understanding of teachers' behavior management approaches. Three profiles of teacher behavior management style emerged, including a (a) Moderate Proactive profile characterized by frequent use of positive strategies and SEL techniques and infrequent use of punitive strategies; (b) Moderate Reactive/Proactive profile characterized by moderate use of both punitive strategies and positive strategies, as well as slightly lower use of SEL techniques; and (c) High Proactive profile characterized by very frequent use of positive strategies and SEL techniques and very infrequent use of punitive strategies. Use of these profiles may enhance understanding of how school psychologists can support teachers' behavior management practices through consultation or professional development to promote effective school and classroom behavior management practices.

Intersite brain MRI volumetric biases persist even in a harmonized multisubject study of multiple sclerosis.

BACKGROUND AND PURPOSE: Multicenter study designs involving a variety of MRI scanners have become increasingly common. However, these present the issue of biases in image-based measures due to scanner or site differences. To assess these biases, we imaged 11 volunteers with multiple sclerosis (MS) with scan and rescan data at four sites. METHODS: Images were acquired on Siemens or Philips scanners at 3 Tesla. Automated white matter lesion detection and whole-brain, gray and white matter, and thalamic volumetry were performed, as well as expert manual delineations of T1 magnetization-prepared rapid acquisition gradient echo and T2 fluid-attenuated inversion recovery lesions. Random-effect and permutation-based nonparametric modeling was performed to assess differences in estimated volumes within and across sites. RESULTS: Random-effect modeling demonstrated model assumption violations for most comparisons of interest. Nonparametric modeling indicated that site explained >50% of the variation for most estimated volumes. This expanded to >75% when data from both Siemens and Philips scanners were included. Permutation tests revealed significant differences between average inter- and intrasite differences in most estimated brain volumes (P < .05). The automatic activation of spine coil elements during some acquisitions resulted in a shading artifact in these images. Permutation tests revealed significant differences between thalamic volume measurements from acquisitions with and without this artifact. CONCLUSION: Differences in brain volumetry persisted across MR scanners despite protocol harmonization. These differences were not well explained by variance component modeling; however, statistical innovations for mitigating intersite differences show promise in reducing biases in multicenter studies of MS.

Cervical Pessary for Prevention of Preterm Birth in Individuals With a Short Cervix: The TOPS Randomized Clinical Trial.

Importance: A short cervix as assessed by transvaginal ultrasound is an established risk factor for preterm birth. Study findings for a cervical pessary to prevent preterm delivery in singleton pregnancies with transvaginal ultrasound evidence of a short cervix have been conflicting. Objective: To determine if cervical pessary placement decreases the risk of preterm birth or fetal death prior to 37 weeks among individuals with a short cervix. Design, Setting, and Participants: We performed a multicenter, randomized, unmasked trial comparing a cervical pessary vs usual care from February 2017 through November 5, 2021, at 12 centers in the US. Study participants were nonlaboring individuals with a singleton pregnancy and a transvaginal ultrasound cervical length of 20 mm or less at gestations of 16 weeks 0 days through 23 weeks 6 days. Individuals with a prior spontaneous preterm birth were excluded. Interventions: Participants were randomized 1:1 to receive either a cervical pessary placed by a trained clinician (n = 280) or usual care (n = 264). Use of vaginal progesterone was at the discretion of treating clinicians. Main Outcome and Measures: The primary outcome was delivery or fetal death prior to 37 weeks. Results: A total of 544 participants (64%) of a planned sample size of 850 were enrolled in the study (mean age, 29.5 years [SD, 6 years]). Following the third interim analysis, study recruitment was stopped due to concern for fetal or neonatal/infant death as well as for futility. Baseline characteristics were balanced between participants randomized to pessary and those randomized to usual care; 98.9% received vaginal progesterone. In an as-randomized analysis, the primary outcome occurred in 127 participants (45.5%) randomized to pessary and 127 (45.6%) randomized to usual care (relative risk, 1.00; 95% CI, 0.83-1.20). Fetal or neonatal/infant death occurred in 13.3% of those randomized to receive a pessary and in 6.8% of those randomized to receive usual care (relative risk, 1.94; 95% CI, 1.13-3.32). Conclusions and Relevance: Cervical pessary in nonlaboring individuals with a singleton gestation and with a cervical length of 20 mm or less did not decrease the risk of preterm birth and was associated with a higher rate of fetal or neonatal/infant mortality. Trial Registration: ClinicalTrials.gov Identifier: NCT02901626.

Early Magnetic Resonance Imaging Features of New Paramagnetic Rim Lesions in Multiple Sclerosis.

OBJECTIVE: To determine early magnetic resonance imaging (MRI) features of new multiple sclerosis (MS) lesions that will develop into paramagnetic rim lesions (PRLs), which have been associated with progressive tissue injury in MS. METHODS: New contrast-enhancing lesions observed on routine clinical MRI were imaged at 7 T within 4 weeks of observation, and 3 and 6 months later. The 6-month MRI was used to classify PRL status (PRL or non-PRL). The relationship between early lesion characteristics and subsequent PRL status was assessed using generalized linear mixed effects models. Random forest classification was performed to classify early predictors of subsequent PRL status. RESULTS: From 93 contrast-enhancing lesions in 23 MS patients, 37 lesions developed into a PRL. In lesions that developed into PRLs compared with those that did not, the average lesion T1 on the initial 7 T MRI was 1994 ms compared with 1,670 ms (p-value <0.001), and the average volume was 168.7 mL compared with 44 mL (p-value <0.001) in lesions that did not. These volume differences were also found on 3 T scans (p-value <0.001), and for intensity-normalized T1 -w (p-value = 0.011) and fluid-attenuated inversion recovery (p-value = 0.005). The area under the receiver operating characteristic curve for the random forest classification with leave-one-out cross-validation was found to be 0.86 using initial 7 T features. INTERPRETATION: New MS lesions that evolve into PRLs can be identified early in lesion evolution. These findings suggest that biological mechanisms underlying PRL development begin early, which has important implications for clinical trials targeting PRLs development and subsequent therapeutics. ANN NEUROL 2023;94:736-744.

Demystifying longitudinal data analyses using structural equation models in school psychology.

Structural equation models (SEM) are a method of latent variable analysis that offer a high degree of flexibility in terms of modeling methods for applied research questions. Recent advancements associated with longitudinal SEM have unlocked innovative ways to decompose variance and to estimate mean trends over time (e.g., Allison et al., 2017; Berry & Willoughby, 2017; Hamaker et al., 2015; McArdle & Nesselroade, 2014). However, these longitudinal methods are not necessarily readily accessible to scholars seeking to advance theory and practice in school psychology. Importantly, not all longitudinal data are the same and not all longitudinal SEMs are the same; thus, analytic approaches must be appropriately matched to specific research aims to meaningfully inform school psychology theory and practice. The present article highlights recent advances in longitudinal SEMs, clarifies their similarities to other-perhaps more familiar-methods, and matches their applications to specific types of research questions. The intent of this work is to promote careful thinking about the correspondence between estimands, developmental theory, and practical applications to foster specificity in testing quantitative questions in school psychology research and advance a more rigorous evaluation of longitudinal trends relevant to research and practice in the field.

The Temporal Relationship Between the Coronavirus Disease 2019 (COVID-19) Pandemic and Preterm Birth.

OBJECTIVE: To evaluate whether preterm birth rates changed in relation to the onset of the coronavirus disease 2019 (COVID-19) pandemic and whether any change depended on socioeconomic status. METHODS: This is an observational cohort study of pregnant individuals with a singleton gestation who delivered in the years 2019 and 2020 at 1 of 16 U.S. hospitals of the Maternal-Fetal Medicine Units Network. The frequency of preterm birth for those who delivered before the onset of the COVID-19 pandemic (ie, in 2019) was compared with that of those who delivered after its onset (ie, in 2020). Interaction analyses were performed for people of different individual- and community-level socioeconomic characteristics (ie, race and ethnicity, insurance status, Social Vulnerability Index (SVI) of a person's residence). RESULTS: During 2019 and 2020, 18,526 individuals met inclusion criteria. The chance of preterm birth before the COVID-19 pandemic was similar to that after the onset of the pandemic (11.7% vs 12.5%, adjusted relative risk 0.94, 95% CI 0.86-1.03). In interaction analyses, race and ethnicity, insurance status, and the SVI did not modify the association between the epoch and the chance of preterm birth before 37 weeks of gestation (all interaction P >.05). CONCLUSION: There was no statistically significant difference in preterm birth rates in relation to the COVID-19 pandemic onset. This lack of association was largely independent of socioeconomic indicators such as race and ethnicity, insurance status, or SVI of the residential community in which an individual lived.

Histone 3.3-related chromatinopathy: missense variants throughout H3-3A and H3-3B cause a range of functional consequences across species.

There has been considerable recent interest in the role that germline variants in histone genes play in Mendelian syndromes. Specifically, missense variants in H3-3A and H3-3B, which both encode Histone 3.3, were discovered to cause a novel neurodevelopmental disorder, Bryant-Li-Bhoj syndrome. Most of the causative variants are private and scattered throughout the protein, but all seem to have either a gain-of-function or dominant negative effect on protein function. This is highly unusual and not well understood. However, there is extensive literature about the effects of Histone 3.3 mutations in model organisms. Here, we collate the previous data to provide insight into the elusive pathogenesis of missense variants in Histone 3.3.

The effects of UPGRADE your performance on employment soft skills of students with intellectual and developmental disabilities: A pilot study of generalization.

Previous research has identified UPGRADE Your Performance as a method for teaching employment soft skills to students with disabilities. UPGRADE Your Performance instruction is a multicomponent intervention including self-evaluation, self-graphing, goal setting, and technology-aided instruction. This pilot study investigated the generalized effects of UPGRADE Your Performance on soft skills of secondary students with intellectual and other developmental disabilities participating in an 18-21 transition program located on a university campus. Results indicated that when students improved in two targeted soft skill areas, generalization occurred to three non-targeted soft skill areas. Implications for practice and suggestions for future research are included.

Deconfounded Dimension Reduction via Partial Embeddings.

Dimension reduction tools preserving similarity and graph structure such as t-SNE and UMAP can capture complex biological patterns in high-dimensional data. However, these tools typically are not designed to separate effects of interest from unwanted effects due to confounders. We introduce the partial embedding (PARE) framework, which enables removal of confounders from any distance-based dimension reduction method. We then develop partial t-SNE and partial UMAP and apply these methods to genomic and neuroimaging data. Our results show that the PARE framework can remove batch effects in single-cell sequencing data as well as separate clinical and technical variability in neuroimaging measures. We demonstrate that the PARE framework extends dimension reduction methods to highlight biological patterns of interest while effectively removing confounding effects.

T1 /T2 ratio from 3T MRI improves multiple sclerosis cortical lesion contrast.

BACKGROUND AND PURPOSE: Cortical demyelinated lesions are prevalent in multiple sclerosis (MS), associated with disability, and have recently been incorporated into MS diagnostic criteria. Presently, advanced and ultrahigh-field MRIs-not routinely available in clinical practice-are the most sensitive methods for detection of cortical lesions. Approaches utilizing MRI sequences obtainable in routine clinical practice remain an unmet need. We plan to assess the sensitivity of the ratio of T1 -weighted and T2 -weighted (T1 /T2 ) signal intensity for focal cortical lesions in comparison to other high-field imaging methods. METHODS: 3-Tesla and 7-Tesla MRI collected from 10 adults with MS were included in the study. T1 /T2 images were calculated by dividing 3T T1 -weighted (T1 w) images by 3T T2 -weighted (T2 w) fluid-attenuated inversion recovery images for each participant. A total of 614 cortical lesions were identified using 7T T2 *w and T1 w images and corresponding voxels were assessed on registered 3T images. Signal intensities were compared across 3T imaging sequences, including T1 /T2 , T1 w, T2 w, and inversion recovery susceptibility-weighted imaging with enhanced T2 weighting (IR-SWIET) images. RESULTS: T1 /T2 images demonstrated a larger contrast between median lesional and nonlesional cortical signal intensity (median ratio = 1.29, range: 1.19-1.38) when compared to T1 w (1.01, 0.97-1.10, p < .002), T2 w (1.17, 1.07-1.26, p < .002), and IR-SWIET (1.21, 1.01-1.29, p < .03). CONCLUSION: T1 /T2 images are sensitive to cortical lesions. Approaches incorporating T1 /T2 could improve the accessibility of cortical lesion detection in research settings and clinical practice.

Automated analysis of low-field brain MRI in cerebral malaria.

A central challenge of medical imaging studies is to extract biomarkers that characterize disease pathology or outcomes. Modern automated approaches have found tremendous success in high-resolution, high-quality magnetic resonance images. These methods, however, may not translate to low-resolution images acquired on magnetic resonance imaging (MRI) scanners with lower magnetic field strength. In low-resource settings where low-field scanners are more common and there is a shortage of radiologists to manually interpret MRI scans, it is critical to develop automated methods that can augment or replace manual interpretation, while accommodating reduced image quality. We present a fully automated framework for translating radiological diagnostic criteria into image-based biomarkers, inspired by a project in which children with cerebral malaria (CM) were imaged using low-field 0.35 Tesla MRI. We integrate multiatlas label fusion, which leverages high-resolution images from another sample as prior spatial information, with parametric Gaussian hidden Markov models based on image intensities, to create a robust method for determining ventricular cerebrospinal fluid volume. We also propose normalized image intensity and texture measurements to determine the loss of gray-to-white matter tissue differentiation and sulcal effacement. These integrated biomarkers have excellent classification performance for determining severe brain swelling due to CM.