HIP: a method for high-dimensional multi-view data integration and prediction accounting for subgroup heterogeneity.

Epidemiologic and genetic studies in many complex diseases suggest subgroup disparities (e.g. by sex, race) in disease course and patient outcomes. We consider this from the standpoint of integrative analysis where we combine information from different views (e.g. genomics, proteomics, clinical data). Existing integrative analysis methods ignore the heterogeneity in subgroups, and stacking the views and accounting for subgroup heterogeneity does not model the association among the views. We propose Heterogeneity in Integration and Prediction (HIP), a statistical approach for joint association and prediction that leverages the strengths in each view to identify molecular signatures that are shared by and specific to a subgroup. We apply HIP to proteomics and gene expression data pertaining to chronic obstructive pulmonary disease (COPD) to identify proteins and genes shared by, and unique to, males and females, contributing to the variation in COPD, measured by airway wall thickness. Our COPD findings have identified proteins, genes, and pathways that are common across and specific to males and females, some implicated in COPD, while others could lead to new insights into sex differences in COPD mechanisms. HIP accounts for subgroup heterogeneity in multi-view data, ranks variables based on importance, is applicable to univariate or multivariate continuous outcomes, and incorporates covariate adjustment. With the efficient algorithms implemented using PyTorch, this method has many potential scientific applications and could enhance multiomics research in health disparities. HIP is available at https://github.com/lasandrall/HIP, a video tutorial at https://youtu.be/O6E2OLmeMDo and a Shiny Application at https://multi-viewlearn.shinyapps.io/HIP_ShinyApp/ for users with limited programming experience.

Recombinant Full-length Plasmodium falciparum Circumsporozoite Protein-Based Vaccine Adjuvanted With Glucopyranosyl Lipid A-Liposome Quillaja saponaria 21: Results of Phase 1 Testing With Malaria Challenge.

BACKGROUND: Malaria is preventable yet causes >600 000 deaths annually. RTS,S, the first marketed malaria vaccine, has modest efficacy, but improvements are needed for eradication. METHODS: We conducted an open-label, dose escalation phase 1 study of a full-length recombinant circumsporozoite protein vaccine (rCSP) administered with adjuvant glucopyranosyl lipid A-liposome Quillaja saponaria 21 formulation (GLA-LSQ) on days 1, 29, and 85 or 1 and 490 to healthy, malaria-naive adults. The primary end points were safety and reactogenicity. The secondary end points were antibody responses and Plasmodium falciparum parasitemia after homologous controlled human malaria infection. RESULTS: Participants were enrolled into 4 groups receiving rCSP/GLA-LSQ: 10 µg × 3 (n = 20), 30 µg × 3 (n = 10), 60 µg × 3 (n = 10), or 60 µg × 2 (n = 9); 10 participants received 30 µg rCSP alone × 3, and there were 6 infectivity controls. Participants experienced no serious adverse events. Rates of solicited and unsolicited adverse events were similar among groups. All 26 participants who underwent controlled human malaria infection 28 days after final vaccinations developed malaria. Increasing vaccine doses induced higher immunoglobulin G titers but did not achieve previously established RTS,S benchmarks. CONCLUSIONS: rCSP/GLA-LSQ had favorable safety results. However, tested regimens did not induce protective immunity. Further investigation could assess whether adjuvant or schedule adjustments improve efficacy. CLINICAL TRIALS REGISTRATION: NCT03589794.

Axial elongation of caudalized human organoids mimics aspects of neural tube development.

Axial elongation of the neural tube is crucial during mammalian embryogenesis for anterior-posterior body axis establishment and subsequent spinal cord development, but these processes cannot be interrogated directly in humans as they occur post-implantation. Here, we report an organoid model of neural tube extension derived from human pluripotent stem cell (hPSC) aggregates that have been caudalized with Wnt agonism, enabling them to recapitulate aspects of the morphological and temporal gene expression patterns of neural tube development. Elongating organoids consist largely of neuroepithelial compartments and contain TBXT+SOX2+ neuro-mesodermal progenitors in addition to PAX6+NES+ neural progenitors. A critical threshold of Wnt agonism stimulated singular axial extensions while maintaining multiple cell lineages, such that organoids displayed regionalized anterior-to-posterior HOX gene expression with hindbrain (HOXB1) regions spatially distinct from brachial (HOXC6) and thoracic (HOXB9) regions. CRISPR interference-mediated silencing of TBXT, a Wnt pathway target, increased neuroepithelial compartmentalization, abrogated HOX expression and disrupted uniaxial elongation. Together, these results demonstrate the potent capacity of caudalized hPSC organoids to undergo axial elongation in a manner that can be used to dissect the cellular organization and patterning decisions that dictate early human nervous system development.

Interpersonal communication, cultural norms, and community perceptions associated with care-seeking for fever among children under age five in Magoé district, Mozambique.

BACKGROUND: Malaria is endemic throughout Mozambique, contributing significantly to the country's burden of disease. Prompt and effective treatment for fevers in children can limit the mortality and morbidity impacts of the disease but many children in the country are not taken for formal care when ill. Using an ideational model of behaviour, this study assesses the magnitude of the relationships for potential drivers of care-seeking, including interpersonal communication, malaria messaging, and knowledge and attitudes about malaria, with actual care-seeking behaviours for under-five children with fever in Magoé district, Mozambique. METHODS: Data on the care-seeking behaviours for fever come from a 2019 household malaria survey in Magoé district. Households were randomly selected for interview from among those with at least one child under age five and one net for every two household members. From 1621 mother-child dyads, the analytical sample consists of 300 children under age five with a fever in the 2 weeks prior to the survey. Multilevel random effects logistic regression models are estimated to test for associations between care-seeking behaviours and hypothesized behavioural determinants, including interpersonal communication (IPC), malaria messaging, ideational factors (e.g., norms, attitudes, beliefs, risk perceptions), and community characteristics. RESULTS: Overall, 18.5% of children under age five (N = 300) were reported to have fever in the previous 2 weeks and, of these, 68.5% were taken to a formal sector health care provider. Multivariate models highlight significant roles for interpersonal communication; care-seeking was highest among mothers who spoke only with friends/community members about malaria (94.0%, p < 0.001), followed by those who spoke only with their husband (78.6%, p = 0.015), relative to 63.3% who spoke with no one. Care-seeking decisions made by a child's grandmother were associated with a 25.0% point (p = 0.001) greater likelihood of seeking care relative to decisions made by the mother alone. Exposure to any malaria messaging was also positively associated with care-seeking (90.5% versus 62.7%, p < 0.001). In contrast, among all individual- and community-level ideational factors, only perceptions of self-efficacy to seek care were related to care-seeking behaviours. CONCLUSIONS: These results suggest that social and behaviour change interventions that focus on encouraging families and community members to talk about malaria and the need to promptly seek treatment for fevers in children may be particularly effective at increasing this behaviour in this and similar settings. Such messaging and IPC should consider grandmothers as a target audience, as they appear to be perceived as highly influential in care-seeking decision-making in this community.

Stress system concordance as a predictor of longitudinal patterns of resilience in adolescence.

Resilience promotes positive adaptation to challenges and may facilitate recovery for adolescents experiencing psychopathology. This work examined concordance across the experience, expression, and physiological response to stress as a protective factor that may predict longitudinal patterns of psychopathology and well-being that mark resilience. Adolescents aged 14-17 at recruitment (oversampled for histories of non-suicidal self-injury; NSSI) were part of a three-wave (T1, T2, T3) longitudinal study. Multi-trajectory modeling produced four distinct profiles of stress experience, expression, and physiology at T1 (High-High-High, Low-Low-Low, High-Low-Moderate, and High-High-Low, respectively). Linear mixed-effect regressions modeled whether the profiles predicted depressive symptoms, suicide ideation, NSSI engagement, positive affect, satisfaction with life, and self-worth over time. Broadly, concordant stress response profiles (Low-Low-Low, High-High-High) were associated with resilient-like patterns of psychopathology and well-being over time. Adolescents with a concordant High-High-High stress response profile showed a trend of greater reduction in depressive symptoms (B = 0.71, p = 0.052), as well as increased global self-worth (B = -0.88, p = 0.055), from T2 to T3 compared to the discordant High-High-Low profile. Concordance across multi-level stress responses may be protective and promote future resilience, whereas blunted physiological responses in the presence of high perceived and expressed stress may indicate poorer outcomes over time.

Ideational factors and their association with insecticide treated net use in Magoe District, Mozambique.

BACKGROUND: Insecticide treated bed nets (ITN) are considered a core malaria vector control tool by the WHO and are the main contributor to the large decline in malaria burden in sub-Saharan Africa over the past 20 years, but they are less effective if they are not broadly and regularly used. ITN use may depend on factors including temperature, relative humidity, mosquito density, seasonality, as well as ideational or psychosocial factors including perceptions of nets and perceptions of net use behaviours. METHODS: A cross-sectional household survey was conducted as part of a planned randomized controlled trial in Magoe District, Mozambique. Interviewers captured data on general malaria and ITN perceptions including ideational factors related to perceived ITN response efficacy, self-efficacy to use an ITN, and community norms around ITN using a standardized questionnaire. Only households with sufficient ITNs present for all children to sleep under (at least one ITN for every two children under the age of five years) were eligible for inclusion in the study. Additional questions were added about seasonality and frequency of ITN use. RESULTS: One-thousand six hundred sixteen mother-child dyads were interviewed. Responses indicated gaps in use of existing nets and net use was largely independent of ideational factors related to ITNs. Self-reported ITN use varied little by season nor meaningfully when different methods were used to solicit responses on net use behaviour. Mothers' perceived response efficacy of ITNS was negatively associated with net use (high perceived response efficacy reduced the log-odds of net use by 0.27 (95% CI - 0.04 to - 0.51), implying that stronger beliefs in the effectiveness of ITNs might result in reduced net use among their children. CONCLUSIONS: In this context, ITN use among children was not clearly related to mothers' ideational factors measured in the study. Scales used in solicitation of ideation around ITN use and beliefs need careful design and testing across a broader range of populations in order to identify ideational factors related to ITN use among those with access.

Hospital pharmacy acquisition of nonstocked antimicrobials-current processes and areas for improvement.

BACKGROUND: The delivery of prompt and appropriate antimicrobial therapy for life-threatening infections is an important antimicrobial stewardship measure and a priority for hospitals. OBJECTIVES: To better understand U.S. hospital pharmacy stocking processes and acquisition of nonstocked antimicrobials and to identify strategies for improving this process. METHODS: This mixed-methods study recruited infectious diseases and antimicrobial stewardship pharmacists. Semistructured interviews with pharmacists in Minnesota were conducted via video conferencing software from January 21, 2021, to March 17, 2021. Audio recordings of the interviews guided survey development and were also transcribed, coded, and qualitatively analyzed. Surveys were distributed throughout the United States via an e-mail listserv, and responses were collected between August 5, 2021, and September 15, 2021. RESULTS: Ten interviews and 78 surveys were included in the analysis. Formulary and stocking practices varied based on institution. Stocking decisions were most frequently based on the frequency of use, clinical utility, and cost of antimicrobials. Nonstocked antimicrobials were often ordered from the wholesale distributor but, if needed urgently, acquired from another local institution. Antibacterial agents were the most frequently needed nonstocked antimicrobials, especially those targeting multidrug-resistant gram-negative bacteria. When acquiring nonstocked antimicrobials, barriers include process inefficiencies, cost, availability, and safety concerns. Improved information sharing between local institutions may help improve this process. CONCLUSION: In this exploratory study, antimicrobial stocking practices varied within U.S. hospitals. Acquisition of nonstocked, urgently needed antimicrobials from neighboring hospitals may be common; however, this process lacks guidance and is often inefficient. Establishing better mechanisms for information sharing may improve this process and should be explored.

School-Based Serosurveys to Assess the Validity of Using Routine Health Facility Data to Target Malaria Interventions in the Central Highlands of Madagascar.

BACKGROUND: In low-malaria-transmission areas of Madagascar, annual parasite incidence (API) from routine data has been used to target indoor residual spraying at subdistrict commune level. To assess validity of this approach, we conducted school-based serological surveys and health facility (HF) data quality assessments in 7 districts to compare API to gold-standard commune-level serological measures. METHODS: At 2 primary schools in each of 93 communes, 60 students were randomly selected with parents and teachers. Capillary blood was drawn for rapid diagnostic tests (RDTs) and serology. Multiplex bead-based immunoassays to detect antibodies to 5 Plasmodium falciparum antigens were conducted, and finite mixture models used to characterize seronegative and seropositive populations. Reversible catalytic models generated commune-level annual seroconversion rates (SCRs). HF register data were abstracted to assess completeness and accuracy. RESULTS: RDT positivity from 12 770 samples was 0.5%. Seroprevalence to tested antigens ranged from 17.9% (MSP-1) to 59.7% (PF13). Median commune-level SCR was 0.0108 (range, 0.001-0.075). Compared to SCRs, API identified 71% (95% confidence interval, 51%-87%) of the 30% highest-transmission communes; sensitivity declined at lower levels. Routine data accuracy did not substantially affect API performance. CONCLUSIONS: API performs reasonably well at identifying higher-transmission communes but sensitivity declined at lower transmission levels.

Implementing a Physical Activity Consultation Clinic during a Global Pandemic.

ABSTRACT: Ten percent of all premature deaths and 117 billion dollars in annual health care costs are attributable to physical inactivity in America. The positive impact exercise can have on overall health is irrefutable. While it is the responsibility of health care providers to assess and counsel for exercise, there are logistical, structural, and educational barriers preventing this counseling. A physical activity consultation clinic led by primary care sports medicine physicians would allow for focused exercise counseling by appropriately trained providers to motivated patients. While previously there have been many institutional and logistical barriers to establishing such a clinic, the COVID-19 pandemic has created a window of opportunity for doing so within a large academic medical center. This article reviews the importance of exercise on overall health, outlines the barriers for establishing a clinical experience dedicated to counseling for physical activity, and details how overcoming those barriers was facilitated by the COVID-19 pandemic.

Differentiation of V2a interneurons from human pluripotent stem cells.

The spinal cord consists of multiple neuronal cell types that are critical to motor control and arise from distinct progenitor domains in the developing neural tube. Excitatory V2a interneurons in particular are an integral component of central pattern generators that control respiration and locomotion; however, the lack of a robust source of human V2a interneurons limits the ability to molecularly profile these cells and examine their therapeutic potential to treat spinal cord injury (SCI). Here, we report the directed differentiation of CHX10+ V2a interneurons from human pluripotent stem cells (hPSCs). Signaling pathways (retinoic acid, sonic hedgehog, and Notch) that pattern the neural tube were sequentially perturbed to identify an optimized combination of small molecules that yielded ∼25% CHX10+ cells in four hPSC lines. Differentiated cultures expressed much higher levels of V2a phenotypic markers (CHX10 and SOX14) than other neural lineage markers. Over time, CHX10+ cells expressed neuronal markers [neurofilament, NeuN, and vesicular glutamate transporter 2 (VGlut2)], and cultures exhibited increased action potential frequency. Single-cell RNAseq analysis confirmed CHX10+ cells within the differentiated population, which consisted primarily of neurons with some glial and neural progenitor cells. At 2 wk after transplantation into the spinal cord of mice, hPSC-derived V2a cultures survived at the site of injection, coexpressed NeuN and VGlut2, extended neurites >5 mm, and formed putative synapses with host neurons. These results provide a description of V2a interneurons differentiated from hPSCs that may be used to model central nervous system development and serve as a potential cell therapy for SCI.

Evaluating the quality of routinely reported data on malaria commodity stocks in Guinea, 2014-2016.

BACKGROUND: Ensuring malaria commodity availability at health facilities is a cornerstone of malaria control. Since 2013, the Guinea National Malaria Control Programme has been routinely collecting data on stock levels of key malaria commodities through a monthly routine malaria information system (RMIS). In parallel, biannual end-user verification (EUV) surveys have also assessed malaria commodity availability at a subset of health facilities, potentially representing a duplication of efforts. METHODS: Data on 12 malaria commodity stock levels verified during four EUV surveys conducted between 2014 and 2016 was compared to data for the corresponding months submitted by the same health facilities through the RMIS. The sensitivity and specificity of the RMIS in detecting stock-outs was calculated, as was the percent difference between average stock levels reported through the two systems. RESULTS: Of the 171 health facilities visited during the four EUV surveys, 129 (75%) had data available in the RMIS. Of 351 commodity stock-outs observed during the EUV in the sampled reporting health facilities, 256 (73%) were also signaled through the corresponding RMIS reports. When the presence of malaria commodity stocks was confirmed during the EUV surveys, the RMIS also reported available stock 87% (677/775) of the time. For all commodities, the median percent difference in average stock levels between the EUV and RMIS was 4% (interquartile range - 7 to 27%). CONCLUSION: The concordance between stock levels reported through the RMIS and those verified during the EUV visits provides certain evidence that RMIS data can inform quantification and procurement decisions. However, lower than acceptable rates of reporting and incomplete detection of stock-outs from facilities that do report suggest that further systems strengthening is needed to improve RMIS reporting completeness and data quality.

Aggregate formation and suspension culture of human pluripotent stem cells and differentiated progeny.

Culture of human pluripotent stem cells (hPSC) as in vitro multicellular aggregates has been increasingly used as a method to model early embryonic development. Three-dimensional assemblies of hPSCs facilitate interactions between cells and their microenvironment to promote morphogenesis, analogous to the multicellular organization that accompanies embryogenesis. In this paper, we describe a method for reproducibly generating and maintaining populations of homogeneous three-dimensional hPSC aggregates using forced aggregation and rotary orbital suspension culture. We propose solutions to several challenges associated with the consistent formation and extended culture of cell spheroids generated from hPSCs and their differentiated progeny. Further, we provide examples to demonstrate how aggregation can be used as a tool to select specific subpopulations of cells to create homotypic spheroids, or as a means to introduce multiple cell types to create heterotypic tissue constructs. Finally, we demonstrate that the aggregation and rotary suspension method can be used to support culture and maintenance of hPSC-derived cell populations representing each of the three germ layers, underscoring the utility of this platform for culturing many different cell types.

A new method for generating high purity motoneurons from mouse embryonic stem cells.

A common problem with using embryonic stem (ES) cells as a source for analysis of gene expression, drug toxicity, or functional characterization studies is the heterogeneity that results from many differentiation protocols. The ability to generate large numbers of high purity differentiated cells from pluripotent stem cells could greatly enhance their utility for in vitro characterization studies and transplantation in pre-clinical injury models. Population heterogeneity is particularly troublesome for post-mitotic neurons, including motoneurons, because they do not proliferate and are quickly diluted in culture by proliferative phenotypes, such as glia. Studies of motoneuron biology and disease, in particular amyotrophic lateral sclerosis, can benefit from high purity motoneuron cultures. In this study, we engineered a transgenic-ES cell line where highly conserved enhancer elements for the motoneuron transcription factor Hb9 were used to drive puromycin N-acetyltransferase expression in ES cell-derived motoneurons. Antibiotic selection with puromycin was then used to obtain high purity motoneuron cultures following differentiation of mouse ES cells. Purity was maintained during maturation allowing the production of consistent, uniform populations of cholinergic ES cell-derived motoneurons. Appropriate functional properties of purified motoneurons were verified by acetylcholinesterase activity and electrophysiology. Antibiotic selection, therefore, can provide an inexpensive alternative to current methods for isolating ES cell-derived motoneurons at high purity that does not require specialized laboratory equipment and provides a unique platform for studies in motoneuron development and degeneration.

A description of malaria sentinel surveillance: a case study in Oromia Regional State, Ethiopia.

BACKGROUND: In the context of the massive scale up of malaria interventions, there is increasing recognition that the current capacity of routine malaria surveillance conducted in most African countries through integrated health management information systems is inadequate. The timeliness of reporting to higher levels of the health system through health management information systems is often too slow for rapid action on focal infectious diseases such as malaria. The purpose of this paper is to: 1) describe the implementation of a malaria sentinel surveillance system in Ethiopia to help fill this gap; 2) describe data use for epidemic detection and response as well as programmatic decision making; and 3) discuss lessons learned in the context of creating and running this system. CASE DESCRIPTION: As part of a comprehensive strategy to monitor malaria trends in Oromia Regional State, Ethiopia, a system of ten malaria sentinel sites was established to collect data on key malaria morbidity and mortality indicators. To ensure the sentinel surveillance system provides timely, actionable data, the sentinel facilities send aggregate data weekly through short message service (SMS) to a central database server. Bland-Altman plots and Poisson regression models were used to investigate concordance of malaria indicator reports and malaria trends over time, respectively. DISCUSSION: This paper describes three implementation challenges that impacted system performance in terms of: 1) ensuring a timely and accurate data reporting process; 2) capturing complete and accurate patient-level data; and 3) expanding the usefulness and generalizability of the system's data to monitor progress towards the national malaria control goals of reducing malaria deaths and eventual elimination of transmission. CONCLUSIONS: The use of SMS for reporting surveillance data was identified as a promising practice for accurately tracking malaria trends in Oromia. The rapid spread of this technology across Africa offers promising opportunities to collect and disseminate surveillance data in a timely way. High quality malaria surveillance in Ethiopia remains a resource intensive activity and extending the generalizability of sentinel surveillance findings to other contexts remains a major limitation of these strategies.

Parental Emotion Socialization of Sadness as a Correlate for Clinical Improvement: A Longitudinal Study of Adolescents with a Range of Nonsuicidal Self-Injury.

Engagement in nonsuicidal self-injury (NSSI) often begins in adolescence, and commonly occurs when a person is emotionally dysregulated. Parental emotion socialization (ES) plays a key role in shaping children's emotional expression, experience, and regulation. Longitudinal work is needed to understand how links between parental ES and adolescent clinical outcomes unfold over time. In this longitudinal study (N = 118; all assigned female at birth with a range of NSSI - from none to severe; age 12-17 years, Mage = 14.98 at the first assessment), for the Time 1 (T1) and Time 2 (T2) annual assessments; adolescents reported NSSI and adolescents and parents reported depressive symptoms. Parents (primarily mothers) reported on their supportive and unsupportive ES responses to youth expressions of sadness, anger, and happiness. We examined (1) concurrent relationships across time points, (2) longitudinal models (T1 to T2 change in parental ES and its associated T1 to T2 changes in adolescent clinical outcomes), and (3) prediction models (T1 parental ES predicting changes in adolescent clinical outcomes). Concurrent associations between parental supportive ES responses to sadness and anger were inversely related to adolescent's depressive symptoms and NSSI episodes. Longitudinal analyses showed that increases in unsupportive responses to sadness correspond with increases in depressive symptoms from T1 to T2. The findings underscore the importance of examining how parents respond to their children's emotions. Next steps are to investigate potential mechanisms of risk and consider interventions that enhance adaptive responses of parents to adolescents embroiled in negative emotional states.

Optimizing the measurement of sample entropy in resting-state fMRI data.

Introduction: The complexity of brain signals may hold clues to understand brain-based disorders. Sample entropy, an index that captures the predictability of a signal, is a promising tool to measure signal complexity. However, measurement of sample entropy from fMRI signals has its challenges, and numerous questions regarding preprocessing and parameter selection require research to advance the potential impact of this method. For one example, entropy may be highly sensitive to the effects of motion, yet standard approaches to addressing motion (e.g., scrubbing) may be unsuitable for entropy measurement. For another, the parameters used to calculate entropy need to be defined by the properties of data being analyzed, an issue that has frequently been ignored in fMRI research. The current work sought to rigorously address these issues and to create methods that could be used to advance this field. Methods: We developed and tested a novel windowing approach to select and concatenate (ignoring connecting volumes) low-motion windows in fMRI data to reduce the impact of motion on sample entropy estimates. We created utilities (implementing autoregressive models and a grid search function) to facilitate selection of the matching length m parameter and the error tolerance r parameter. We developed an approach to apply these methods at every grayordinate of the brain, creating a whole-brain dense entropy map. These methods and tools have been integrated into a publicly available R package ("powseR"). We demonstrate these methods using data from the ABCD study. After applying the windowing procedure to allow sample entropy calculation on the lowest-motion windows from runs 1 and 2 (combined) and those from runs 3 and 4 (combined), we identified the optimal m and r parameters for these data. To confirm the impact of the windowing procedure, we compared entropy values and their relationship with motion when entropy was calculated using the full set of data vs. those calculated using the windowing procedure. We then assessed reproducibility of sample entropy calculations using the windowed procedure by calculating the intraclass correlation between the earlier and later entropy measurements at every grayordinate. Results: When applying these optimized methods to the ABCD data (from the subset of individuals who had enough windows of continuous "usable" volumes), we found that the novel windowing procedure successfully mitigated the large inverse correlation between entropy values and head motion seen when using a standard approach. Furthermore, using the windowed approach, entropy values calculated early in the scan (runs 1 and 2) are largely reproducible when measured later in the scan (runs 3 and 4), although there is some regional variability in reproducibility. Discussion: We developed an optimized approach to measuring sample entropy that addresses concerns about motion and that can be applied across datasets through user-identified adaptations that allow the method to be tailored to the dataset at hand. We offer preliminary results regarding reproducibility. We also include recommendations for fMRI data acquisition to optimize sample entropy measurement and considerations for the field.

A single-cell transcriptomic map of the developing Atoh1 lineage identifies neural fate decisions and neuronal diversity in the hindbrain.

Proneural transcription factors establish molecular cascades to orchestrate neuronal diversity. One such transcription factor, Atonal homolog 1 (Atoh1), gives rise to cerebellar excitatory neurons and over 30 distinct nuclei in the brainstem critical for hearing, breathing, and balance. Although Atoh1 lineage neurons have been qualitatively described, the transcriptional programs that drive their fate decisions and the full extent of their diversity remain unknown. Here, we analyzed single-cell RNA sequencing and ATOH1 DNA binding in Atoh1 lineage neurons of the developing mouse hindbrain. This high-resolution dataset identified markers for specific brainstem nuclei and demonstrated that transcriptionally heterogeneous progenitors require ATOH1 for proper migration. Moreover, we identified a sizable population of proliferating unipolar brush cell progenitors in the mouse Atoh1 lineage, previously described in humans as the origin of one medulloblastoma subtype. Collectively, our data provide insights into the developing mouse hindbrain and markers for functional assessment of understudied neuronal populations.

Exercise for patients with COPD: an integral yet underutilized intervention.

Chronic obstructive pulmonary disease (COPD) was the third leading cause of mortality in the United States in 2009 and accounts for millions of dollars in health care expenses annually. It is characterized by slow declines in functional ability and exercise tolerance, which are strongly predictive of poor health-related quality of life and survival. The cycle of physical, social, and psychosocial consequences of COPD is more easily prevented than remedied; therefore, maintaining baseline respiratory function is a key goal of early treatment. Although medical management of COPD is generally well understood and implemented by most primary care physicians, multidisciplinary approaches that include nonpharmacologic modalities (eg, exercise training) are not often used. Exercise training can alleviate dyspnea and improve exercise tolerance and health-related quality of life in patients with mild-to-severe COPD. Pulmonary rehabilitation, which includes exercise training, nutritional and psychological counseling, and patient education, is an important component of COPD treatment and management programs, and is currently underutilized in the United States. This article addresses the role of exercise as part of a multidisciplinary approach to the management of COPD, especially with regard to pulmonary rehabilitation.

Histopathologic Features of Breast Tissue From Transgender Men and Their Associations With Androgen Therapy.

OBJECTIVES: To assess the histopathologic features of breast tissue of transgender men (TM) undergoing gender-affirming bilateral mastectomies in relation to androgen therapy (AT). METHODS: We reviewed 374 transgender bilateral mastectomy cases from 2017 to 2020. Of these, 314 (84.4%) patients received preoperative AT. We compared these with 127 cases of cisgender females undergoing elective breast reduction. RESULTS: Breast specimens from TM on AT, compared with cisgender women, showed a median higher gross percentage of fibrous tissue (P < .001), reduced lobular density (P = .004), higher amount of lobular atrophy (P < .001), and lower incidence of cysts (P < .001), apocrine metaplasia (P < .001), calcifications (P < .001), columnar cell change (P = .002), and atypia (P = .003). Each additional month of AT was associated with a 2% decrease in the odds of having nonapocrine cysts (P = .02), a 5% decrease in the odds of having usual ductal hyperplasia (P = .007), and a 0.14% decrease in median lobular density (95% confidence interval, -0.18 to -0.05). CONCLUSIONS: In this study, breast specimens from TM, particularly with a history of AT, had a higher proportion of fibrous tissue, fewer lobules, and a higher degree of lobular atrophy than cisgender females. Rare cases of atypia were not predicted by preoperative imaging or gross findings, supporting routine microscopic evaluation of these specimens.

Atoh1 drives the heterogeneity of the pontine nuclei neurons and promotes their differentiation.

Pontine nuclei (PN) neurons mediate the communication between the cerebral cortex andthe cerebellum to refine skilled motor functions. Prior studies showed that PN neurons fall into two subtypes based on their anatomic location and region-specific connectivity, but the extent of their heterogeneity and its molecular drivers remain unknown. Atoh1 encodes a transcription factor that is expressed in the PN precursors. We previously showed that partial loss of Atoh1 function in mice results in delayed PN development and impaired motor learning. In this study, we performed single-cell RNA sequencing to elucidate the cell state-specific functions of Atoh1 during PN development and found that Atoh1 regulates cell cycle exit, differentiation, migration, and survival of PN neurons. Our data revealed six previously not known PN subtypes that are molecularly and spatially distinct. We found that the PN subtypes exhibit differential vulnerability to partial loss of Atoh1 function, providing insights into the prominence of PN phenotypes in patients with ATOH1 missense mutations.