Automated Spatial Omics Landscape Analysis Approach Reveals Novel Tissue Architectures in Ulcerative Colitis.

The utility of spatial omics in leveraging cellular interactions in normal and diseased states for precision medicine is hampered by a lack of strategies for matching disease states with spatial heterogeneity-guided cellular annotations. Here we use a spatial context-dependent approach that matches spatial pattern detection to cell annotation. Using this approach in existing datasets from ulcerative colitis patient colonic biopsies, we identified architectural complexities and associated difficult-to-detect rare cell types in ulcerative colitis germinal-center B cell follicles. Our approach deepens our understanding of health and disease pathogenesis, illustrates a strategy for automating nested architecture detection for highly multiplexed spatial biology data, and informs precision diagnosis and therapeutic strategies.

Deploying Machine Learning Based Segmentation for Scientific Imaging Analysis at Synchrotron Facilities.

Scientific user facilities present a unique set of challenges for image processing due to the large volume of data generated from experiments and simulations. Furthermore, developing and implementing algorithms for real-time processing and analysis while correcting for any artifacts or distortions in images remains a complex task, given the computational requirements of the processing algorithms. In a collaborative effort across multiple Department of Energy national laboratories, the "MLExchange" project is focused on addressing these challenges. MLExchange is a Machine Learning framework deploying interactive web interfaces to enhance and accelerate data analysis. The platform allows users to easily upload, visualize, label, and train networks. The resulting models can be deployed on real data while both results and models could be shared with the scientists. The MLExchange web-based application for image segmentation allows for training, testing, and evaluating multiple machine learning models on hand-labeled tomography data. This environment provides users with an intuitive interface for segmenting images using a variety of machine learning algorithms and deep-learning neural networks. Additionally, these tools have the potential to overcome limitations in traditional image segmentation techniques, particularly for complex and low-contrast images.

Certified Nurse-Midwives as Teachers: Expanding Interprofessional Collaboration Learning Opportunities for Medical Students on the Obstetrics and Gynecology Clerkship.

INTRODUCTION: Interprofessional experiences provide critical exposure to collaborative health care teams, yet medical students often lack this experience during clinical clerkships. We created a labor and delivery triage rotation exclusively staffed by certified nurse-midwives in the obstetrics and gynecology clerkship to address this gap. We sought to evaluate the clinical learning experiences of medical students rotating on this midwife-supervised collaborative team. METHODS: Between 2018 and 2020, we electronically sent all medical students an evaluation after each required clerkship. Our primary outcome was the quality of teaching score, as defined by level of agreement on a 5-point Likert scale with a statement regarding teaching quality. A secondary outcome evaluated scores from the National Board of Medical Examiners (NBME) Obstetrics and Gynecology subject examination taken by all students at the end of the rotation. Evaluations and assessments were compared between students rotating on labor and delivery triage and those who did not. Evaluation comments from students rotating on labor and delivery triage were collated to identify common themes. RESULTS: Of 374 students, 370 (98.9%) completed the end-of-clerkship course evaluation and 312 (83.4%) completed teaching evaluations. Sixty-seven students (17.9%) rotated in labor and delivery triage; of these, 52 (77.6%) completed both the course and triage rotation evaluations. There were no differences in the mean quality of teaching scores (3.9 ± 1.2 versus 3.8 ± 1.2, p = 0.54) or in NBME Obstetrics and Gynecology subject examination scores between students rotating in labor and delivery triage compared to all other rotations (79.9% ± 7.2% vs 80.2% ± 7.8%, P = 0.436). Comments from teaching evaluations highlighted student exposure to the midwifery philosophy of care model. DISCUSSION: This work demonstrates the feasibility and benefits of this midwife-led authentic interprofessional collaborative experience for medical students. This model can serve as an example of how to implement and evaluate interprofessional collaboration experiences in the clinical setting.

Association of a longitudinal, preclinical ultrasound curriculum with medical student performance.

INTRODUCTION: Point-of-care ultrasound (US) is used in clinical practice across many specialties. Ultrasound (US) curricula for medical students are increasingly common. Optimal timing, structure, and effect of ultrasound education during medical school remains poorly understood. This study aims to retrospectively determine the association between participation in a preclinical, longitudinal US curriculum and medical student academic performance. METHODS: All first-year medical students at a medical school in the Midwest region of the United States were offered a voluntary longitudinal US curriculum. Participants were selected by random lottery. The curriculum consisted of five three-hour hands on-sessions with matching asynchronous content covering anatomy and pathologic findings. Content was paired with organ system blocks in the standard first year curriculum at our medical school. Exam scores between the participating and non-participating students were compared to evaluate the objective impact of US education on performance in an existing curriculum. We hypothesized that there would be an association between participation in the curriculum and improved medical student performance. Secondary outcomes included shelf exam scores for the surgery, internal medicine, neurology clerkships and USMLE Step 1. A multivariable linear regression model was used to evaluate the association of US curriculum participation with student performance. Scores were adjusted for age, gender, MCAT percentile, and science or engineering degree. RESULTS: 76 of 178 students applied to participate in the curriculum, of which 51 were accepted. US curriculum students were compared to non-participating students (n = 127) from the same class. The US curriculum students performed better in cardiovascular anatomy (mean score 92.1 vs. 88.7, p = 0.048 after adjustment for multiple comparisons). There were no significant differences in cumulative cardiovascular exam scores, or in anatomy and cumulative exam scores for the gastroenterology and neurology blocks. The effect of US curriculum participation on cardiovascular anatomy scores was estimated to be an improvement of 3.48 points (95% CI 0.78-6.18). No significant differences were observed for USMLE Step 1 or clerkship shelf exams. There were no significant differences in either preclinical, clerkship or Step 1 score for the 25 students who applied and were not accepted and the 102 who did not apply. CONCLUSIONS: Participation in a preclinical longitudinal US curriculum was associated with improved exam performance in cardiovascular anatomy but not examination of other cardiovascular system concepts. Neither anatomy or comprehensive exam scores for neurology and gastrointestinal organ system blocks were improved.

Concealment of a Sexual Minority Identity in the Workplace: The Role of Workplace Climate and Identity Centrality.

Concealing a sexual minority identity at work has been linked to adverse health and employment outcomes. The authors of this paper examine whether LGBQ employee levels of concealment from coworkers and supervisors are linked to perceived workplace climate and LGBQ-identity centrality. Rainbow Illinois 2010-2011 data were used; N = 319 LGBQ full or part-time employees. Multiple regression with moderation was used to test the hypotheses. Support and hostility in the workplace each had a negative main effect on concealment from coworkers as well as supervisors. The interaction between support and centrality was also significant. LGBQ employees who placed greater importance on their sexual orientation were more likely to disclose that identity to supervisors in the face of hostility than those with less central identities. Thus, sexual minorities may be more responsive to workplace climate when they have more central identities.

MLExchange: A web-based platform enabling exchangeable machine learning workflows for scientific studies.

Machine learning (ML) algorithms are showing a growing trend in helping the scientific communities across different disciplines and institutions to address large and diverse data problems. However, many available ML tools are programmatically demanding and computationally costly. The MLExchange project aims to build a collaborative platform equipped with enabling tools that allow scientists and facility users who do not have a profound ML background to use ML and computational resources in scientific discovery. At the high level, we are targeting a full user experience where managing and exchanging ML algorithms, workflows, and data are readily available through web applications. Since each component is an independent container, the whole platform or its individual service(s) can be easily deployed at servers of different scales, ranging from a personal device (laptop, smart phone, etc.) to high performance clusters (HPC) accessed (simultaneously) by many users. Thus, MLExchange renders flexible using scenarios-users could either access the services and resources from a remote server or run the whole platform or its individual service(s) within their local network.

COVID-19 and medical education in Africa: a cross sectional analysis of the impact on medical students.

BACKGROUND: The African continent currently experiences 25% of the global burden of disease with only 1.3% of the world's healthcare workers. The COVID-19 pandemic has caused unprecedented disruption to medical education systems, increasing the strain on already-vulnerable regions. Our study examines the impact of COVID-19 on medical students across 33 countries in the African continent. METHODS: A 39-item anonymous electronic survey was developed and distributed to medical students across Africa through social networks to assess the impact of the COVID-19 pandemic on medical education. The survey assessed the domains of: class structure changes and timing, patient interactions, exam administration, learning environment satisfaction, mental health impacts, and volunteer opportunities/engagement. RESULTS: 694 students across 33 countries participated. 80% of respondents had their classes suspended for varied lengths of time during the pandemic, and from these students 59% of them resumed their classes. 83% of students felt they were in a supportive learning environment before the pandemic, which dropped to 32% since the start. The proportion of students taking exams online increased (6-26%, p<0.001) and there was a decrease in the proportion of students seeing patients as a part of their education (72-19%, p<0.001). CONCLUSIONS: COVID-19 is harming medical students in Africa and is likely to worsen the shortage of the future's healthcare workforce in the region. Pandemic-related impacts have led to a degradation of the learning environment of medical students. Medical schools have shifted online to differing degrees and direct patient-care in training of students has decreased. This study highlights the urgent need for flexible and innovative approaches to medical education in Africa.

Autonomous adaptive data acquisition for scanning hyperspectral imaging.

Non-invasive and label-free spectral microscopy (spectromicroscopy) techniques can provide quantitative biochemical information complementary to genomic sequencing, transcriptomic profiling, and proteomic analyses. However, spectromicroscopy techniques generate high-dimensional data; acquisition of a single spectral image can range from tens of minutes to hours, depending on the desired spatial resolution and the image size. This substantially limits the timescales of observable transient biological processes. To address this challenge and move spectromicroscopy towards efficient real-time spatiochemical imaging, we developed a grid-less autonomous adaptive sampling method. Our method substantially decreases image acquisition time while increasing sampling density in regions of steeper physico-chemical gradients. When implemented with scanning Fourier Transform infrared spectromicroscopy experiments, this grid-less adaptive sampling approach outperformed standard uniform grid sampling in a two-component chemical model system and in a complex biological sample, Caenorhabditis elegans. We quantitatively and qualitatively assess the efficiency of data acquisition using performance metrics and multivariate infrared spectral analysis, respectively.

Creating Supportive Environments for LGBT Older Adults: An Efficacy Evaluation of Staff Training in a Senior Living Facility.

Supportive housing later in life tends to be a key concern for lesbian, gay, bisexual, and transgender (LGBT) elders. Most senior care providers are un(der)prepared to meet the needs of older LGBT adults. This study evaluated the efficacy of a 4 hours, face-to-face, research-based, LGBT-diversity training designed to improve senior housing facility staff's cultural competency regarding the needs of LGBT elders. Findings from this study found a significant increase in LGBT content knowledge between pre- and post-intervention assessments and a significant decrease in perceived preparedness when working with LGBT elders. These effects remained significant after controlling for staff designation, religion, educational attainment, and training session. Findings suggest that staff's cultural competence affected their perceived readiness to address LGBT elders' needs. Implications are related to the concept of cultural humility or the lifelong process of understanding others' experiences based on the recognition of lack of un(der)preparedness to create a culturally supportive residential environment.

Sensitive Detection and Analysis of Neoantigen-Specific T Cell Populations from Tumors and Blood.

Neoantigen-specific T cells are increasingly viewed as important immunotherapy effectors, but physically isolating these rare cell populations is challenging. Here, we describe a sensitive method for the enumeration and isolation of neoantigen-specific CD8+ T cells from small samples of patient tumor or blood. The method relies on magnetic nanoparticles that present neoantigen-loaded major histocompatibility complex (MHC) tetramers at high avidity by barcoded DNA linkers. The magnetic particles provide a convenient handle to isolate the desired cell populations, and the barcoded DNA enables multiplexed analysis. The method exhibits superior recovery of antigen-specific T cell populations relative to literature approaches. We applied the method to profile neoantigen-specific T cell populations in the tumor and blood of patients with metastatic melanoma over the course of anti-PD1 checkpoint inhibitor therapy. We show that the method has value for monitoring clinical responses to cancer immunotherapy and might help guide the development of personalized mutational neoantigen-specific T cell therapies and cancer vaccines.

Creating assessments as an active learning strategy: what are students' perceptions? A mixed methods study.

Background: Teaching students how to create assessments, such as those involving multiple-choice questions (MCQs), has the potential to be a useful active learning strategy. In order to optimize students' learning, it is essential to understand how they engage with such activities. Objective: To explore medical students' perceptions of how completing rigorous MCQ training and subsequently writing MCQs affects their learning. Design: In this mixed methods exploratory qualitative study, eighteen second-year medical students, trained in MCQ-writing best practices, collaboratively generated a question bank. Subsequently, the authors conducted focus groups with eight students to probe impressions of the process and the effect on learning. Responses partially informed a survey consisting of open-ended and Likert rating scale questions that the remaining ten students completed. Focus group and survey data from the eighteen participants were iteratively coded and categorized into themes related to perceptions of training and of collaborative MCQ writing. Results: Medical students felt that training in MCQ construction affected their appreciation for MCQ examinations and their test-taking strategy. They perceived that writing MCQs required more problem-solving and content-integration compared to their preferred study strategies. Specifically, generating plausible distractors required the most critical reasoning to make subtle distinctions between diagnoses and treatments. Additionally, collaborating with other students was beneficial in providing exposure to different learning and question-writing approaches. Conclusions: Completing MCQ-writing training increases appreciation for MCQ assessments. Writing MCQs requires medical students to make conceptual connections, distinguish between diagnostic and therapeutic options, and learn from colleagues, but requires extensive time and knowledge base.

Identifying Medical Student Mistreatment in the Obstetrics and Gynecology Clerkship.

OBJECTIVE: To characterize the mistreatment identified within the University of Michigan's Obstetrics and Gynecology (Ob/Gyn) clerkship and compare the rates of mistreatment to that of other clerkships in an effort to improve the learning environment. DESIGN: This is a retrospective cohort study looking at multiple sources of data from 2015 to 2018 about student mistreatment including end-of-rotation and teaching evaluations completed by students, as well as an online reporting system available to medical students. For evaluations, students were asked to rate their agreement with statements on a 5-point Likert scale (1 = strongly disagree, to 5 = strongly agree). Narrative comments were also solicited and evaluated. SETTING: University of Michigan Medical School and Michigan Medicine Ob/Gyn Department, Ann Arbor, Michigan. PARTICIPANTS: A total of 513 students rotated through the Ob/Gyn clerkship between 2015 and 2018 and were asked to complete evaluations. RESULTS: Five hundred and five of the 513 students completed evaluations between 2015 and 2018. In response to the statement, "Students are treated in a professional/respectful manner in this clerkship," the Ob/Gyn clerkship's mean scores on a 5-point scale were 4.45 (in 2015-2016), 4.52 (in 2016-2017), and 4.27 (in 2017-2018). These means, as well as the means to 3 other professionalism questions, were lower than the range of 4.42 to 4.84 for all other third-year clerkships over this time. The mean scores were also lower for Ob/gyn when compared to the Surgery clerkship. A total of 32 narrative comments were submitted by students between 2015 and 2017 related to mistreatment or unprofessional behavior. Frequent themes included students being treated as "stupid" or discouraged from asking questions (8 comments), being treated in an unprofessional manner by staff (7 comments), feeling ignored or marginalized by faculty (4 comments), and faculty unprofessional behavior toward others (4 comments). CONCLUSIONS: Students on the Ob/Gyn clerkship reported a higher rate of mistreatment compared to other clerkships. Efforts are being made by the Ob/Gyn department to communicate these data on mistreatment to educators in order to improve the Ob/Gyn culture and learning environment for medical students.

The effects of minority stressors in the workplace on same-sex relationships: A collective case study of female couples.

The purpose of this study is to explore the relational effects of minority stress processes experienced at work by female sexual minority employees. Lesbians, in particular, warrant attention in the work environment, as their experiences with homophobia may be exacerbated by sexist overtones. While scholars have linked hostility in the work environment to individual health and employment outcomes for LGBQ employees, less attention has been given to the cross-contextual effects from work to family life. This collective case study examines the experiences of three lesbian employees and their partners in various workplaces using minority stress border theory. Results show that, for these women, there are negative effects on their same-sex relationships; surprisingly though, several women also discussed positive changes in their relationship as a result of experiences with minority stress processes in the workplace. Implications for future research are discussed.

Reconsidering the LGBT Climate Inventory: Understanding Support and Hostility for LGBTQ Employees in the Workplace.

Workplace climate matters significantly for lesbian, gay, bisexual, queer, or other sexual minority (LGBQ) employees, given that the presence of workplace hostility or support can affect well-being. The Lesbian, Gay, Bisexual, and Transgender Climate Inventory (LGBTCI) is a measure of workplace climate for LGBQ individuals, intended to capture the full range of workplace climate from hostility to support. The purpose of this article is to provide evidence that the recommended scoring approach of the LGBTCI needs to be reconsidered. We used latent class analysis to estimate classes of work-related experiences in our sample of 442 LGBQ employees who completed the LGBTCI. A four-class solution fit the data best. Characteristics of each class were identified and consequently labeled: supportive work climate, tolerant work climate, ambiguous work climate, and hostile work climate. Findings suggest that a more accurate measure of workplace climate would include independent scales for support and hostility.

Tolerance Versus Support: Perceptions of Residential Community Climate Among LGB Parents.

OBJECTIVE: To understand which aspects of residential communities are most salient for determining whether sexual minority parents classify their residential community climates as tolerant versus supportive. BACKGROUND: Metropolitan hubs for lesbian, gay, and bisexual (LGB) parents are well established, but less is known about nonmetropolitan community climates for LGB parents. Residential community climate toward nonmetropolitan LGB persons may be particularly important to LGB parents because of the potential influences on child and family well-being. METHOD: Open- and closed-ended survey data from a sample of 55 LGB parents were collected along with publically available data regarding their residential communities. Self-reported residential community climate (tolerant vs. supportive) and community involvement, as well as objective county and municipal climate were analyzed. RESULTS: Compared with LGB parents who perceived their communities to be tolerant (n = 38), parents who considered their residential communities to be supportive (n = 17) were more likely to live in counties characterized by legal support and broad social acceptance, were personally more likely to participate in LGB-focused social and political activities, had children with more exposure to other LGB families, and attended church less frequently. CONCLUSION: Having basic features of equity such as city ordinances and LGB organizations provides a foundation for tolerance in a community; however, individuals in a community must access personal and social supports and activities beyond work and church to feel truly supported. IMPLICATIONS: LGB parents' perceptions of climate reveal specific community features that need to be strengthened to promote family well-being.

Theoretical Extensions of Minority Stress Theory for Sexual Minority Individuals in the Workplace: A Cross-Contextual Understanding of Minority Stress Processes.

Minority stress theory posits that stress processes specific to a sexual minority orientation can affect the psychological health and well-being of lesbian, gay, bisexual, or queer-identified (LGBQ) individuals. In the workplace, LGBQ employees experiencing minority stress report poor mental health outcomes and decreased job satisfaction and commitment. However, few scholars have examined the cross-contextual effects minority stressors that individuals experience in the workplace may have on couples. That is, given the literature highlighting the work-family interface, how do minority stressors at work affect the sexual minority employee within the family dynamics of same-sex couples at home? The purpose of this article is to propose a multi-theoretical approach which includes elements of minority stress theory and work-family border theory to guide future research in examining the cross-contextual effects of minority stress for couple- and family-level outcomes.

High pCO2-induced exopolysaccharide-rich ballasted aggregates of planktonic cyanobacteria could explain Paleoproterozoic carbon burial.

The contribution of planktonic cyanobacteria to burial of organic carbon in deep-sea sediments before the emergence of eukaryotic predators ~1.5 Ga has been considered negligible owing to the slow sinking speed of their small cells. However, global, highly positive excursion in carbon isotope values of inorganic carbonates ~2.22-2.06 Ga implies massive organic matter burial that had to be linked to oceanic cyanobacteria. Here to elucidate that link, we experiment with unicellular planktonic cyanobacteria acclimated to high partial CO2 pressure (pCO2) representative of the early Paleoproterozoic. We find that high pCO2 boosts generation of acidic extracellular polysaccharides (EPS) that adsorb Ca and Mg cations, support mineralization, and aggregate cells to form ballasted particles. The down flux of such self-assembled cyanobacterial aggregates would decouple the oxygenic photosynthesis from oxidative respiration at the ocean scale, drive export of organic matter from surface to deep ocean and sustain oxygenation of the planetary surface.

Palliative Care Matters: Lessons From the Loss of a Facility Dog.

Animal-assisted intervention is gaining attention as a stress reduction modality. Quantitative data demonstrate its effectiveness, as a recent study published in AJHPM supported that a Veterans Affairs (VA) hospital facility dog paired with a palliative care psychologist had a measurable impact on salivary cortisol levels and heart rate in hospitalized veterans. There remains an important role for qualitative insights. The Denver VA palliative care team learned a range of lessons from the sudden loss of their facility dog, many of which relate directly to palliative care. The importance of communication, adjusting to changing teams, and the need for consultation and support based in shared goals and values all became evident in the course of the facility dog's illness. After her death, lessons shifted to grief and loss and how providers, patients, and a community care for each other. People's connection to the facility dog ultimately proved to be a critical factor in helping them connect with one another.

Tracking Student Mistreatment Data to Improve the Emergency Medicine Clerkship Learning Environment.

INTRODUCTION: Medical student mistreatment is a prevalent and significant challenge for medical schools across the country, associated with negative emotional and professional consequences for students. The Association of American Medical Colleges and Liaison Committee on Medical Education have increasingly emphasized the issue of mistreatment in recent years, and medical schools are tasked with creating a positive learning climate. METHODS: The authors describe the efforts of an emergency department (ED) to improve its clerkship learning environment, using a multifaceted approach for collecting mistreatment data and relaying them to educators and clerkship leadership. Data are gathered through end-of-rotation evaluations, teaching evaluations, and an online reporting system available to medical students. Mistreatment data are then relayed to the ED during semi-annual meetings between clerkship leadership and medical school assistant deans, and through annual mistreatment reports provided to department chairs. RESULTS: Over a two-year period, students submitted a total of 56 narrative comments related to mistreatment or unprofessional behavior during their emergency medicine (EM) clerkship. Of these comments, 12 were submitted in 2015-16 and 44 were submitted in 2016-17. The most frequently observed themes were students feeling ignored or marginalized by faculty (14 comments); students being prevented from speaking or working with patients and/or attending faculty (11 comments); and students being treated in an unprofessional manner by staff (other than faculty, 8 comments). CONCLUSION: This article details an ED's efforts to improve its EM clerkship learning environment by tracking mistreatment data and intentionally communicating the results to educators and clerkship leadership. Continued mistreatment data collection and faculty development will be necessary for these efforts to have a measurable effect on the learning environment.

Effects of VA Facility Dog on Hospitalized Veterans Seen by a Palliative Care Psychologist: An Innovative Approach to Impacting Stress Indicators.

The United States is home to 23 million veterans. In many instances, veterans with serious illness who seek healthcare at the VA receive care from a palliative care service. Animal-assisted intervention (AAI) is gaining attention as a therapeutic stress reducing modality; however, its effects have not been well studied in veterans receiving palliative care in an acute care setting. A crossover repeated-measures study was conducted to examine the effects of an animal-assisted intervention (AAI) in the form of a therapy dog on stress indicators in 25 veterans on the palliative care service at the VA Eastern Colorado Healthcare System in Denver, CO. Veterans had a visit from a therapy dog and the dog's handler, a clinical psychologist (experimental condition) and an unstructured visit with the clinical psychologist alone (control condition). Blood pressure, heart rate, and the salivary biomarkers cortisol, alpha-amylase, and immunoglobulin A were collected before, after, and 30-minutes after both the experimental and control conditions. Significant decreases in cortisol were found when the before time period was compared to the 30-minutes after time period for both the experimental ( p = 0.007) and control condition ( p = 0.036). A significant decrease in HR was also found when the before time period was compared to the 30-minutes after time period for both the experimental ( p = 0.0046) and control ( p = 0.0119) condition. Results of this study supported that a VA facility dog paired with a palliative care psychologist had a measurable impact on salivary cortisol levels and HR in veterans.