From compost to culver: genome sequence and annotation of a cluster CQ1 Gordonia phage.

Phage Culver, with a siphovirus morphology, was isolated using Gordonia terrae CAG3. Culver is assigned to phage cluster CQ1 based on gene content similarity to actinobacteriophages. Notably, Culver is predicted to encode eight tRNAs, lysin A by two adjacent genes, and, unlike other CQ1 phages, two putative integrase genes.

Assessment of Medical Education on Transgender Health: A Scoping Literature Review.

Little is known about how physician learners are assessed following educational interventions about providing gender-affirming care to transgender and gender diverse (TGD) people. The inclusion of learner assessments with educational interventions is essential to understand and measure health professionals' knowledge and skills. We seek to describe how the medical literature has approached the assessment of learners following educational interventions about TGD health. A scoping literature review was done. The guiding research question was "What are the current learner-assessment practices in medical education pedagogy about TGD health?" A total of 270 manuscripts were reviewed. 17 manuscripts were included for data extraction. Miller's pyramid was used to categorize results. 15 used pre- and post-intervention knowledge questionaries to assess learners. Six used simulated patient encounters to assess learners. Most assessments of TGD knowledge and skills among physician learners are pre- and post-surveys. There is sparse literature on higher level assessment following educational interventions that demonstrate learner skills, behaviors, or impact on patient outcomes. Discrete, one-time interventions that are lecture or workshop-based have yet to rigorously assess learners' ability to provide clinical care to TGD patients that is both culturally humble and clinically astute.

A comparative analysis of gene and protein expression in chronic and acute models of photoreceptor degeneration in adult zebrafish.

Background: Adult zebrafish are capable of photoreceptor (PR) regeneration following acute phototoxic lesion (AL). We developed a chronic low light (CLL) exposure model that more accurately reflects chronic PR degeneration observed in many human retinal diseases. Methods: Here, we characterize the morphological and transcriptomic changes associated with acute and chronic models of PR degeneration at 8 time-points over a 28-day window using immunohistochemistry and 3'mRNA-seq. Results: We first observed a differential sensitivity of rod and cone PRs to CLL. Next, we found no evidence for Müller glia (MG) gliosis or regenerative cell-cycle re-entry in the CLL model, which is in contrast to the robust gliosis and proliferative response from resident MG in the AL model. Differential responses of microglia between the models was also observed. Transcriptomic comparisons between the models revealed gene-specific networks of PR regeneration and degeneration, including genes that are activated under conditions of chronic PR stress. Finally, we showed that CLL is at least partially reversible, allowing for rod and cone outer segment outgrowth and replacement of rod cell nuclei via an apparent upregulation of the existing rod neurogenesis mechanism. Discussion: Collectively, these data provide a direct comparison of the morphological and transcriptomic PR degeneration and regeneration models in zebrafish.

Probing the conserved roles of cut in the development and function of optically different insect compound eyes.

Astonishing functional diversity exists among arthropod eyes, yet eye development relies on deeply conserved genes. This phenomenon is best understood for early events, whereas fewer investigations have focused on the influence of later transcriptional regulators on diverse eye organizations and the contribution of critical support cells, such as Semper cells (SCs). As SCs in Drosophila melanogaster secrete the lens and function as glia, they are critical components of ommatidia. Here, we perform RNAi-based knockdowns of the transcription factor cut (CUX in vertebrates), a marker of SCs, the function of which has remained untested in these cell types. To probe for the conserved roles of cut, we investigate two optically different compound eyes: the apposition optics of D. melanogaster and the superposition optics of the diving beetle Thermonectus marmoratus. In both cases, we find that multiple aspects of ocular formation are disrupted, including lens facet organization and optics as well as photoreceptor morphogenesis. Together, our findings support the possibility of a generalized role for SCs in arthropod ommatidial form and function and introduces Cut as a central player in mediating this role.

Global Gene Expression Analysis Reveals Complex Cuticle Organization of the Tribolium Compound Eye.

The red flour beetle Tribolium castaneum is a resource-rich model for genomic and developmental studies. To extend previous studies on Tribolium eye development, we produced transcriptomes for normal-eyed and eye-depleted heads of pupae and adults to identify differentially transcript-enriched (DE) genes in the visual system. Unexpectedly, cuticle-related genes were the largest functional class in the pupal compound eye DE gene population, indicating differential enrichment in three distinct cuticle components: clear lens facet cuticle, highly melanized cuticle of the ocular diaphragm, which surrounds the Tribolium compound eye for internal fortification, and newly identified facet margins of the tanned cuticle, possibly enhancing external fortification. Phylogenetic, linkage, and high-throughput gene knockdown data suggest that most cuticle proteins (CPs) expressed in the Tribolium compound eye stem from the deployment of ancient CP genes. Consistent with this, TcasCPR15, which we identified as the major lens CP gene in Tribolium, is a beetle-specific but pleiotropic paralog of the ancient CPR RR-2 CP gene family. The less abundant yet most likely even more lens-specific TcasCP63 is a member of a sprawling family of noncanonical CP genes, documenting a role of local gene family expansions in the emergence of the Tribolium compound eye CP repertoire. Comparisons with Drosophila and the mosquito Anopheles gambiae reveal a steady turnover of lens-enriched CP genes during insect evolution.

Training clinicians in culturally relevant care: a curriculum to improve knowledge and comfort with the transgender and gender diverse population.

PURPOSE: To design a replicable simulation curriculum collaboratively with the transgender and gender diverse community to improve clinician knowledge and comfort with providing reproductive care to this population. METHODS: This is a prospective, single arm pre-post analysis of obstetrics and gynecology residents at a single academic institution after completion of a novel simulation curriculum. The primary outcome was the change in resident comfort and knowledge in providing transgender and gender diverse patient care. A thematic analysis of learner and standardized patient free text responses was analyzed for insights on perceived learner experiences. RESULTS: This curriculum was created with iterative feedback from the transgender community and involved only transgender and gender diverse-identified standardized patients. Thirty residents participated, with 22 responding to both the pre-and post-curriculum surveys, and 11 responding to a 6-month post-curriculum survey. There were significant improvements in learner comfort and knowledge after participation that were found to persist at 6 months. Qualitative analysis demonstrated that this was a positive and powerful learning experience for both residents and standardized patients. CONCLUSIONS: This simulation curriculum may be an effective and impactful tool to increase trainee comfort and knowledge of transgender and gender diverse patient care, which is important given the lack of physician training in the care for these individuals. By building the foundation with resident learners, the ultimate goal is to enhance the pool of clinicians confident and capable of caring for transgender and gender diverse patients, to increase access to care, and to improve health outcomes in this vulnerable population.

EyeVolve, a modular PYTHON based model for simulating developmental eye type diversification.

Vision is among the oldest and arguably most important sensory modalities for animals to interact with their external environment. Although many different eye types exist within the animal kingdom, mounting evidence indicates that the genetic networks required for visual system formation and function are relatively well conserved between species. This raises the question as to how common developmental programs are modified in functionally different eye types. Here, we approached this issue through EyeVolve, an open-source PYTHON-based model that recapitulates eye development based on developmental principles originally identified in Drosophila melanogaster. Proof-of-principle experiments showed that this program's animated timeline successfully simulates early eye tissue expansion, neurogenesis, and pigment cell formation, sequentially transitioning from a disorganized pool of progenitor cells to a highly organized lattice of photoreceptor clusters wrapped with support cells. Further, tweaking just five parameters (precursor pool size, founder cell distance and placement from edge, photoreceptor subtype number, and cell death decisions) predicted a multitude of visual system layouts, reminiscent of the varied eye types found in larval and adult arthropods. This suggests that there are universal underlying mechanisms that can explain much of the existing arthropod eye diversity. Thus, EyeVolve sheds light on common principles of eye development and provides a new computational system for generating specific testable predictions about how development gives rise to diverse visual systems from a commonly specified neuroepithelial ground plan.

Prednisone and deflazacort in Duchenne muscular dystrophy: a patient perspective and plain language summary publication of the Cincinnati study.

WHAT IS THIS SUMMARY ABOUT?: This is a summary of an article about the Cincinnati study, which was published in the Journal of Comparative Effectiveness Research in January 2020. The Cincinnati study reviewed data from 435 males with Duchenne muscular dystrophy, also known as DMD, who were treated at the Cincinnati Children's Hospital Medical Center. DMD is a rare disease that worsens over time. People with DMD experience inflammation in their muscles and muscle loss over time. They also experience bone problems such as an abnormally bent spine, also known as scoliosis, as well as heart and lung problems. WHAT HAPPENED IN THE CINCINNATI STUDY?: Prednisone and deflazacort are steroids that help to reduce muscle inflammation and are used as treatments for DMD. The study researchers wanted to further understand the differences between using prednisone and deflazacort in males with DMD by reviewing data from past medical records of patients seen in clinics rather than in clinical studies. This is known as gathering real-world evidence. In the Cincinnati study, the researchers compared males with DMD who started taking prednisone as their first steroid treatment with males who started taking deflazacort as their first steroid treatment. WHAT WERE THE RESULTS?: Overall, the researchers found that the participants who took deflazacort were able to walk until a later age before they needed to use a wheelchair, compared with those who took prednisone. They also had a lower risk of scoliosis and developed it at a later age. WHAT DO THE RESULTS OF THE STUDY MEAN?: These results helped the researchers to learn more about the differences between how well prednisone and deflazacort work in males with DMD based on their medical records.

Comparing Electronic Health Record Domains' Utility to Identify Transgender Patients.

Purpose: Earlier literature has reported on the utility of diagnostic codes and demographic information for identifying transgender patients. We aim to assess which method identifies the most transgender patients utilizing readily available tools from within the electronic health record (EHR). Methods: A de-identified patient database from a single EHR that allows for searching any discrete data point in the EHR was used to query International Statistical Classification of Diseases and Related Health Problems, 10th Revision (ICD-10) diagnostic codes and demographic data specific to transgender patients from January 2011 to April 2019. Results: Demographic data and ICD-10 codes yielded 1494 individual EHRs with transgender-specific data domains. ICD-10 diagnostic codes alone identified 942 (63.05%) unique EHRs. Demographics alone identified 218 (14.59%) unique EHRs. A total of 334 (22.36%) unique EHRs had both ICD-10 and demographic identifiers. Of those identified by transgender-specific demographic data (552), 294 (53.26%) were trans masculine, 215 (38.95%) were trans feminine, and 43 (7.79%) were nonbinary. Of the 552 demographic-identified transgender patients, 141 (25.86%) were identified by a two-part gender identity demographic question. Conclusions: ICD-10 diagnostic codes, not demographic data, identified the most transgender patient records, but neither diagnostic codes alone nor demographic data captured the full population. Only 26.36% of the charts identified as transgender patients had both ICD-10 codes and demographic data. We recommend that when identifying transgender populations through EHR domains, a combination of diagnostic codes and demographic data be used. Furthermore, research is needed to optimize disclosure and collection of demographic information for gender minority populations.

Semper's cells in the insect compound eye: Insights into ocular form and function.

The arthropod compound eye represents one of two major eye types in the animal kingdom and has served as an essential experimental paradigm for defining fundamental mechanisms underlying sensory organ formation, function, and maintenance. One of the most distinguishing features of the compound eye is the highly regular array of lens facets that define individual eye (ommatidial) units. These lens facets are produced by a deeply conserved quartet of cuticle-secreting cells, called Semper cells (SCs). Also widely known as cone cells, SCs were originally identified for their secretion of the dioptric system, i.e. the corneal lens and underlying crystalline cones. Additionally, SCs are now known to execute a diversity of patterning and glial functions in compound eye development and maintenance. Here, we present an integrated account of our current knowledge of SC multifunctionality in the Drosophila compound eye, highlighting emerging gene regulatory modules that may drive the diverse roles for these cells. Drawing comparisons with other deeply conserved retinal glia in the vertebrate single lens eye, this discussion speaks to glial cell origins and opens new avenues for understanding sensory system support programs.

Development and characterization of a chronic photoreceptor degeneration model in adult zebrafish that does not trigger a regenerative response.

Zebrafish (Danio rerio) have become a highly-utilized model system in the field of regenerative biology because of their endogenous ability to regenerate many tissues and organs, including the retina. The vast majority of previous research on retinal regeneration in adult zebrafish utilizes acute methodologies for retinal damage. Acute retinal cell death triggers a reactive gliosis response of Müller glia (MG), the resident macroglia of the retina. In addition, each activated MG undergoes asymmetric cell division to produce a neuronal progenitor, which continues to divide and ultimately gives rise to new retinal neurons. Studies using these approaches have uncovered many crucial mechanisms by which MG respond to acute damage. However, they may not adequately mimic the chronic neuronal degeneration observed in many human retinal degenerative diseases. The current study aimed to develop a new long-term, chronic photoreceptor damage and degeneration model in adult zebrafish. Comparing the subsequent cellular responses to that of the commonly-used acute high-intensity model, we found that low, continuous light exposure damaged the outer segments of both rod and cone photoreceptors, but did not result in significant apoptotic cell death, MG gliosis, or MG cell-cycle re-entry. Instead, chronic light nearly completely truncated photoreceptor outer segments and resulted in a recruitment of microglia to the area. Together, these studies present a chronic photoreceptor model that can be performed in a relatively short time frame (21 days), that may lend insight into the cellular events underlying non-regenerative photoreceptor degeneration observed in other model systems.

Sexual Orientation Demographic Data in a Clinical Cohort of Transgender Patients.

BACKGROUND: There are specific issues regarding sexual orientation (SO) collection and analysis among transgender and nonbinary patients. A limitation to meaningful SO and gender identity (GI) data collection is their consideration as a fixed trait or demographic data point. METHODS: A de-identified patient database from a single electronic health record (EHR) that allows for searching any discrete data point in the EHR was used to query demographic data (sex assigned at birth and current GI) for transgender individuals from January 2011 to March 2020 at a large urban tertiary care academic health center. RESULTS: A cohort of transgender individuals were identified by using EHR data from a two-step demographic question. Almost half of male identified (46.70%, n = 85) and female identified (47.51%, n = 86) individuals had "heterosexual/straight" input for SO. Overall, male and female identified (i.e., binary) GI aggregate categories had similar SO responses. Assigned male at birth (AMAB) nonbinary individuals (n = 6) had "homosexual/gay" SO data input. Assigned female at birth (AFAB) nonbinary individuals (n = 56) had almost half "something else" SO data input (41.67%, n = 15). Individuals with "choose not to disclose" for GI (n = 249) almost all had "choose not to disclose" SO data (96.27%, n = 232). CONCLUSION: Current SO categories do not fully capture transgender individuals' identities and experiences, and limit the clinical and epidemiological utility of collecting this data in the current form. Anatomical assumptions based on SO should be seen as a potential shortcoming in over-reliance on SO as an indicator of screening needs and risk factors.

Assessment of Racial/Ethnic Disparities in Hospitalization and Mortality in Patients With COVID-19 in New York City.

Importance: Black and Hispanic populations have higher rates of coronavirus disease 2019 (COVID-19) hospitalization and mortality than White populations but lower in-hospital case-fatality rates. The extent to which neighborhood characteristics and comorbidity explain these disparities is unclear. Outcomes in Asian American populations have not been explored. Objective: To compare COVID-19 outcomes based on race and ethnicity and assess the association of any disparities with comorbidity and neighborhood characteristics. Design, Setting, and Participants: This retrospective cohort study was conducted within the New York University Langone Health system, which includes over 260 outpatient practices and 4 acute care hospitals. All patients within the system's integrated health record who were tested for severe acute respiratory syndrome coronavirus 2 between March 1, 2020, and April 8, 2020, were identified and followed up through May 13, 2020. Data were analyzed in June 2020. Among 11 547 patients tested, outcomes were compared by race and ethnicity and examined against differences by age, sex, body mass index, comorbidity, insurance type, and neighborhood socioeconomic status. Exposures: Race and ethnicity categorized using self-reported electronic health record data (ie, non-Hispanic White, non-Hispanic Black, Hispanic, Asian, and multiracial/other patients). Main Outcomes and Measures: The likelihood of receiving a positive test, hospitalization, and critical illness (defined as a composite of care in the intensive care unit, use of mechanical ventilation, discharge to hospice, or death). Results: Among 9722 patients (mean [SD] age, 50.7 [17.5] years; 58.8% women), 4843 (49.8%) were positive for COVID-19; 2623 (54.2%) of those were admitted for hospitalization (1047 [39.9%] White, 375 [14.3%] Black, 715 [27.3%] Hispanic, 180 [6.9%] Asian, 207 [7.9%] multiracial/other). In fully adjusted models, Black patients (odds ratio [OR], 1.3; 95% CI, 1.2-1.6) and Hispanic patients (OR, 1.5; 95% CI, 1.3-1.7) were more likely than White patients to test positive. Among those who tested positive, odds of hospitalization were similar among White, Hispanic, and Black patients, but higher among Asian (OR, 1.6, 95% CI, 1.1-2.3) and multiracial patients (OR, 1.4; 95% CI, 1.0-1.9) compared with White patients. Among those hospitalized, Black patients were less likely than White patients to have severe illness (OR, 0.6; 95% CI, 0.4-0.8) and to die or be discharged to hospice (hazard ratio, 0.7; 95% CI, 0.6-0.9). Conclusions and Relevance: In this cohort study of patients in a large health system in New York City, Black and Hispanic patients were more likely, and Asian patients less likely, than White patients to test positive; once hospitalized, Black patients were less likely than White patients to have critical illness or die after adjustment for comorbidity and neighborhood characteristics. This supports the assertion that existing structural determinants pervasive in Black and Hispanic communities may explain the disproportionately higher out-of-hospital deaths due to COVID-19 infections in these populations.

How Do OSCE Cases Activate Learners About Transgender Health?

PURPOSE: To describe the effect of transgender health-related objective structured clinical examination (THOSCE) case exposure on learner activation regarding gender-affirming care. METHOD: A modified grounded theory approach was applied to identify the educational value of THOSCE cases. Focus groups with current and former primary care internal medicine residents who participated in THOSCE cases were conducted in 2018-2019. Transcripts were analyzed and coded until saturation to identify themes. RESULTS: Eighteen (72%) eligible learners participated in the focus groups. Themes were identified relating to gender-affirming care, and modified grounded theory analysis was used as a framework to organize the themes into 4 stages of learner activation: (1) believing the learner role is important, (2) having the confidence and knowledge necessary to take action, (3) taking action to maintain and improve one's skills, and (4) staying the course even under stress. CONCLUSIONS: Residents were grateful for the opportunity to practice the skills involved in transgender health in a simulation. Many felt unprepared and were concerned about how they were perceived by the standardized patient and faculty. Residents identified feeling more comfortable with gender-affirming language in the inpatient setting, which may provide an opportunity for learning in the future. Residents identified the psychosocial skills of gender-affirming care as more directly relevant while biomedical aspects of gender-affirming care seemed less accessible to residents, given the lack of outpatient experience. The authors propose a staged approach to teaching the skills of gender-affirming care using simulation to address learners of all levels.

Interrupting Microaggressions in Health Care Settings: A Guide for Teaching Medical Students.

Introduction: Microaggressions are connected to broader conceptualizations of the impact of implicit bias and systems of inequity. The body of evidence supporting the need for more-open discussions in medical education about race, racism, and their impact on health disparities continues to grow. Some have advocated for the importance of bringing anti-racist pedagogy into medical education curricula, which involves explicitly attempting to move beyond people's comfort zones and acknowledging that discomfort can be a catalyst for growth. To discuss the intent and impact of microaggressions in health care settings and how we might go about responding to them, we developed a workshop for third-year undergraduate medical students within a longitudinal undergraduate medical education diversity and inclusion curriculum. Methods: This workshop occurred during a regularly scheduled clerkship intersession during the 2016-2017 academic year for third-year undergraduate medical students (N = 154). Prior to the workshop, the students were asked to anonymously submit critical incident reports on any microaggressions experienced or witnessed to develop case studies for problem-based learning. Teaching modalities included lecture, problem-based learning with case studies, pair and share, and facilitated small- and large-group debriefs. Results: The session was evaluated using a 4-point Likert scale to assess students' comfort in learning about the information presented. Ninety-eight percent felt confident in identifying microaggressions, and 85% felt confident in interrupting microaggressions when they occur. Discussion: This personalized workshop exposes students to microaggressions personally experienced by colleagues with an attempt to interrupt them using empathy, awareness, and communication techniques.

Gendered Expectations: Strategies for Navigating Structural Challenges in Support of Transgender and Nonbinary Trainees in Academic Medicine.

Members of the lesbian, gay, bisexual, transgender, and queer community experience marginalization, bias, and discrimination, including in the world of academic medicine. People who are transgender and nonbinary (TGNB) experience further marginalization compared with individuals who are lesbian, gay, bisexual, and queer. According to a recent survey, more than half of medical students who are TGNB chose not to disclose their gender identities during training due to fears of discrimination, feeling a lack of support, and concerns about future career options. Academic medicine has historically pathologized TGNB individuals, perpetuating discrimination structurally and reinforcing discriminatory behaviors of peers and faculty. In this Perspective, the authors provide a comprehensive overview of the challenges that administrators and educators face in creating a learning environment that is inclusive of TGNB trainees. They outline opportunities for change and provide strategies to address administrative and educational challenges, including those related to institutional climate, policies, data collection, physical spaces, health care, curriculum, mentoring, and the evaluation of TGNB trainees. Finally, the authors issue a call to action for medical educators and administrators to create environments in which trainees who are TGNB can fulfill their educational mission: to learn the practice of medicine.

Experiences of Transgender and Gender Nonbinary Medical Students and Physicians.

Purpose: To explore the experiences of transgender and gender nonbinary (TGNB) medical students and physicians in the United States. Methods: The authors conducted a 79-item online survey using Likert-type and open-ended questions to assess the experiences of TGNB-identified U.S. medical students and physicians. Variables included demographic data, disclosure of TGNB status, exposure to transphobia, and descriptions of educational and professional experiences. Recruitment was conducted using snowball sampling through Lesbian, Gay, Bisexual, Transgender, Queer professional groups, list-servs, and social media. The survey was open from June 2017 through November 2017. Results: Respondents included 21 students and 15 physicians (10 transgender women, 10 transgender men, and 16 nonbinary participants). Half (50%; 18) of the participants and 60% (9) of physicians had not disclosed their TGNB identity to their medical school or residency program, respectively. Respondents faced barriers on the basis of gender identity/expression when applying to medical school (22%; 11) and residency (43%; 6). More than three-quarters (78%; 28) of participants censored speech and/or mannerisms half of the time or more at work/school to avoid unintentional disclosure of their TGNB status. More than two-thirds (69%; 25) heard derogatory comments about TGNB individuals at medical school, in residency, or in practice, while 33% (12) witnessed discriminatory care of a TGNB patient. Conclusion: TGNB medical students and physicians faced significant barriers during medical training, including having to hide their identities and witnessing anti-TGNB stigma and discrimination. This study, the first to exclusively assess experiences of TGNB medical students and physicians, reveals that significant disparities still exist on the basis of gender identity.

Opposing transcriptional and post-transcriptional roles for Scalloped in binary Hippo-dependent neural fate decisions.

The Hippo tumor suppressor pathway plays many fundamental cell biological roles during animal development. Two central players in controlling Hippo-dependent gene expression are the TEAD transcription factor Scalloped (Sd) and its transcriptional co-activator Yorkie (Yki). Hippo signaling phosphorylates Yki, thereby blocking Yki-dependent transcriptional control. In post-mitotic Drosophila photoreceptors, a bistable negative feedback loop forms between the Hippo-dependent kinase Warts/Lats and Yki to lock in green vs blue-sensitive neuronal subtype choices, respectively. Previous experiments indicate that sd and yki mutants phenocopy each other's functions, both being required for promoting the expression of the blue photoreceptor fate determinant melted (melt) and the blue-sensitive opsin Rh5. Here, we demonstrate that Sd ensures the robustness of this neuronal fate decision via multiple antagonistic gene regulatory roles. In Hippo-positive (green) photoreceptors, Sd directly represses both melt and Rh5 gene expression through defined TEAD binding sites, a mechanism that is antagonized by Yki in Hippo-negative (blue) cells. Additionally, in blue photoreceptors, Sd is required to promote the translation of the Rh5 protein through a 3'UTR-dependent and microRNA-mediated process. Together, these studies reveal that Sd can drive context-dependent cell fate decisions through opposing transcriptional and post-transcriptional mechanisms.