Gut virome in early life: origins and implications

The human body is colonized by a multitude of bacteria, fungi, and viruses, which play important roles in health and disease. Microbial colonization during early life is thought to be a particularly important period with lasting consequences for health. Viral populations in the gut are particularly dynamic in early life before they stabilize in adulthood. The composition of the early-life virome is increasingly recognized as a determinant of disease later in life. Here, we review the development of the virome in healthy infants, as well as the role of the early-life virome in the development of disease states including diarrhea, malnutrition, and autoimmune diseases.

Sluggish Cognitive Tempo in Pediatric Sickle Cell Disease

Background

Sickle cell disease (SCD) imparts risk for a range of neurodevelopmental and neurocognitive disorders. Sluggish cognitive tempo (SCT) is a distinct syndrome that often co-occurs with attention-deficit/hyperactivity disorder (ADHD) but has not been described in SCD. We investigated the reliability and validity of a SCT measure in SCD and examined associations with biopsychosocial risk factors and functional outcomes.

Materials and Methods

Caregivers (n = 85) of children with SCD ages 7-16 reported on socio-demographics and the Kiddie-Sluggish Cognitive Tempo (K-SCT) measure, Behavior Rating Inventory of Executive Function, and Conners 3. Disease-related characteristics were extracted from health records.

Results

The K-SCT demonstrated excellent internal consistency (α = 0.92) and test-retest reliability (r = 0.82, p < 0.001). K-SCT scores were correlated with ADHD-Inattention (r = 0.64, p < 0.001) and ADHD-Hyperactive/Impulsive (r = 0.46, p < 0.001) scores, as well as functional outcomes, including learning problems (r = 0.69, p < 0.001). In multivariate analyses controlling for ADHD symptoms, SCT accounted for unique variance in learning (b = 9.67, p < 0.01) and executive functioning (b = 5.93, p < 0.01). Nearly all participants (93%) with elevated levels of co-occurring SCT and ADHD-Inattention symptoms had significant learning problems.

Conclusion

The K-SCT is a reliable and valid measure of SCT in SCD. SCT symptoms are associated with learning difficulties even after controlling for ADHD symptoms. Further research is needed to understand the biopsychosocial factors that lead to SCT symptoms in SCD and examine long-term implications of SCT.

Subclinical hepatic fibrosis is associated with coronary microvascular dysfunction by myocardial perfusion reserve index: a retrospective cohort study

The heart-liver axis is of growing importance. Previous studies have identified independent association of liver dysfunction and fibrosis with adverse cardiac outcomes, but mechanistic pathways remain uncertain. We sought to understand the relations between the degree of hepatic fibrosis identified by the Fibrosis-4 (Fib-4) risk score and comprehensive cardiac MRI (CMR) measures of subclinical cardiac disease. We conducted a retrospective single-center cohort study of patients between 2011 and 2021. We identified consecutive patients who underwent a comprehensive CMR imaging protocol including contrast enhanced with stress/rest perfusion, and lacked pre-existing cardiovascular disease or perfusion abnormalities on CMR. We examined the association of hepatic fibrosis, using the Fib-4 score, with subclinical cardiac disease on CMR while adjusting for cardiometabolic traits. Given known associations of hepatic disease and coronary microvascular dysfunction, we prioritized analyses with the myocardial perfusion reserve index (MPRI), a marker of coronary microvascular function. Of the 66 patients in our study cohort, 54 were female (81%) and the mean age was 53.7 ± 15.3 years. We found that higher Fib-4 was associated with reduction in the MPRI (β [SE] - 1.12 [0.46], P = 0.02), after adjusting for cardiometabolic risk factors. Importantly, Fib-4 was not significantly associated with any other CMR phenotypes including measures of cardiac remodeling, inflammation, fibrosis, or dysfunction. We found evidence that hepatic fibrosis associated with coronary microvascular dysfunction, in the absence of overt associations with any other subclinical cardiac disease measures. These findings highlight a potentially important precursor pathway leading to development of subsequent heart-liver disease.

The impact of a health systems strengthening initiative on child morbidity: The case of the Ghana Essential Health Interventions Program in rural northern Ghana

BACKGROUND

Improving child and maternal health remains a core objective of global health priorities, extending from the millennium development goal (MDG) era to the current focus on the Sustainable Development Goals (SGDs). This paper analyses the childhood morbidity effects of the Ghana Essential Heath Interventions Program (GEHIP), a community-based health systems strengthening in rural northern Ghana. GEHIP was a five-year embedded implementation science plausibility trial that implemented a set of health systems strengthening strategies and tested the proposition that their combined effect at the district, subdistrict and community levels could foster effective community engagement and thereby improve maternal and child health outcomes.

METHODS

A two stage random sample survey of reproductive-aged women residing in treatment and comparison districts at the GEHIP baseline and end line was used for Heckman Difference-in-differences (DiD) regression models for estimating the incremental effect of GEHIP exposure on three child morbidity conditions (diarrhea, fever and cough), as recalled by maternal respondents in the course of survey interviews.

RESULTS

After controlling for child age and gender, maternal age, education, marital status, health insurance status, religion, ethnicity, occupation and household wealth index, regression results show that GEHIP had a statistically significant 45% reduction in fever (OR = 0.55, CI = 0.31-0.98) and 47% reduction in cough (OR = 0.53, CI = 0.30-0.94), over and above temporal reductions that prevailed in study districts. Although not significant, GEHIP also had 38% reduction in the incidence of diarrhea.

CONCLUSION

Previous research has shown that GEHIP had a pronounced positive effect with a reduction in mortality. Our results show that household location in GEHIP districts also led to a significant reduction in morbidity due to cough and fever among under-five children. This association is a likely outcome of GEHIP's impact on the accessibility of primary health care services. Results lend further support to the growing body of evidence that strengthening health systems in rural Africa through the provision of community-based strategies enhances prospects for achieving the United Nations child health SDGs.

Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness

Repeated emergence of SARS-CoV-2 variants with increased fitness underscores the value of rapid detection and characterization of new lineages. We have developed PyR₀, a hierarchical Bayesian multinomial logistic regression model that infers relative prevalence of all viral lineages across geographic regions, detects lineages increasing in prevalence, and identifies mutations relevant to fitness. Applying PyR₀ to all publicly available SARS-CoV-2 genomes, we identify numerous substitutions that increase fitness, including previously identified spike mutations and many non-spike mutations within the nucleocapsid and nonstructural proteins. PyR₀ forecasts growth of new lineages from their mutational profile, ranks the fitness of lineages as new sequences become available, and prioritizes mutations of biological and public health concern for functional characterization.

Neuropathic-like Pain in Fibrous Dysplasia/McCune-Albright Syndrome

CONTEXT

Pain is a major symptom in adults with fibrous dysplasia/McCune-Albright syndrome (FD/MAS) and response to current treatments, including bisphosphonates and standard analgesics (nonsteroidal anti-inflammatory drugs and opiates) is unpredictable. No studies have explored whether the type of pain is variable in this patient group.

OBJECTIVE

To determine the frequency of neuropathic-like pain in patients with FD/MAS.

DESIGN

Retrospective, dual registry study.

SETTING

Community.

PATIENTS

FD/MAS online registries: the US-based Familial Dysautonomia Foundation (FDF) and the UK-based Rare and Undiagnosed Diseases (RUDY) study.

INTERVENTION

Subjects completed questionnaires to evaluate the presence of features of neuropathic-like pain (painDETECT) and the impact on sleep quality (Pittsburgh Sleep Quality Index) and mental health (Hospital Anxiety and Depression Scale). Descriptive statistics were used to characterize the prevalence and associated burden of neuropathic-like pain.

MAIN OUTCOME MEASURES

Incidence of neuropathic, nociceptive, and unclear pain.

RESULTS

Of 249 participants, one third experienced neuropathic-like pain. This group had statistically significantly (P < 0.001) worse mental well-being and sleep in comparison to those with predominately nociceptive pain.

CONCLUSIONS

Neuropathic-like pain is common in patients with FD/MAS and associated with worse quality of life. Evaluation of pain in patients with FD/MAS should include assessment of neuropathic-like pain to guide personalized approaches to treatment and inform future research.

The resistance within: Antibiotic disruption of the gut microbiome and resistome dynamics in infancy

Intestinal host-microbiota interactions during the first year of life are critical for infant development. Early-life antibiotic exposures disrupt stereotypical gut microbiota maturation and adversely affect childhood health. Furthermore, antibiotics increase the abundance of resistant bacteria and enrich the resistome-the compendium of antibiotic resistance genes-within the gut microbiota. Here, we discuss acute and persistent impacts of antibiotic exposure during infancy on pediatric health, the gut microbiome, and, particularly, the resistome. Reviewing our current understanding of antibiotic resistance acquisition and dissemination within and between microbiomes, we highlight open questions, which are imperative to resolve in the face of rising bacterial resistance.

CT angiographic radiomics signature for risk stratification in anterior large vessel occlusion stroke

BACKGROUND AND PURPOSE

As "time is brain" in acute stroke triage, the need for automated prognostication tools continues to increase, particularly in rapidly expanding tele-stroke settings. We aimed to create an automated prognostication tool for anterior circulation large vessel occlusion (LVO) stroke based on admission CTA radiomics.

METHODS

We automatically extracted 1116 radiomics features from the anterior circulation territory on admission CTAs of 829 acute LVO stroke patients who underwent mechanical thrombectomy in two academic centers. We trained, optimized, validated, and compared different machine-learning models to predict favorable outcome (modified Rankin Scale ≤ 2) at discharge and 3-month follow-up using four different input sets: "Radiomics", "Radiomics + Treatment" (radiomics, post-thrombectomy reperfusion grade, and intravenous thrombolysis), "Clinical + Treatment" (baseline clinical variables and treatment), and "Combined" (radiomics, treatment, and baseline clinical variables).

RESULTS

For discharge outcome prediction, models were optimized/trained on n = 494 and tested on an independent cohort of n = 100 patients from Yale. Receiver operating characteristic analysis of the independent cohort showed no significant difference between best-performing Combined input models (area under the curve, AUC = 0.77) versus Radiomics + Treatment (AUC = 0.78, p = 0.78), Radiomics (AUC = 0.78, p = 0.55), or Clinical + Treatment (AUC = 0.77, p = 0.87) models. For 3-month outcome prediction, models were optimized/trained on n = 373 and tested on an independent cohort from Yale (n = 72), and an external cohort from Geisinger Medical Center (n = 232). In the independent cohort, there was no significant difference between Combined input models (AUC = 0.76) versus Radiomics + Treatment (AUC = 0.72, p = 0.39), Radiomics (AUC = 0.72, p = 0.39), or Clinical + Treatment (AUC = 76, p = 0.90) models; however, in the external cohort, the Combined model (AUC = 0.74) outperformed Radiomics + Treatment (AUC = 0.66, p < 0.001) and Radiomics (AUC = 0.68, p = 0.005) models for 3-month prediction.

CONCLUSION

Machine-learning signatures of admission CTA radiomics can provide prognostic information in acute LVO stroke candidates for mechanical thrombectomy. Such objective and time-sensitive risk stratification can guide treatment decisions and facilitate tele-stroke assessment of patients. Particularly in the absence of reliable clinical information at the time of admission, models solely using radiomics features can provide a useful prognostication tool.

Discordance in patient and physician global assessment in relapsing polychondritis

OBJECTIVES

Relapsing polychondritis (RP) is a rare, heterogeneous, systemic inflammatory disease that targets cartilage. Patient-reported outcome measures may differ from physician assessment. This study compared patient global assessment (PtGA) and physician global assessment (PhGA) scores in a prospective cohort of patients with RP.

METHODS

Adult patients with RP underwent a standardized comprehensive evaluation at ∼6 month intervals. At each visit, three physicians scored PhGA by consensus. The patient independently completed four patient-reported outcomes: PtGA, 36-item Short Form Health Survey (SF-36), Brief Illness Perception Questionnaire (BIPQ) and Multidimensional Fatigue Inventory (MFI). Patient-physician discordance was defined as a difference between PtGA and PhGA of ≥3 on a 0-10 scale.

RESULTS

A total of 76 patients were evaluated over 154 visits. The median PhGA was 3 [interquartile range (IQR) 2-3] and the median PtGA was 5 (IQR 4-7). PtGA and PhGA were concordant in 66 visits (42.9%) and patients scored disease severity ≥3 points higher than physicians scored disease activity (positive discordance) in 84 visits (54.5%). Compared with visits with concordance, visits with positive discordance were associated with significantly worse scores on the MFI, BIPQ, SF-36 physical component score and SF-36 mental component score.

CONCLUSION

Patients with RP typically self-report high PtGA that does not align with PhGA. Discordance is likely driven by the high physical and psychological burden of illness experienced by patients. Multifaceted treatment approaches that address the burden of disease in RP from the patient perspective are needed.

Glial-mediated neuroinflammatory mechanisms in age-related macular degeneration

Age-related macular degeneration (AMD) is a neurodegenerative disorder characterized by photoreceptor and retinal pigment epithelium loss often complicated by neovascularization and is one of the leading causes of irreversible vision loss worldwide. However, the precise pathophysiology of AMD remains to date unclear, and there is a dearth of effective therapies for the early stages of the disease. A growing body of evidence has identified microglia-mediated neuroinflammation as a key driver of neuronal damage in AMD, presenting a novel avenue for the development of pharmacological agents targeting this cell population. The local microglial response interacts with other glia as well as engages in crosstalk with peripheral immunological niches. This article presents a review of the current evidence regarding the involvement of glia in the pathophysiology of AMD, an overview of the key immune circuits and effector mechanisms shown to be active in AMD, and potential therapeutic avenues targeting glial involvement.

"Our Hands Are Tied Until Your Doctor Gets Here": Nursing Perspectives on Inter-hospital Transfers

BACKGROUND

The transfer of patients between hospitals (inter-hospital transfer, or IHT) is a common occurrence for patients, but guidelines to ensure safe and effective IHTs are lacking. Poor IHTs result in higher rates of mortality, longer lengths of stay, and higher hospitalization costs compared to admissions from the emergency department. Nurses are often the first point of contact for IHT patients and can provide valuable insights on key challenges to IHT processes.

OBJECTIVE

To characterize the experiences of inpatient floor-level bedside nurses caring for IHT patients and identify care coordination challenges and solutions.

DESIGN/PARTICIPANTS/APPROACH

Qualitative study using semi-structured focus groups and interviews conducted from October 2019 to July 2020 with 21 inpatient floor-level nurses caring for adult medicine patients at an academic hospital. Nurses were recruited using a purposive convenience sampling approach. A combined inductive and deductive coding approach guided by thematic analysis was used for data analysis.

KEY RESULTS

Results from this study are mapped to the Agency for Healthcare Research and Quality Care Coordination Measurement Framework domains of communication, assessing needs and goals, and negotiating accountability. The following key themes characterize nurses' experiences with IHT related to these domains: (1) challenges with information exchange and team communication during IHT, (2) environmental and information preparation needed to anticipate transfers, and (3) determining responsibility and care plans after the IHT patient has arrived at the accepting facility.

CONCLUSIONS

Nurses described the absence of standardized processes to coordinate care before or at the time of patient arrival. Challenges to communication and coordination during IHTs negatively impacted patient care and nursing professional satisfaction. To streamline care for IHT patients and reduce nursing stress, future IHT interventions should include standardized handoff reports, timely identification and easy access to admitting clinicians, and timely clinician evaluation and orders.

Fertility after Curative Therapy for Sickle Cell Disease: A Comprehensive Review to Guide Care

Curative therapy for sickle cell disease (SCD) currently requires gonadotoxic conditioning that can impair future fertility. Fertility outcomes after curative therapy are likely affected by pre-transplant ovarian reserve or semen analysis parameters that may already be abnormal from SCD-related damage or hydroxyurea treatment. Outcomes are also likely affected by the conditioning regimen. Conditioning with myeloablative busulfan and cyclophosphamide causes serious gonadotoxicity particularly among post-pubertal females. Reduced-intensity and non-myeloablative conditioning may be acutely less gonadotoxic, but more short and long-term fertility outcome data after these approaches is needed. Fertility preservation including oocyte/embryo, ovarian tissue, sperm, and experimental testicular tissue cryopreservation should be offered to patients with SCD pursing curative therapy. Regardless of HSCT outcome, longitudinal post-HSCT fertility care is required.

Factors associated with a history of treatment interruption among pregnant women living with HIV in Malawi: A cross-sectional study

Introduction

Long-term care engagement of women on antiretroviral therapy (ART) is essential to effective HIV public health measures. We sought to explore factors associated with a history of HIV treatment interruption among pregnant women living with HIV presenting to an antenatal clinic in Lilongwe, Malawi.

Methods

We performed a cross-sectional study of pregnant women living with HIV who had a history of ART interruption presenting for antenatal care. Women were categorized as either retained in HIV treatment or reinitiating care after loss-to-follow up (LTFU). To understand factors associated with treatment interruption, we surveyed socio-demographic and partner relationship characteristics. Crude and adjusted prevalence ratios (aPR) for factors associated with ART interruption were estimated using modified Poisson regression with robust variance. We additionally present patients’ reasons for ART interruption.

Results

We enrolled 541 pregnant women living with HIV (391 retained and 150 reinitiating). The median age was 30 years (interquartile range (IQR): 25–34). Factors associated with a history of LTFU were age <30 years (aPR 1.46; 95% CI: 1.33–1.63), less than a primary school education (aPR 1.25; CI: 1.08–1.46), initiation of ART during pregnancy or breastfeeding (aPR 1.49, CI: 1.37–1.65), nondisclosure of HIV serostatus to their partner (aPR 1.39, CI: 1.24–1.58), lack of awareness of partner’s HIV status (aPR 1.41, CI: 1.27–1.60), and no contraception use at conception (aPR 1.60, CI 1.40–1.98). Access to care challenges were the most common reasons reported by women for treatment interruption (e.g., relocation, transport costs, or misplacing health documentation).

Conclusions

Interventions that simplify the ART clinic transfer process, facilitate partner disclosure, and provide counseling about the importance of lifelong ART beyond pregnancy and breastfeeding should be further evaluated for improving retention in ART treatment of women living with HIV in Malawi.

Radiomics: A Primer on Processing Workflow and Analysis

Quantitative analysis of medical images can provide objective tools for diagnosis, prognostication, and disease monitoring. Radiomics refers to automated extraction of a large number of quantitative features from medical images for characterization of underlying pathologies. In this review, we will discuss the principles of radiomics, image preprocessing, feature extraction workflow, and statistical analysis. We will also address the limitations and future directions of radiomics.

Understanding the challenges faced by Michigan's family farmers: race/ethnicity and the impacts of a pandemic

Michigan is a critical agricultural state, and small family farms are a crucial component of the state's food sector. This paper examines how the race/ethnicity of the family farm owners/operators is related to farm characteristics, financing, and impacts of the pandemic. It compares 75 farms owned/operated solely by Whites and 15 with People of Color owners/operators. The essay examines how farmers finance their farm operations and the challenges they face doing so. The article also explores how the Coronavirus-19 (COVID-19) pandemic affected farming operations, the financial viability of farms, and how farmers responded to the challenges posed by the pandemic. The study found that People of Color farm owners/operators were younger than White farm owners/operators. The People of Color farm owners/operators tended to manage smaller farms for shorter periods than White farm owners/operators. Though two-thirds of the Farmers of Color owned their farms, they were more financially vulnerable than White farm owners/operators. The farmers studied had difficulty obtaining loans to finance their farms. Farmers reported increasing requests from people for food assistance during the pandemic. Farmers responded to the pandemic by participating in government programs such as the Farm to Families Food Box Program that purchased their produce. It allowed farmers to supply emergency food assistance programs with products from their farms. The products went to families receiving food assistance from soup kitchens, food banks, and other community-based nonprofits.

Forgotten frontline workers: Environmental health service employees' perspectives on working during the COVID-19 pandemic

BACKGROUND

Environmental Health Service employees (EVS) sanitize healthcare facilities and are critical to preventing infection, but are under-resourced during the COVID-19 pandemic and at risk of burnout.

OBJECTIVE

Understand demands on EVS' work and strain on resources during COVID-19.

DESIGN

Qualitative descriptive study conducted in winter 2020-2021.

SETTING

One quaternary care academic medical center in Colorado.

PARTICIPANTS

A convenience sample of 16 EVS out of 305 eligible at the medical center. Fifty percent identified as Black, 31% as Hispanic, 6% as Asian, and 6% as White (another 6% identified as mixed race). Sixty-nine percent were female, and half were born in a country outside the United States.

MEASURES

Semistructured telephone interviews. Interviews were audio-recorded and transcribed, and thematic analysis was used to identify key themes.

RESULTS

Four themes illustrate EVS experiences with job strain and support during COVID-19: (1) Needs for ongoing training/education, (2) Emotional challenges of patient care, (3) Resource/staffing barriers, and (4) Lack of recognition as frontline responders. Despite feeling unrecognized during the pandemic, EVS identified structural supports with potential to mitigate job strain, including opportunities for increased communication with interdisciplinary colleagues, intentional acknowledgment, and education for those who speak languages other than English. Strategies that can increase physical and emotional resources and reduce job demands have potential to combat EVS burnout.

CONCLUSIONS

As the surge of COVID-19 cases continues to overwhelm healthcare facilities, healthcare systems and interdisciplinary colleagues can adopt policies and practices that ensure lower-wage healthcare workers have access to resources, education, and emotional support.

Targeting of RecQ Helicases as a Novel Therapeutic Strategy for Ovarian Cancer

RecQ helicases are essential for DNA replication, recombination, DNA damage repair, and other nucleic acid metabolic pathways required for normal cell growth, survival, and genome stability. More recently, RecQ helicases have been shown to be important for replication fork stabilization, one of the major mechanisms of PARP inhibitor resistance. Cancer cells often have upregulated helicases and depend on these enzymes to repair rapid growth-promoted DNA lesions. Several studies are now evaluating the use of RecQ helicases as potential biomarkers of breast and gynecologic cancers. Furthermore, RecQ helicases have attracted interest as possible targets for cancer treatment. In this review, we discuss the characteristics of RecQ helicases and their interacting partners that may be utilized for effective treatment strategies (as cancers depend on helicases for survival). We also discuss how targeting helicase in combination with DNA repair inhibitors (i.e., PARP and ATR inhibitors) can be used as novel approaches for cancer treatment to increase sensitivity to current treatment to prevent rise of treatment resistance.

Out-of-home placement, sleep problems, and later mental health and crime: A prospective investigation

Previous research suggests that out-of-home placement experiences increase the risk for mental health problems and criminal involvement. However, few studies have examined the mechanisms whereby out-of-home placement increases the risk for these outcomes. The present study examines whether sleep problems in part explain the relationship between childhood placement experiences and depression and anxiety and criminal arrests in adulthood. Data are from a prospective longitudinal study of 531 children with documented cases of childhood maltreatment (14% with no out-of-home placement, 68% placed solely for abuse and/or neglect, and 18% placed for maltreatment and delinquency) who were followed up into adulthood. Cases are from 1967 to 1971 from a metropolitan county in the Midwest. Sleep problems were assessed in young adulthood (M_age = 29 years). Depression and anxiety symptoms and arrest records were assessed in middle adulthood (M_age = 40 years). Structural equation modeling was used to test hypotheses. Both types of out-of-home placement experiences (for maltreatment only and for maltreatment and delinquency) predicted more sleep problems in adulthood across all models. Sleep problems in young adulthood predicted higher levels of anxiety and depression in middle adulthood, but not criminal arrests. Sleep problems mediated the relationship between placement only and internalizing symptoms and results differed for male, female, White, and Black individuals examined separately. Using court-substantiated cases of childhood abuse and neglect, this study demonstrates the long-term negative consequences of out-of-home placement experiences for sleep problems and anxiety and depression in adulthood. More attention is needed to insure adequate sleep for maltreated children. (PsycInfo Database Record (c) 2022 APA, all rights reserved).

Targeted Mutational Analysis of Cortisol-Producing Adenomas

CONTEXT

Somatic gene mutations have been identified in only about half of cortisol-producing adenomas (CPAs). Affected genes include PRKACA, GNAS, PRKAR1A, and CTNNB1.

OBJECTIVE

This work aims to expand our understanding of the prevalence of somatic mutations in CPAs from patients with overt Cushing syndrome (OCS) and "subclinical" mild autonomous cortisol excess (MACE), with an immunohistochemistry (IHC)‒guided targeted amplicon sequencing approach using formalin-fixed paraffin-embedded (FFPE) tissue.

METHODS

We analyzed FFPE adrenal tissue from 77 patients (n = 12 men, 65 women) with either OCS (n = 32) or MACE (n = 45). Using IHC for 17α-hydroxylase/17,20-lyase (CYP17A1) and 3β-hydroxysteroid dehydrogenase (HSD3B2), we identified 78 CPAs (32 OCS CPAs and 46 MACE CPAs). Genomic DNA was isolated from the FFPE CPAs and subjected to targeted amplicon sequencing for identification of somatic mutations.

RESULTS

Somatic mutations were identified in 71.8% (56/78) of the CPAs. While PRKACA was the most frequently mutated gene in OCS CPAs (14/32, 43.8%), somatic genetic aberrations in CTNNB1 occurred in 56.5% (26/46) of the MACE CPAs. Most GNAS mutations were observed in MACE CPAs (5/7, 71.4%). No mutations were observed in PRKAR1A. In addition to the known mutations, we identified one previously unreported mutation in PRKACA. Two patients with MACE harbored 2 adjacent tumors within the same adrenal gland - one patient had 2 CPAs, and the other patient had a CPA and an aldosterone-producing adenoma (identified by IHC for aldosterone synthase).

CONCLUSION

A comprehensive FFPE IHC-guided gene-targeted sequencing approach identified somatic mutations in 71.8% of the CPAs. OCS CPAs demonstrated a distinct mutation profile compared to MACE CPAs.

Identifying clinically applicable machine learning algorithms for glioma segmentation: recent advances and discoveries

Background

While there are innumerable machine learning (ML) research algorithms used for segmentation of gliomas, there is yet to be a US FDA cleared product. The aim of this study is to explore the systemic limitations of research algorithms that have prevented translation from concept to product by a review of the current research literature.

Methods

We performed a systematic literature review on 4 databases. Of 11 727 articles, 58 articles met the inclusion criteria and were used for data extraction and screening using TRIPOD.

Results

We found that while many articles were published on ML-based glioma segmentation and report high accuracy results, there were substantial limitations in the methods and results portions of the papers that result in difficulty reproducing the methods and translation into clinical practice.

Conclusions

In addition, we identified that more than a third of the articles used the same publicly available BRaTS and TCIA datasets and are responsible for the majority of patient data on which ML algorithms were trained, which leads to limited generalizability and potential for overfitting and bias.

Overlapping needs for sexual and reproductive health and HIV prevention in women with substance use disorders

OBJECTIVES

Women with substance use disorders have high unmet needs for HIV prevention and drug treatment and face challenges accessing care for other unique health issues, including their sexual and reproductive health.

METHODS

We did a cross-sectional evaluation of sexual and reproductive health behaviors and outcomes among women with substance use disorders, who were enrolled in one of two concurrent clinical trials of pre-exposure prophylaxis for HIV prevention. Descriptive analyses and bivariate logistic regression were used to assess factors driving contraceptive use, and other essential sexual and reproductive health services utilization and outcomes.

RESULTS

Among 226 women, 173 (76.5%) were of reproductive age. Most women had histories of unintended pregnancy (79.2%) or miscarriage (45.1%) and high HIV risk behaviors (53.5%). Most (61%) participants did not use any form of contraception at the time of assessment, although few (15%) reported pregnancy intentions. In bivariate models, ongoing criminal justice involvement was associated with 2.22 higher odds of not using contraception (95% confidence interval = 1.09-4.53; p = 0.03) and hazardous drinking was protective against not using contraception (odds ratio = 0.33, 95% confidence interval = 0.13-0.81; p = 0.02). Contraception use was not significantly associated with any other individual characteristics or need factors.

CONCLUSIONS

This is the first study that identifies the unmet sexual and reproductive health needs of women with substance use disorders who are engaging with pre-exposure prophylaxis. We found that women accessed some health services but not in a way that holistically addresses the full scope of their needs. Integrated sexual and reproductive care should align women's expressed sexual and reproductive health intentions with their behaviors and outcomes, by addressing social determinants of health.

mAb Das-1 recognizes 3'-Sulfated Lewis A/C, which is aberrantly expressed during metaplastic and oncogenic transformation of several gastrointestinal Epithelia

INTRODUCTION

Multiple previous studies have shown the monoclonal antibody Das-1 (formerly called 7E12H12) is specifically reactive towards metaplastic and carcinomatous lesions in multiple organs of the gastrointestinal system (e.g. Barrett's esophagus, intestinal-type metaplasia of the stomach, gastric adenocarcinoma, high-grade pancreatic intraepithelial neoplasm, and pancreatic ductal adenocarcinoma) as well as in other organs (bladder and lung carcinomas). Beyond being a useful biomarker in tissue, mAb Das-1 has recently proven to be more accurate than current paradigms for identifying cysts harboring advanced neoplasia. Though this antibody has been used extensively for clinical, basic science, and translational applications for decades, its epitope has remained elusive.

METHODS

In this study, we chemically deglycosylated a standard source of antigen, which resulted in near complete loss of the signal as measured by western blot analysis. The epitope recognized by mAb Das-1 was determined by affinity to a comprehensive glycan array and validated by inhibition of a direct ELISA.

RESULTS

The epitope recognized by mAb Das-1 is 3'-Sulfo-Lewis A/C (3'-Sulfo-LeA/C). 3'-Sulfo-LeA/C is broadly reexpressed across numerous GI epithelia and elsewhere during metaplastic and carcinomatous transformation.

DISCUSSION

3'-Sulfo-LeA/C is a clinically important antigen that can be detected both intracellularly in tissue using immunohistochemistry and extracellularly in cyst fluid and serum by ELISA. The results open new avenues for tumorigenic risk stratification of various gastrointestinal lesions.

Defining genome-wide CRISPR-Cas genome-editing nuclease activity with GUIDE-seq

Genome-wide unbiased identification of double-stranded breaks enabled by sequencing (GUIDE-seq) is a sensitive, unbiased, genome-wide method for defining the activity of genome-editing nucleases in living cells. GUIDE-seq is based on the principle of efficient integration of an end-protected double-stranded oligodeoxynucleotide tag into sites of nuclease-induced DNA double-stranded breaks, followed by amplification of tag-containing genomic DNA molecules and high-throughput sequencing. Here we describe a detailed GUIDE-seq protocol including cell transfection, library preparation, sequencing and bioinformatic analysis. The entire protocol including cell culture can be completed in 9 d. Once tag-integrated genomic DNA is isolated, library preparation, sequencing and analysis can be performed in 3 d. The result is a genome-wide catalog of off-target sites ranked by nuclease activity as measured by GUIDE-seq read counts. GUIDE-seq is one of the most sensitive cell-based methods for defining genome-wide off-target activity and has been broadly adopted for research and therapeutic use.

"This is not your Life…and it becomes your Life": A Qualitative Exploration of Deployment-related Stress and Support needs in National Guard and Reserve spouses who are Mothers of Young Children

The adverse effects of deployment-related stress (DRS) on military service members, spouses, and children are well documented. Findings from a recent Consensus Report on Military Families by the National Academies of Science, Engineering, and Medicine (2019) underscore the priority of gaining a more comprehensive understanding of the diversity of today's military families and their needs and well-being. While social support is generally regarded as helpful during times of stress, it has not been studied extensively in National Guard/Reserve spouses who are parents of young children. This qualitative study of 30 women examines the unique ways in which DRS affects women who are National Guard/Reserve spouses and mothers of young children, as well as the processes through which they encountered support to manage these stressors. Salient themes spanned experiences involving deployment cycle phases of separation and reintegration and included both anticipated and unanticipated changes in family-related division of labor, dynamics, and communication patterns. These were complicated by geographic, social, and cultural isolation and misguided efforts to support spouses initiated by civilians. Women managed these stressors primarily through seeking, acquiring, and repurposing existing sources of informal social support for themselves and formal supports for their children, with varying degrees of success.

Patient-derived iPSCs link elevated mitochondrial respiratory complex I function to osteosarcoma in Rothmund-Thomson syndrome

Rothmund-Thomson syndrome (RTS) is an autosomal recessive genetic disorder characterized by poikiloderma, small stature, skeletal anomalies, sparse brows/lashes, cataracts, and predisposition to cancer. Type 2 RTS patients with biallelic RECQL4 pathogenic variants have multiple skeletal anomalies and a significantly increased incidence of osteosarcoma. Here, we generated RTS patient-derived induced pluripotent stem cells (iPSCs) to dissect the pathological signaling leading to RTS patient-associated osteosarcoma. RTS iPSC-derived osteoblasts showed defective osteogenic differentiation and gain of in vitro tumorigenic ability. Transcriptome analysis of RTS osteoblasts validated decreased bone morphogenesis while revealing aberrantly upregulated mitochondrial respiratory complex I gene expression. RTS osteoblast metabolic assays demonstrated elevated mitochondrial respiratory complex I function, increased oxidative phosphorylation (OXPHOS), and increased ATP production. Inhibition of mitochondrial respiratory complex I activity by IACS-010759 selectively suppressed cellular respiration and cell proliferation of RTS osteoblasts. Furthermore, systems analysis of IACS-010759-induced changes in RTS osteoblasts revealed that chemical inhibition of mitochondrial respiratory complex I impaired cell proliferation, induced senescence, and decreased MAPK signaling and cell cycle associated genes, but increased H19 and ribosomal protein genes. In summary, our study suggests that mitochondrial respiratory complex I is a potential therapeutic target for RTS-associated osteosarcoma and provides future insights for clinical treatment strategies.