Informing Equitable Prevention Practices: A Statewide Disaggregated Analysis of Suicide for Ethnoracially Minoritized Adolescents.

The increase in adolescent suicide rates in the United States is a pervasive public health issue, and ethnoracial youth with diverse identities are disproportionately impacted, yet less studied. National planning efforts reinforce state-level approaches to suicide prevention through an equitable lens to prevent adolescent suicide. This study examined disaggregated state-level data over time to determine changes to suicide outcomes based on race/ethnicity, sex, sexual orientation, and the intersection of these identities and determined which sub-groups had higher odds of suicide outcomes. Data from the 1991-2019 Centers for Disease Control and Prevention Youth Risk Behavioral Surveillance System were analyzed for 17,419 ethnoracially minoritized high school adolescents in North Carolina. Descriptive analyses and multinominal logistic regression models were employed. Findings indicated that subgroups within categories of ethnoracial populations, specifically Black female adolescents unsure of their sexual orientation, reported higher rates of suicide attempts. Additionally, Multiracial adolescents reported higher means for suicide consideration and attempts over time. Recommendations for investigating state-level suicide data by focusing on diverse intersecting identities to illuminate areas for potential prevention efforts and support health equity are provided.

Sixty years of learning and teaching physiology.

This is a memoir of my experiences in learning and teaching Physiology. It begins in 1962 when I entered the University of Washington as a medical student and began research in a physiology laboratory, which led to a Ph.D. degree in Physiology and Biophysics to go with my M.D. degree in 1968. At this time, both groups of students participated in the same physiology course containing both lectures and laboratories. After postdoctoral research at the NIH and in Cambridge, UK, in 1973 I joined the faculty of the Department of Physiology, University of California, San Francisco where I participated in the teaching of medical students and graduate students for nearly 15 years. By this time, the teaching of medical and graduate students had largely separated. In 1987, I moved to the University of Michigan as Professor and Chair of Physiology where my role in teaching was organizational as well as participatory for the next 35 years. In this work, I compare the teaching of medical students as well as graduate students and focus on how it has changed over this 60-year period. Over this time both medical and graduate Ph.D. education have become more integrative. Medical education is now taught in organ blocks rather than courses, and I participated in organizing the teaching of the gastrointestinal block. At Michigan, there is no longer a separate medical school class in Physiology, and graduate students enter a combined, "Program in Biomedical Science" for a year before choosing a mentor and department.NEW & NOTEWORTHY Teaching remains an important part of the career of academic physiologists. It is important for schools offering the Ph.D. to provide instruction and experience in teaching. The American Physiology Society has developed new programs to assist teachers and many universities have centers on learning and teaching.

Redefining ß-blocker response in heart failure patients with sinus rhythm and atrial fibrillation: a machine learning cluster analysis.

BACKGROUND: Mortality remains unacceptably high in patients with heart failure and reduced left ventricular ejection fraction (LVEF) despite advances in therapeutics. We hypothesised that a novel artificial intelligence approach could better assess multiple and higher-dimension interactions of comorbidities, and define clusters of ß-blocker efficacy in patients with sinus rhythm and atrial fibrillation. METHODS: Neural network-based variational autoencoders and hierarchical clustering were applied to pooled individual patient data from nine double-blind, randomised, placebo-controlled trials of ß blockers. All-cause mortality during median 1·3 years of follow-up was assessed by intention to treat, stratified by electrocardiographic heart rhythm. The number of clusters and dimensions was determined objectively, with results validated using a leave-one-trial-out approach. This study was prospectively registered with ClinicalTrials.gov (NCT00832442) and the PROSPERO database of systematic reviews (CRD42014010012). FINDINGS: 15 659 patients with heart failure and LVEF of less than 50% were included, with median age 65 years (IQR 56-72) and LVEF 27% (IQR 21-33). 3708 (24%) patients were women. In sinus rhythm (n=12 822), most clusters demonstrated a consistent overall mortality benefit from ß blockers, with odds ratios (ORs) ranging from 0·54 to 0·74. One cluster in sinus rhythm of older patients with less severe symptoms showed no significant efficacy (OR 0·86, 95% CI 0·67-1·10; p=0·22). In atrial fibrillation (n=2837), four of five clusters were consistent with the overall neutral effect of ß blockers versus placebo (OR 0·92, 0·77-1·10; p=0·37). One cluster of younger atrial fibrillation patients at lower mortality risk but similar LVEF to average had a statistically significant reduction in mortality with ß blockers (OR 0·57, 0·35-0·93; p=0·023). The robustness and consistency of clustering was confirmed for all models (p<0·0001 vs random), and cluster membership was externally validated across the nine independent trials. INTERPRETATION: An artificial intelligence-based clustering approach was able to distinguish prognostic response from ß blockers in patients with heart failure and reduced LVEF. This included patients in sinus rhythm with suboptimal efficacy, as well as a cluster of patients with atrial fibrillation where ß blockers did reduce mortality. FUNDING: Medical Research Council, UK, and EU/EFPIA Innovative Medicines Initiative BigData@Heart.

Early onset of immune-mediated diseases in minority ethnic groups in the UK.

BACKGROUND: The prevalence of some immune-mediated diseases (IMDs) shows distinct differences between populations of different ethnicities. The aim of this study was to determine if the age at diagnosis of common IMDs also differed between different ethnic groups in the UK, suggestive of distinct influences of ethnicity on disease pathogenesis. METHODS: This was a population-based retrospective primary care study. Linear regression provided unadjusted and adjusted estimates of age at diagnosis for common IMDs within the following ethnic groups: White, South Asian, African-Caribbean and Mixed-race/Other. Potential disease risk confounders in the association between ethnicity and diagnosis age including sex, smoking, body mass index and social deprivation (Townsend quintiles) were adjusted for. The analysis was replicated using data from UK Biobank (UKB). RESULTS: After adjusting for risk confounders, we observed that individuals from South Asian, African-Caribbean and Mixed-race/Other ethnicities were diagnosed with IMDs at a significantly younger age than their White counterparts for almost all IMDs. The difference in the diagnosis age (ranging from 2 to 30 years earlier) varied for each disease and by ethnicity. For example, rheumatoid arthritis was diagnosed at age 49, 48 and 47 years in individuals of African-Caribbean, South Asian and Mixed-race/Other ethnicities respectively, compared to 56 years in White ethnicities. The earlier diagnosis of most IMDs observed was validated in UKB although with a smaller effect size. CONCLUSION: Individuals from non-White ethnic groups in the UK had an earlier age at diagnosis for several IMDs than White adults.

Evaluating semantic similarity methods for comparison of text-derived phenotype profiles.

BACKGROUND: Semantic similarity is a valuable tool for analysis in biomedicine. When applied to phenotype profiles derived from clinical text, they have the capacity to enable and enhance 'patient-like me' analyses, automated coding, differential diagnosis, and outcome prediction. While a large body of work exists exploring the use of semantic similarity for multiple tasks, including protein interaction prediction, and rare disease differential diagnosis, there is less work exploring comparison of patient phenotype profiles for clinical tasks. Moreover, there are no experimental explorations of optimal parameters or better methods in the area. METHODS: We develop a platform for reproducible benchmarking and comparison of experimental conditions for patient phentoype similarity. Using the platform, we evaluate the task of ranking shared primary diagnosis from uncurated phenotype profiles derived from all text narrative associated with admissions in the medical information mart for intensive care (MIMIC-III). RESULTS: 300 semantic similarity configurations were evaluated, as well as one embedding-based approach. On average, measures that did not make use of an external information content measure performed slightly better, however the best-performing configurations when measured by area under receiver operating characteristic curve and Top Ten Accuracy used term-specificity and annotation-frequency measures. CONCLUSION: We identified and interpreted the performance of a large number of semantic similarity configurations for the task of classifying diagnosis from text-derived phenotype profiles in one setting. We also provided a basis for further research on other settings and related tasks in the area.

Employing the Urban Education Typology Through a Critical Race Spatial Analysis.

The urban education typology put forth by Milner (Urban Educ 47(3):556-561, 2012) offered a conceptual demarcation of three different, yet interconnected types of urban school districts (i.e., urban intensive, urban emergent, and urban characteristic). Nearly one decade after Milner's seminal urban education typology, few empirical or conceptual articles have operationalized this typology across multiple school districts in one region. We enter this scholarly space to reaffirm the typology and its utility in identifying the conditions that create varying educational inequities and transformative opportunities. Through a critical race spatial analysis, we attempt to capture, crystalize, and expand Milner's typology by examining a multitude of data points and intentionally drawing on geospatial data from five linked school districts in Harris County, Texas. Our findings, as viewed through lenses of Critical Race Theory and the Chicana Feminist conceptual framework known as borderlands, accentuate two major implications; (1) while there are physical spaces of restriction inside and around schools and school districts, regularly school districts contend with identical challenges despite their urban education typology categorical classification; and (2) when employing the urban education typology, it is imperative that researchers deeply contextualize the physical, temporal, historical, social, and racialized spaces that schools and school districts exist in.

The Contribution of Autophagy and LncRNAs to MYC-Driven Gene Regulatory Networks in Cancers.

MYC is a target of the Wnt signalling pathway and governs numerous cellular and developmental programmes hijacked in cancers. The amplification of MYC is a frequently occurring genetic alteration in cancer genomes, and this transcription factor is implicated in metabolic reprogramming, cell death, and angiogenesis in cancers. In this review, we analyse MYC gene networks in solid cancers. We investigate the interaction of MYC with long non-coding RNAs (lncRNAs). Furthermore, we investigate the role of MYC regulatory networks in inducing changes to cellular processes, including autophagy and mitophagy. Finally, we review the interaction and mutual regulation between MYC and lncRNAs, and autophagic processes and analyse these networks as unexplored areas of targeting and manipulation for therapeutic gain in MYC-driven malignancies.

Biomarker Prioritisation and Power Estimation Using Ensemble Gene Regulatory Network Inference.

Inferring the topology of a gene regulatory network (GRN) from gene expression data is a challenging but important undertaking for gaining a better understanding of gene regulation. Key challenges include working with noisy data and dealing with a higher number of genes than samples. Although a number of different methods have been proposed to infer the structure of a GRN, there are large discrepancies among the different inference algorithms they adopt, rendering their meaningful comparison challenging. In this study, we used two methods, namely the MIDER (Mutual Information Distance and Entropy Reduction) and the PLSNET (Partial least square based feature selection) methods, to infer the structure of a GRN directly from data and computationally validated our results. Both methods were applied to different gene expression datasets resulting from inflammatory bowel disease (IBD), pancreatic ductal adenocarcinoma (PDAC), and acute myeloid leukaemia (AML) studies. For each case, gene regulators were successfully identified. For example, for the case of the IBD dataset, the UGT1A family genes were identified as key regulators while upon analysing the PDAC dataset, the SULF1 and THBS2 genes were depicted. We further demonstrate that an ensemble-based approach, that combines the output of the MIDER and PLSNET algorithms, can infer the structure of a GRN from data with higher accuracy. We have also estimated the number of the samples required for potential future validation studies. Here, we presented our proposed analysis framework that caters not only to candidate regulator genes prediction for potential validation experiments but also an estimation of the number of samples required for these experiments.

HIF1-alpha Regulates Acinar Cell Function and Response to Injury in Mouse Pancreas.

We investigated whether intrapancreatic coagulation, with deposition of the fibrinogen-γ dimer (Fib-γD) and hypoxia, affect the severity of acute pancreatitis (AP) in mice. Pancreata of mice with AP induced by administration of cerulein or by L-arginine, or from patients with pancreatitis, had increased deposition of Fib-γD compared with control pancreata. Heparin administration protected mice from cerulein-induced AP and prevented Fib-γD formation. Cerulein administration resulted in activation and stabilization of hypoxia-inducible factor-1α (HIF1α) in pancreata of oxygen-dependent degradation domain-luciferase HIF1α reporter mice. Cerulein also led to induction of genes regulated by HIF1α, including Vegfa and Ero1a, before evidence of Fib-γD deposition or histologic features of AP. Expression of tissue factor, which is regulated by vascular endothelial growth factor, also increased following cerulein administration. Mice with acinar cell-specific disruption of Hif1a (Hif1aAc-/-) developed spontaneous endoplasmic reticulum stress and less severe AP, but did not accumulate Fib-γD following administration of cerulein. Feeding mice increased pancreatic expression of HIF1α, indicating a physiologic role in the exocrine pancreas. Therefore, HIF1α has bifunctional roles, in exocrine pancreas homeostasis and progression of AP that is promoted by intrapancreatic coagulation.

Lamin A/C Maintains Exocrine Pancreas Homeostasis by Regulating Stability of RB and Activity of E2F.

Lamins have important roles in nuclear structure and cell signaling. Several diseases are associated with mutations in the lamin A/C gene (LMNA in humans). Patients with familial partial lipodystrophy caused by LMNA mutations develop pancreatitis, but lamin function in the pancreas and how these mutations affect pancreatic regulation are unknown. We generated mice with inducible exocrine pancreas-specific disruption of Lmna and showed that LMNA is lost from most exocrine pancreas cells. LMNA-knockout pancreata develop endoplasmic reticulum stress with loss of acinar cell markers, increased autophagy, apoptosis, and cell proliferation, compared to CreERT2- mice (littermate controls). Disruption of Lmna led to a phenotype that resembled chronic pancreatitis, with increased Sirius Red staining and α-smooth muscle actin in male LMNA-knockout mice compared to littermate males, but not in female mice. LMNA-knockout pancreata have reduced levels of RB and activation of E2F, based on increased expression of E2F target genes. Therefore, lamins maintain pancreatic homeostasis by regulating RB stability and E2F activity.

-Omics biomarker identification pipeline for translational medicine.

BACKGROUND: Translational medicine (TM) is an emerging domain that aims to facilitate medical or biological advances efficiently from the scientist to the clinician. Central to the TM vision is to narrow the gap between basic science and applied science in terms of time, cost and early diagnosis of the disease state. Biomarker identification is one of the main challenges within TM. The identification of disease biomarkers from -omics data will not only help the stratification of diverse patient cohorts but will also provide early diagnostic information which could improve patient management and potentially prevent adverse outcomes. However, biomarker identification needs to be robust and reproducible. Hence a robust unbiased computational framework that can help clinicians identify those biomarkers is necessary. METHODS: We developed a pipeline (workflow) that includes two different supervised classification techniques based on regularization methods to identify biomarkers from -omics or other high dimension clinical datasets. The pipeline includes several important steps such as quality control and stability of selected biomarkers. The process takes input files (outcome and independent variables or -omics data) and pre-processes (normalization, missing values) them. After a random division of samples into training and test sets, Least Absolute Shrinkage and Selection Operator and Elastic Net feature selection methods are applied to identify the most important features representing potential biomarker candidates. The penalization parameters are optimised using 10-fold cross validation and the process undergoes 100 iterations and a combinatorial analysis to select the best performing multivariate model. An empirical unbiased assessment of their quality as biomarkers for clinical use is performed through a Receiver Operating Characteristic curve and its Area Under the Curve analysis on both permuted and real data for 1000 different randomized training and test sets. We validated this pipeline against previously published biomarkers. RESULTS: We applied this pipeline to three different datasets with previously published biomarkers: lipidomics data by Acharjee et al. (Metabolomics 13:25, 2017) and transcriptomics data by Rajamani and Bhasin (Genome Med 8:38, 2016) and Mills et al. (Blood 114:1063-1072, 2009). Our results demonstrate that our method was able to identify both previously published biomarkers as well as new variables that add value to the published results. CONCLUSIONS: We developed a robust pipeline to identify clinically relevant biomarkers that can be applied to different -omics datasets. Such identification reveals potentially novel drug targets and can be used as a part of a machine-learning based patient stratification framework in the translational medicine settings.

Fabrication of precise aperiodic multichannel fibre Bragg grating filters for spectral line suppression in hydrogenated standard telecommunications fibre.

We demonstrate the design and fabrication of multichannel fibre Bragg gratings (FBGs) with aperiodic channel spacings. These will be suitable for the suppression of specific spectral lines such as OH emission lines in the near infrared (NIR) which degrade ground based astronomical imaging. We discuss the design process used to meet a given specification and the fabrication challenges that can give rise to errors in the final manufactured device. We propose and demonstrate solutions to meet these challenges.

Glucagon-like peptide-1 receptor is present in pancreatic acinar cells and regulates amylase secretion through cAMP.

Glucagon-like peptide-1 (GLP-1) is a glucoincretin hormone that can act through its receptor (GLP-1R) on pancreatic ß-cells and increase insulin secretion and production. GLP-1R agonists are used clinically to treat type 2 diabetes. GLP-1 may also regulate the exocrine pancreas at multiple levels, including inhibition through the central nervous system, stimulation indirectly through insulin, and stimulation directly on acinar cells. However, it has been unclear whether GLP-1R is present in pancreatic acini and what physiological functions these receptors regulate. In the current study we utilized GLP-1R knockout (KO) mice to study the role of GLP-1R in acinar cells. RNA expression of GLP-1R was detected in acutely isolated pancreatic acini. Acinar cell morphology and expression of digestive enzymes were not affected by loss of GLP-1R. GLP-1 induced amylase secretion in wild-type (WT) acini. In GLP-1R KO mice, this effect was abolished, whereas vasoactive intestinal peptide-induced amylase release in KO acini showed a pattern similar to that in WT acini. GLP-1 stimulated cAMP production and increased protein kinase A-mediated protein phosphorylation in WT acini, and these effects were absent in KO acini. These data show that GLP-1R is present in pancreatic acinar cells and that GLP-1 can regulate secretion through its receptor and cAMP signaling pathway.

Genetic deletion of Rab27B in pancreatic acinar cells affects granules size and has inhibitory effects on amylase secretion.

Small G protein Rab27B is expressed in various secretory cell types and plays a role in mediating secretion. In pancreatic acinar cells, Rab27B was found to be expressed on the zymogen granule membrane and by overexpression to regulate the secretion of zymogen granules. However, the effect of Rab27B deletion on the physiology of pancreatic acinar cells is unknown. In the current study, we utilized the Rab27B KO mouse model to better understand the role of Rab27B in the secretion of pancreatic acinar cells. Our data show that Rab27B deficiency had no obvious effects on the expression of major digestive enzymes and other closely related proteins, e.g. similar small G proteins, such as Rab3D and Rab27A, and putative downstream effectors. The overall morphology of acinar cells was not changed in the knockout pancreas. However, the size of zymogen granules was decreased in KO acinar cells, suggesting a role of Rab27B in regulating the maturation of secretory granules. The secretion of digestive enzymes was moderately decreased in KO acini, compared with the WT control. These data indicate that Rab27B is involved at a different steps of zymogen granule maturation and secretion, which is distinct from that of Rab3D.

GLP-1 mimetic drugs and the risk of exocrine pancreatic disease: Cell and animal studies.

BACKGROUND: Glucagon Like Peptide 1 (GLP-1) mimetic drugs or degradation inhibitors mimic the action of native GLP-1 as a incretin hormone and have become a common second line of therapy for Type 2 diabetes. However, an important clinical issue is whether these drugs increase the incidence of pancreatitis and pancreatic cancer. OBJECTIVE: This paper reviews the physiology of GLP-1 including its synthesis, secretion and action of the peptide. Reported effects of the mimetic drugs on the exocrine pancreas in animal studies are also reviewed. RESULTS: GLP-1 is synthesized in a specific class of enteroendocrine cell, the L-cell, by post-translational processing of proglucagon. It is released in response to the presence of nutrients in the small intestine and stimulates vagal afferent nerve endings as well as entering the blood where it is rapidly degraded by dipeptidyl peptidase IV. Its actions are mediated by specific G-protein coupled receptors. The major target tissues are the pancreatic islet beta cells, the brain and the heart but GLP-1 also affects gastrointestinal motility and secretion including the exocrine pancreas where its major systemic action is to inhibit secretion. In some animal, as well as human studies, the GLP-1 mimetic drugs are associated with pancreatitis or precursor lessions to pancreatic cancer but a mechanism is not clear. The most common occurrence of pathology in rodents is when the drugs are combined with a high fat diet. CONCLUSIONS: There is nothing in the physiology of GLP-1 or animal toxicology studies to support a mechanism of action or a major concern about the action of GLP-1 mimetic drugs on the exocrine pancreas. Further studies are warranted using animal models of disease and high fat diets.

A technique for mitigating the effect of the writing-beam profile on fibre Bragg grating fabrication.

We propose and demonstrate a pre-compensation mechanism to account for the writing-beam profile which when applied to the design of advanced fibre Bragg gratings helps to achieve a desired design spectral response. We use the example of a complex multi-channel grating as an example to demonstrate the improvement achievable using the pre-compensation and find good agreement between experimental results and numerical calculations.

EPI64B acts as a GTPase-activating protein for Rab27B in pancreatic acinar cells.

The small GTPase Rab27B localizes to the zymogen granule membranes and plays an important role in regulating protein secretion by pancreatic acinar cells, as does Rab3D. A common guanine nucleotide exchange factor (GEF) for Rab3 and Rab27 has been reported; however, the GTPase-activating protein (GAP) specific for Rab27B has not been identified. In this study, the expression in mouse pancreatic acini of two candidate Tre-2/Bub2/Cdc16 (TBC) domain-containing proteins, EPI64 (TBC1D10A) and EPI64B (TBC1D10B), was first demonstrated. Their GAP activity on digestive enzyme secretion was examined by adenovirus-mediated overexpression of EPI64 and EPI64B in isolated pancreatic acini. EPI64B almost completely abolished the GTP-bound form of Rab27B, without affecting GTP-Rab3D. Overexpression of EPI64B also enhanced amylase release. This enhanced release was independent of Rab27A, but dependent on Rab27B, as shown using acini from genetically modified mice. EPI64 had a mild effect on both GTP-Rab27B and amylase release. Co-overexpression of EPI64B with Rab27B can reverse the inhibitory effect of Rab27B on amylase release. Mutations that block the GAP activity decreased the inhibitory effect of EPI64B on the GTP-bound state of Rab27B and abolished the enhancing effect of EPI64B on the amylase release. These data suggest that EPI64B can serve as a potential physiological GAP for Rab27B and thereby participate in the regulation of exocytosis in pancreatic acinar cells.