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The COVID-19 pandemic highlighted the need for potent community-based tools to improve preparedness. We developed a community health-safety climate (HSC) measure to assess readiness to adopt health behaviors during a pandemic. We conducted a mixed-methods study incorporating qualitative methods (e.g., focus groups) to generate items for the measure and quantitative data from a February 2021 national survey to test reliability, multilevel construct, and predictive and nomologic validities. The 20-item HSC measure is unidimensional (Cronbach α = 0.87). All communities had strong health-safety climates but with significant differences between communities (F = 10.65; p

Abstract Background Refeeding syndrome is the gravest possible medical complication in malnourished patients undergoing refeeding in the hospital. We previously reported that males with malnutrition secondary to eating disorders required more calories and had longer hospital stays than females; however, sex differences in electrolyte abnormalities indicating refeeding syndrome risk remain unknown. The objective of this study was to assess differences in electrolyte abnormalities indicating refeeding syndrome risk among male and female adolescents and young adults with eating disorders hospitalized for medical instability. Methods We retrospectively reviewed the electronic medical records of 558 patients aged 9–25 years admitted to the University of California, San Francisco Eating Disorders Program for medical instability between May 2012 and August 2020. Serum was drawn per standard of care between 5 and 7 am each morning and electrolyte abnormalities indicating refeeding syndrome risk were defined as: hypophosphatemia (

ABSTRACT The gain of mobile elements, such as prophages, can introduce cargo to the recipient bacterium that could facilitate its persistence in or expansion to a new environment, such as a host. While previous studies have focused on identifying and characterizing the genetic diversity of prophages, analyses characterizing the cargo that prophages carry have not been extensively explored. We characterized prophage regions from 303 Salmonella spp. genomes (representing 254 unique serovars) to assess the distribution of prophages in diverse Salmonella. On average, prophages accounted for 3.7% (0.1%–8.8%) of the total genomic content of each isolate. Prophage regions annotated as Gifsy 1 and Salmon Fels 1 were the most commonly identified intact prophages, suggesting that they are common throughout the Salmonella genus. Among 21,687 total coding sequences (CDSs) from intact prophage regions in subsp. enterica genomes, 7.5% (median; range: 1.1%–47.6%) were categorized as having a function not related to prophage integration or phage structure, some of which could potentially provide a functional attribute to the host Salmonella cell. These predicted functions could be broadly categorized into CDSs involved in: (i) modification of cell surface structures (i.e., glycosyltransferases); (ii) modulation of host responses (e.g., SodC/SodA, SopE, ArtAB, and typhoid toxin); (iii) conferring resistance to heavy metals and antimicrobials; (iv) metabolism of carbohydrates, amino acids, and nucleotides; and (v) DNA replication, repair, and regulation. Overall, our systematic analysis of prophage cargo highlights a broader role for prophage cargo in influencing the metabolic, virulence, and resistance characteristics of Salmonella.IMPORTANCELysogenic bacteriophages (phages) can integrate their genome into a bacterial host's genome, potentially introducing genetic elements that can affect the fitness of the host bacterium. The functions of prophage-encoded genes are important to understand as these genes could be mobilized and transferred to a new host. Using a large genomic dataset representing >300 isolates from all known subspecies and species of Salmonella, our study contributes important new findings on the distribution of prophages and the types of cargo that diverse Salmonella prophages carry. We identified a number of coding sequences (CDSs) annotated as having cell surface-modifying attributes, suggesting that prophages may have played an important role in shaping Salmonella's diverse surface antigen repertoire. Furthermore, our characterization of prophages suggests that they play a broader role in facilitating the acquisition and transfer of CDSs associated with metabolism, DNA replication and repair, virulence factors, and to a lesser extent, antimicrobial resistance.

The incidence of Clostridioides difficile infection (CDI) has been increasing compared to pre-COVID-19 pandemic levels. The COVID-19 infection and CDI relationship can be affected by gut dysbiosis and poor antibiotic stewardship. As the COVID-19 pandemic transitions into an endemic stage, it has become increasingly important to further characterize how concurrent infection with both conditions can impact patient outcomes. We performed a retrospective cohort study utilizing the 2020 NIS Healthcare Cost Utilization Project (HCUP) database with a total of 1,659,040 patients, with 10,710 (0.6%) of those patients with concurrent CDI. We found that patients with concurrent COVID-19 and CDI had worse outcomes compared to patients without CDI including higher in-hospital mortality (23% vs. 13.4%, aOR: 1.3, 95% CI: 1.12–1.5, p = 0.01), rates of in-hospital complications such as ileus (2.7% vs. 0.8%, p < 0.001), septic shock (21.0% vs. 7.2%, aOR: 2.3, 95% CI: 2.1–2.6, p < 0.001), length of stay (15.1 days vs. 8 days, p < 0.001) and overall cost of hospitalization (USD 196,012 vs. USD 91,162, p < 0.001). Patients with concurrent COVID-19 and CDI had increased morbidity and mortality, and added significant preventable burden on the healthcare system. Optimizing hand hygiene and antibiotic stewardship during in-hospital admissions can help to reduce worse outcomes in this population, and more efforts should be directly made to reduce CDI in hospitalized patients with COVID-19 infection.

BackgroundThe narrative free-text data in electronic medical records (EMRs) contain valuable clinical information for analysis and research to inform better patient care. However, the release of free text for secondary use is hindered by concerns surrounding personally identifiable information (PII), as protecting individuals' privacy is paramount. Therefore, it is necessary to deidentify free text to remove PII. Manual deidentification is a time-consuming and labor-intensive process. Numerous automated deidentification approaches and systems have been attempted to overcome this challenge over the past decade. ObjectiveWe sought to develop an accurate, web-based system deidentifying free text (DEFT), which can be readily and easily adopted in real-world settings for deidentification of free text in EMRs. The system has several key features including a simple and task-focused web user interface, customized PII types, use of a state-of-the-art deep learning model for tagging PII from free text, preannotation by an interactive learning loop, rapid manual annotation with autosave, support for project management and team collaboration, user access control, and central data storage. MethodsDEFT comprises frontend and backend modules and communicates with central data storage through a filesystem path access. The frontend web user interface provides end users with a user-friendly workspace for managing and annotating free text. The backend module processes the requests from the frontend and performs relevant persistence operations. DEFT manages the deidentification workflow as a project, which can contain one or more data sets. Customized PII types and user access control can also be configured. The deep learning model is based on a Bidirectional Long Short-Term Memory-Conditional Random Field (BiLSTM-CRF) with RoBERTa as the word embedding layer. The interactive learning loop is further integrated into DEFT to speed up the deidentification process and increase its performance over time. ResultsDEFT has many advantages over existing deidentification systems in terms of its support for project management, user access control, data management, and an interactive learning process. Experimental results from DEFT on the 2014 i2b2 data set obtained the highest performance compared to 5 benchmark models in terms of microaverage strict entity–level recall and F1-scores of 0.9563 and 0.9627, respectively. In a real-world use case of deidentifying clinical notes, extracted from 1 referral hospital in Sydney, New South Wales, Australia, DEFT achieved a high microaverage strict entity–level F1-score of 0.9507 on a corpus of 600 annotated clinical notes. Moreover, the manual annotation process with preannotation demonstrated a 43% increase in work efficiency compared to the process without preannotation. ConclusionsDEFT is designed for health domain researchers and data custodians to easily deidentify free text in EMRs. DEFT supports an interactive learning loop and end users with minimal technical knowledge can perform the deidentification work with only a shallow learning curve.

Autoimmune hemolytic anemia (AIHA) is a rare complication following heart transplantation and has been attributed to several etiologies including infections, immunosuppressive medications, and post-transplant lymphoproliferative disorders. We report a 23-year-old male presenting 22 years after heart transplantation with severe AIHA. Laboratory findings were notable for positive IgG autoantibody against RBCs and high titer Epstein-Barr virus (EBV) viremia. Shortly after the first unit of irradiated RBC transfusion and high dose steroids, the patient developed acute dyspnea and hypoxia requiring intubation. Further workup demonstrated that the patient had Methicillin-sensitive Staphylococcus aureus (MSSA) pneumonia (PNA) and bacteremia, requiring antibiotics. Patient was subsequently treated with high-dose steroids, IVIG, as well as rituximab. Following treatment, the patient was successfully extubated and eventually showed complete resolution of the anemia. This case is novel as it represents AIHA likely secondary to EBV viremia in a post-cardiac transplant patient complicated by a severe transfusion reaction. In this circumstance, rituximab in conjunction with standard of care remains an effective treatment of choice.

Plain English summary Medical complications of eating disorders in males are understudied compared to females. Little is known about vitamin D levels in male adolescents and young adults with eating disorders. We studied vitamin D levels in male and female adolescents and young adults hospitalized at the University of California, San Francisco between 2012 and 2020. We found that 44% of males had low vitamin D levels. Despite nearly half of males having low vitamin D, few were receiving calcium, vitamin D, or multivitamin supplementation prior to the hospitalization. White race, prior calcium or vitamin D supplementation, and higher calcium levels were associated with higher vitamin D levels. Medical providers should consider assessing for low vitamin D levels among males and females with eating disorders.

BackgroundInsulin resistance (IR) with associated compensatory hyperinsulinemia (HI) are early abnormalities in the etiology of prediabetes (preT2D) and type 2 diabetes (T2D). IR and HI also associate with increased erythrocytosis. Hemoglobin A1c (HbA1c) is commonly used to diagnose and monitor preT2D and T2D, but can be influenced by erythrocytosis independent of glycemia.MethodsWe undertook bidirectional Mendelian randomization (MR) in individuals of European ancestry to investigate potential causal associations between increased fasting insulin adjusted for BMI (FI), erythrocytosis and its non-glycemic impact on HbA1c. We investigated the association between the triglyceride-glucose index (TGI), a surrogate measure of IR and HI, and glycation gap (difference between measured HbA1c and predicted HbA1c derived from linear regression of fasting glucose) in people with normoglycemia and preT2D.ResultsInverse variance weighted MR (IVWMR) suggested that increased FI increases hemoglobin (Hb, b=0.54 ± 0.09, p=2.7 x 10-10), red cell count (RCC, b=0.54 ± 0.12, p=5.38x10-6) and reticulocyte (RETIC, b=0.70 ± 0.15, p=2.18x10-6). Multivariable MR indicated that increased FI did not impact HbA1c (b=0.23 ± 0.16, p=0.162) but reduced HbA1c after adjustment for T2D (b=0.31 ± 0.13, p=0.016). Increased Hb (b=0.03 ± 0.01, p=0.02), RCC (b=0.02 ± 0.01, p=0.04) and RETIC (b=0.03 ± 0.01, p=0.002) might modestly increase FI. In the observational cohort, increased TGI associated with decreased glycation gap, (i.e., measured HbA1c was lower than expected based on fasting glucose, (b=-0.09 ± 0.009, p

Chronic myeloid leukemia (CML) is a clonal myeloproliferative neoplasm (MPN) that accounts for 10% of pregnancy-associated leukemias. The Philadelphia chromosome balanced translocation, t (9:22) (q34; q11.2), is the classic mutation seen in CML. The BCR-ABL oncoprotein encoded by this mutation is a constitutively active tyrosine kinase. Tyrosine kinase inhibitor (TKI) therapy is considered a first-line treatment for CML. However, the literature has revealed risks of teratogenicity with TKI therapy during pregnancy. Understanding the risks and benefits of TKI therapy and alternative therapies such as interferon-alpha (IFN-α) will help clinicians and pregnant patients develop a personalized CML treatment plan. This manuscript presents a case series detailing the management of five pregnancies in two pregnant patients with CML and a literature review of CML management in pregnancy.

Emerging evidence indicates that intracellular calcium (Ca2+) levels and their regulatory proteins play essential roles in normal stem cell proliferation and differentiation. Cancer stem-like cells (CSCs) are subpopulations of cancer cells that retain characteristics similar to stem cells and play an essential role in cancer progression. Recent studies have reported that the Orai3 calcium channel plays an oncogenic role in human cancer. However, its role in CSCs remains underexplored. In this study, we explored the effects of Orai3 in the progression and stemness of oral/oropharyngeal squamous cell carcinoma (OSCC). During the course of OSCC progression, the expression of Orai3 exhibited a stepwise augmentation. Notably, Orai3 was highly enriched in CSC populations of OSCC. Ectopic Orai3 expression in non-tumorigenic immortalized oral epithelial cells increased the intracellular Ca2+ levels, acquiring malignant growth and CSC properties. Conversely, silencing of the endogenous Orai3 in OSCC cells suppressed the CSC phenotype, indicating a pivotal role of Orai3 in CSC regulation. Moreover, Orai3 markedly increased the expression of inhibitor of DNA binding 1 (ID1), a stemness transcription factor. Orai3 and ID1 exhibited elevated expression within CSCs compared to their non-CSC counterparts, implying the functional importance of the Orai3/ID1 axis in CSC regulation. Furthermore, suppression of ID1 abrogated the CSC phenotype in the cell with ectopic Orai3 overexpression and OSCC. Our study reveals that Orai3 is a novel functional CSC regulator in OSCC and further suggests that Orai3 plays an oncogenic role in OSCC by promoting cancer stemness via ID1 upregulation.

Background: Behcet’s disease (BD) is a complex inflammatory vascular disorder that follows a relapsing-remitting course with diverse clinical manifestations. The prevalence of the disease varies throughout the globe and targets different age-groups. There are many variations of BD; however, intestinal BD is not only more common but has many signs and symptoms. Summary: BD is a relapsing-remitting inflammatory vascular disorder with multiple system involvement, affecting vessels of all types and sizes that targets young adults. The etiology of BD is unknown but many factors including genetic mechanisms, vascular changes, hypercoagulability, and dysregulation of immune function are believed to be responsible. BD usually presents with signs and symptoms of ulcerative disease of the small intestine; endoscopy being consistent with the clinical manifestations. The mainstay of treatment depends upon the severity of the disease. Corticosteroids are recommended for severe forms of the disease and aminosalicylic acids are used in maintaining remission in mild to moderate forms of the disease. Key Messages: In this review, we have tried to summarize in the present review the clinical manifestations, differential diagnoses, and management of intestinal BD. Hopefully, this review will enable health policymakers to ponder over establishing clear endpoints for treatment, surveillance investigations, and creating robust algorithms.

Rationale & Objective: Patients with a high-risk Apolipoprotein L1 (APOL1) genotype are more likely to develop chronic kidney disease and kidney failure. It is unclear whether this increased risk is entirely mediated by the development of proteinuria. Study Design: Retrospective observational study of the African American Study of Kidney Disease and Hypertension cohort and Chronic Renal Insufficiency Cohort. Exposures & Predictors: Self-identified race (Black/non-Black) and presence of high-risk APOL1 genotype. The primary model was adjusted for age, sex, diabetes, estimated glomerular filtration rate, and urinary protein-creatinine ratio. Outcomes: Time to kidney failure defined as time to dialysis or transplantation. Analytical Approach: We used Cox proportional hazard models to study how proteinuria mediates the association between APOL1 and kidney failure. We modeled proteinuria at baseline and as a time-varying covariate. Results: A high-risk APOL1 genotype was associated with a significantly higher risk of kidney failure, even for patients with minimal proteinuria (HR, 1.87; 95% CI, 1.23-2.84). The association was not significant among patients with high proteinuria (HR, 1.22; 95% CI, 0.93-1.61). When modeling proteinuria as a time-varying covariate, a high-risk APOL1 genotype was associated with higher kidney failure risk even among patients who never developed proteinuria (HR, 2.04; 95% CI, 1.10-3.77). Compared to non-Black patients, Black patients without the high-risk genotype did not have higher risk of kidney failure (HR, 0.96; 95% CI, 0.85-1.10). Limitations: Two datasets were combined to increase statistical power. Limited generalizability beyond the study cohorts. Residual confounding common to observational studies. Conclusions: A high-risk APOL1 genotype is significantly associated with increased kidney failure risk, especially among patients without baseline proteinuria. Although our results suggest that the risk is partially mediated through proteinuria, higher kidney failure risk was present even among patients who never developed proteinuria. Providers should consider screening for the high-risk APOL1 genotype, especially among Black patients without proteinuria in populations with chronic kidney disease.

Abstract As healthcare providers receive fixed amounts of reimbursement for given services under DRG (Diagnosis-Related Groups) payment, DRG codes are valuable for cost monitoring and resource allocation. However, coding is typically performed retrospectively post-discharge. We seek to predict DRGs and DRG-based case mix index (CMI) at early inpatient admission using routine clinical text to estimate hospital cost in an acute setting. We examined a deep learning-based natural language processing (NLP) model to automatically predict per-episode DRGs and corresponding cost-reflecting weights on two cohorts (paid under Medicare Severity (MS) DRG or All Patient Refined (APR) DRG), without human coding efforts. It achieved macro-averaged area under the receiver operating characteristic curve (AUC) scores of 0·871 (SD 0·011) on MS-DRG and 0·884 (0·003) on APR-DRG in fivefold cross-validation experiments on the first day of ICU admission. When extended to simulated patient populations to estimate average cost-reflecting weights, the model increased its accuracy over time and obtained absolute CMI error of 2·40 (1·07%) and 12·79% (2·31%), respectively on the first day. As the model could adapt to variations in admission time, cohort size, and requires no extra manual coding efforts, it shows potential to help estimating costs for active patients to support better operational decision-making in hospitals.

Mantle cell lymphoma (MCL) is a type of non-Hodgkin lymphoma (NHL) characterized by a hallmark translocation of t (11; 14). CD10 negativity has been used to differentiate MCL from other NHL types; however, recently, there has been an increase in the number of reported cases of CD10-positive MCL. This warrants further investigation into this rarer immunophenotype and its clinical significance. BCL6, which is a master transcription factor for the regulation of cell proliferation and key oncogene in B cell lymphomagenesis, has been reported to have co-expression with CD10 in MCL. The clinical significance of this aberrant antigen expression remains unknown. We conducted a systematic review by searching four databases and selected five retrospective analyses and five case series. Two survival analyses were conducted to determine if BCL6 positivity conferred a survival difference: 1. BCL6+ vs. BCL6− MCL. 2. BCL6+/CD10+ vs. BCL6−/CD10+ MCL. Correlation analysis was conducted to determine if BCL6 positivity correlated with the Ki67 proliferation index (PI). Overall survival (OS) rates were performed by the Kaplan–Meier method and log-rank test. Our analyses revealed that BCL6+ MCL had significantly shorter overall survival (median OS: 14 months vs. 43 months; p = 0.01), BCL6+/CD10+ MCL had an inferior outcome vs. BCL6+/CD10− MCL (median OS: 20 months vs. 55 months p = 0.1828), BCL6+ MCL had significantly higher percentages of Ki67% (Ki67% difference: 24.29; p = 0.0094), and BCL6 positivity had a positive correlation with CD10+ status with an odds ratio 5.11 (2.49, 10.46; p = 0.0000286). Our analysis showed that BCL6 expression is correlated with CD10 positivity in MCL, and BCL6 expression demonstrated an inferior overall survival. The higher Ki67 PI in BCL6+ MCL compared to BCL6− MCL further supports the idea that the BCL6+ immunophenotype may have prognostic value in MCL. MCL management should consider incorporating prognostic scoring systems adjusted for BCL6 expression. Targeted therapies against BCL6 may offer potential therapeutic options for managing MCL with aberrant immunophenotypes.

Patient‐derived samples present an advantage over current cell line models of high‐grade serous ovarian cancer (HGSOC) that are not always reliable and phenotypically faithful models of in vivo HGSOC. To improve upon cell line models of HGSOC, we set out to characterize a panel of patient‐derived cells and determine their epithelial and mesenchymal characteristics. We analyzed RNA and protein expression levels in patient‐derived xenograft (PDX) models of HGSOC, and functionally characterized these models using flow cytometry, wound healing assays, invasion assays, and spheroid cultures. Besides in vitro work, we also evaluated the growth characteristics of PDX in vivo (orthotopic PDX). We found that all samples had hybrid characteristics, covering a spectrum from an epithelial‐to‐mesenchymal state. Samples with a stronger epithelial phenotype were more active in self‐renewal assays and more tumorigenic in orthotopic xenograft models as compared to samples with a stronger mesenchymal phenotype, which were more migratory and invasive. Additionally, we observed an inverse association between microRNA let‐7 (lethal‐7) expression and stemness, consistent with the loss of let‐7 being an important component of the cancer stem cell phenotype. We observed that lower let‐7 levels were associated with the epithelial state and a lower epithelial mesenchymal transition (EMT) score, more efficient spheroid and tumor formation, and increased sensitivity to platinum‐based chemotherapy. Surprisingly, in these HGSOC cells, stemness could be dissociated from invasiveness: Cells with lower let‐7 levels were more tumorigenic, but less migratory, and with a lower EMT score, than those with higher let‐7 levels. We conclude that let‐7 expression and epithelial/mesenchymal state are valuable predictors of HGSOC proliferation, in vitro self‐renewal, and tumor burden in vivo.

Hepatic encephalopathy is a common complication in chronic liver disease and cirrhosis. Here we describe two patients with hepatic encephalopathy who did not respond to standard empiric treatment and were found to have non-convulsive status epilepticus. Both patients improved with antiepileptic therapy. Non-convulsive status epilepticus should be considered in the differential diagnosis of patients with suspected hepatic encephalopathy who do not respond to empiric treatment.

Abstract Objective To explore the efficacy of primary chemoradiation with cisplatin versus cetuximab with respect to HPV/p16 and smoking statuses. Methods We retrospectively reviewed patients from our center with locally advanced non-nasopharyngeal head and neck squamous cell carcinoma (HNSCC) who received primary chemoradiation with cisplatin or cetuximab between 2006 and 2018. Results The median OS for cisplatin (n = 66) was not reached versus 132 months when treated with cetuximab (n = 55) (p = 0.03). For HPV/p16-positive patients, we found the median OS for cisplatin (n = 34) was not reached versus 60 months with cetuximab (n = 21) (p = 0.036). In the smoking group, the median OS was not reached in the cisplatin group (n = 44) versus 60 months when treated with cetuximab (n = 32) (p = 0.03). Conclusion HPV/p16-positive and smoking cohorts treated with cisplatin-based chemoradiotherapy had a significantly better OS versus cetuximab.

Patients with co-morbidities like cirrhosis are at risk of worse outcome from COVID-19 infection. Given limited prior studies, we evaluated outcomes associated with COVID-19 infection in alcoholic and non-alcoholic steatohepatitis cirrhotic (CC+) versus cirrhotic without COVID-19 (CC−). We performed retrospective analysis of 822,604 patients including 28,610 COVID-19 patients from the National Inpatient Sample database with alcoholic and NASH cirrhosis enrolled between 1 January 2020 to 31 December 2020, with univariate and multivariate regression analyses. Primary outcome was mortality and secondary outcomes was mechanical ventilation, vasopressor use, length of stay, hospitalization expense and predictors of mortality. In-hospital mortality was three time higher in the CC+ group compared to those in the CC− group(18.6% vs. 5.96%, p < 0.001, adjusted odds ratio (OR)3.39 (95% 3.08–3.74 CI). Hospitalization was more likely for underrepresented racial and ethnic groups with COVID-19 and cirrhosis. CC+ group had over twice the rates of mechanical ventilation (19.92% vs. 9.07%, adjusted OR 2.71 2.71 (95% 2.51–2.93 CI)),1.7 times likelihood of receiving vasopressors (4.12% vs. 2.45%, p < 0.001, adjusted OR 1.71 (95% CI 1.46–2.01). COVID-19 is associated with increased mortality in patients with alcoholic and NASH cirrhosis, and patients with alcoholic cirrhosis and COVID-19 have a slightly higher mortality compared to NASH cirrhosis.

Alcohol consumption is associated with an increased risk of several cancers, including oral/oropharyngeal squamous cell carcinoma (OSCC). Alcohol also enhances the progression and aggressiveness of existing cancers; however, its underlying molecular mechanism remains elusive. Especially, the local carcinogenic effects of alcohol on OSCC in closest contact with ingestion of alcohol are poorly understood. We demonstrated that chronic ethanol exposure to OSCC increased cancer stem cell (CSC) populations and their stemness features, including self-renewal capacity, expression of stem cell markers, ALDH activity, and migration ability. The ethanol exposure also led to a significant increase in aerobic glycolysis. Moreover, increased aerobic glycolytic activity was required to support the stemness phenotype of ethanol-exposed OSCC, suggesting a molecular coupling between cancer stemness and metabolic reprogramming. We further demonstrated that chronic ethanol exposure activated NFAT (nuclear factor of activated T cells) signaling in OSCC. Functional studies revealed that pharmacological and genetic inhibition of NFAT suppressed CSC phenotype and aerobic glycolysis in ethanol-exposed OSCC. Collectively, chronic ethanol exposure promotes cancer stemness and aerobic glycolysis via activation of NFAT signaling. Our study provides a novel insight into the roles of cancer stemness and metabolic reprogramming in the molecular mechanism of alcohol-mediated carcinogenesis.

Objective Medical research studies often rely on the manual collection of data from scanned typewritten clinical records, which can be laborious, time consuming and error prone because of the need to review individual clinical records. We aimed to use text mining to assist with the extraction of clinical features from complex text-based scanned pathology records for medical research studies.Design Text mining performance was measured by extracting and annotating three distinct pathological features from scanned photocopies of endometrial carcinoma clinical pathology reports, and comparing results to manually abstracted terms. Inclusion and exclusion keyword trigger terms to capture leiomyomas, endometriosis and adenomyosis were provided based on expert knowledge. Terms were expanded with character variations based on common optical character recognition (OCR) error patterns as well as negation phrases found in sample reports. The approach was evaluated on an unseen test set of 1293 scanned pathology reports originating from laboratories across Australia.Setting Scanned typewritten pathology reports for women aged 18–79 years with newly diagnosed endometrial cancer (2005–2007) in Australia.Results High concordance with final abstracted codes was observed for identifying the presence of three pathology features (94%–98% F-measure). The approach was more consistent and reliable than manual abstractions, identifying 3%–14% additional feature instances.Conclusion Keyword trigger-based automation with OCR error correction and negation handling proved not only to be rapid and convenient, but also providing consistent and reliable data abstractions from scanned clinical records. In conjunction with manual review, it can assist in the generation of high-quality data abstractions for medical research studies.

High-grade serous carcinoma of the ovary is a deadly gynecological cancer with poor long-term survival. Dysregulation of microRNAs has been shown to contribute to the formation of cancer stem cells (CSCs), an important part of oncogenesis and tumor progression. The let-7 family of microRNAs has previously been shown to regulate stemness and has tumor suppressive actions in a variety of cancers, including ovarian. Here, we demonstrate tumor suppressor actions of let-7i: repression of cancer cell stemness, inhibition of migration and invasion, and promotion of apoptosis, features important for cancer progression, relapse, and metastasis. Let-7i over-expression results in increased sensitivity to the PARP inhibitor olaparib in samples without BRCA mutations, consistent with induction of BRCAness phenotype. We also show that let-7i inhibits the expression of several factors involved in the homologous recombination repair (HRR) pathway, providing potential mechanisms by which the BRCAness phenotype could be induced. These actions of let-7i add to the rationale for use of this miRNA as a treatment for ovarian cancer patients, including those without mutations in the HRR pathway.

Dengue virus (DV) is a compact, icosahedrally symmetric, enveloped particle, covered by 90 dimers of envelope protein (E), which mediates viral attachment and membrane fusion. Fusion requires a dimer-to-trimer transition and membrane engagement of hydrophobic ‘fusion loops’. We previously characterized the steps in membrane fusion for the related West Nile virus (WNV), using recombinant, WNV virus-like particles (VLPs) for single-particle experiments (Chao et al., 2014). Trimerization and membrane engagement are rate-limiting; fusion requires at least two adjacent trimers; availability of competent monomers within the contact zone between virus and target membrane creates a trimerization bottleneck. We now report an extension of that work to dengue VLPs, from all four serotypes, finding an essentially similar mechanism. Small-molecule inhibitors of dengue virus infection that target E block its fusion-inducing conformational change. We show that ~12–14 bound molecules per particle (~20–25% occupancy) completely prevent fusion, consistent with the proposed mechanism.

Viruses have long been implicated in the pathogenesis of autoimmunity, yet their contribution remains circumstantial partly due to the lack of well-documented information on infections prior to autoimmune disease onset. Here, we used the lymphocytic choriomeningitis virus (LCMV) as a model to mechanistically dissect the impact of viral infection on lupus-like autoimmunity. Virus persistence strongly enhanced disease in mice with otherwise weak genetic predisposition but not in highly predisposed or non-autoimmune mice, indicating a synergistic interplay between genetic susceptibility and virus infection. Moreover, endosomal Toll-like receptors (TLRs) and plasmacytoid dendritic cells (pDCs) were both strictly required for disease acceleration, even though LCMV also induces strong TLR-independent type I interferon (IFN-I) production via RNA helicases and MAVS in conventional DCs. These results suggest that LCMV enhances systemic autoimmunity primarily by providing stimulatory nucleic acids for endosomal TLR engagement, whereas overstimulation of the MAVS-dependent cytosolic pathway in the absence of endosomal TLR signaling is insufficient for disease induction.

A sinus of Valsalva aneurysm is a rare malformation of the aortic root that can fistulize to another cardiac structure such as the right atrium. Although transthoracic echocardiography and computed tomography angiography have demonstrated utility for the diagnosis of a sinus of Valsalva-to-right atrial fistula, there are few cases where a misdiagnosis may occur. Intraoperative transesophageal echocardiography may be an essential imaging tool for the diagnosis and management of incidental findings such as a sinus of Valsalva-to-right atrial fistula during cardiac surgery and should be used routinely.

The eukaryotic chaperonin TRiC/CCT uses ATP cycling to fold many essential proteins that other chaperones cannot fold. This 1 MDa hetero-oligomer consists of two identical stacked rings assembled from eight paralogous subunits, each containing a conserved ATP-binding domain. Here, we report a dramatic asymmetry in the ATP utilization cycle of this ring-shaped chaperonin, despite its apparently symmetric architecture. Only four of the eight different subunits bind ATP at physiological concentrations. ATP binding and hydrolysis by the low-affinity subunits is fully dispensable for TRiC function in vivo. The conserved nucleotide-binding hierarchy among TRiC subunits is evolutionarily modulated through differential nucleoside contacts. Strikingly, high- and low-affinity subunits are spatially segregated within two contiguous hemispheres in the ring, generating an asymmetric power stroke that drives the folding cycle. This unusual mode of ATP utilization likely serves to orchestrate a directional mechanism underlying TRiC/CCT's unique ability to fold complex eukaryotic proteins.

Following the Evidence Based Medicine (EBM) practice, practitioners make use of the existing evidence to make therapeutic decisions. This evidence, in the form of scientific statements, is usually found in scholarly publications such as randomised control trials and systematic reviews. However, finding such information in the overwhelming amount of published material is particularly challenging. Approaches have been proposed to automatically extract scientific artefacts in EBM using standardised schemas. Our work takes this stream a step forward and looks into consolidating extracted artefacts-i.e., quantifying their degree of similarity based on the assumption that they carry the same rhetorical role. By semantically connecting key statements in the literature of EBM, practitioners are not only able to find available evidence more easily, but also can track the effects of different treatments/outcomes in a number of related studies. We devise a regression model based on a varied set of features and evaluate it both on a general English corpus (the SICK corpus), as well as on an EBM corpus (the NICTA-PIBOSO corpus). Experimental results show that our approach performs on par with the state of the art on the general English and achieves encouraging results on the biomedical text when compared against human judgement.

Despite the iconic association of palms with semi-arid regions, most are introduced and can invade natural areas. Along the San Diego River (San Diego, California, USA), the introduced Canary Island date palm (Phoenix canariensis) forms dense patches among native riparian shrubs like arroyo willow (Salix lasiolepis). The structural differences between the palm and native shrubs are visually obvious, but little is known about palm's effects on the ecosystem. We tested for the effects of the palm on a riparian invertebrate community in June 2011 by comparing the faunal and environmental variables associated with palm and willow canopies, trunks and ground beneath each species. The palm invertebrate community had lower abundance and diversity, fewer taxa feeding on the host (e.g., specialized hemipterans), and more taxa likely using only the plant's physical structure (e.g., web-builders, oak moths, willow hemipterans). There were no observed effects on the ground-dwelling fauna. Faunal differences were due to the physical and trophic changes associated with palm presence, namely increased canopy density, unpalatable leaves, trunk rugosity, and litter accumulations. Palm presence and resulting community shifts may have further ecosystem-level effects through alteration of physical properties, food, and structural resources. These results were consistent with a recent study of invasive palm effects on desert spring arthropods, illustrating that effects may be relatively generalizable. Since spread of the palm is largely localized, but effects are dramatic where it does occur, we recommend combining our results with several further investigations in order to prioritize management decisions.

The use of visual content in applications of the digital computer has increased dramatically with the advent of the Internet and world wide web. Image coding standards such as JPEG 2000 have been developed to provide scalable and progressive compression of imagery. Advances in image and video analysis are also making human-computer interaction multi-modal rather than through the use of a keyboard or mouse. An eye tracker is an example input device that can be used by an application that displays visual content to adapt to the viewer. Many features are required of the format to facilitate this adaptation, and some are already part of image coding standards such as JPEG 2000. This paper presents a system incorporating the use of eye tracking and JPEG 2000, called Gaze-J2K, to allow a customised encoding of an image by using a user’s gaze pattern. The gaze pattern is used to automatically determine and assign importance to fixated regions in an image, and subsequently constrain the encoding of the image to these regions.