Patterns of Failure in Patients With Borderline Resectable/Locally Advanced Pancreatic Cancer After Preoperative Chemotherapy and Stereotactic Body Radiation Therapy.

Purpose: The role of preoperative stereotactic body radiation therapy (SBRT) in pancreatic cancer is controversial, and questions regarding the optimal dose and radiation treatment field remain. To better inform future investigations of SBRT dose and radiation fields, we evaluated the patterns of failure in patients with borderline resectable/locally advanced pancreatic cancer (BR/LAPC) after preoperative chemotherapy and SBRT in patients who underwent surgical resection. Methods and Materials: We performed a single-institution retrospective review of consecutive patients treated from September 2017 to January 2022 with BR/LAPC. Patients who underwent preoperative chemotherapy and SBRT followed by surgical resection were reviewed. SBRT was delivered to a dose of 33 Gy in 5 fractions. Kaplan-Meier overall survival and progression-free survival estimates were calculated. Results: In total, 18 patients (12 BRPC, 6 LAPC) were included. Median age was 69 years (range 41-84 years). Median follow-up was 30 months (range 13-59 months). Seventeen patients (94%) had a R0 resection and 13 (72%) underwent vascular reconstruction. Median overall survival and progression-free survival was 42 months (range 13-59 months) and 23 months (range 1-45 months), respectively. In total, 61% (11/18) patients experienced progression at any point during follow-up. Of the patients who experienced recurrence, 27% (3/11) experienced local progression as component of their first recurrence, whereas 100% (11/11) experienced distant progression as a component of their first recurrence. When examining all recurrences that occurred at any point in follow-up, 28% (5/18) of patients experienced local or locoregional recurrence and 61% (11/18) experienced distant progression. Conclusions: Local control and margin negative resection rates were excellent with preoperative chemotherapy and nondose-escalated SBRT in surgically resected patients with BR/LAPC. Distant recurrence was the predominant site of failure with lower incidences of isolated locoregional recurrences. Additional research is needed to determine the ideal treatment volume and patients who may benefit from dose escalation.

Analyses of potential causal contributors to increased waist/hip ratio-associated cardiometabolic disease: A combined and sex-stratified Mendelian randomization study.

BACKGROUND: Increased waist/hip ratio (WHR) contributes to type 2 diabetes, fatty liver, dyslipidaemia, hypertension and coronary artery disease, with potential sex-differential effects. Postulated mediators include increased lipid flux, branched-chain amino acids, glycine and glycoprotein acetyl, but their relative contributions and sex-specific impact on WHR-associated cardiometabolic disease (CMD) are not established. METHODS: We therefore undertook combined and sex-stratified Mendelian randomization (MR) to assess the relative causal contributions of these mediators to WHR-associated CMD using summary statistics from the largest genome-wide association studies in European ancestries. RESULTS: In sex-combined MR analyses, increased WHR significantly reduces high-density lipoprotein (beta = -0.416, SE = 0.029, p = 2.87E-47), increases triglyceride (beta = 0.431, SE = 0.029, p = 1.87E-50), type 2 diabetes (odds ratio = 2.747, SE = 0.09, p = 26E-23), coronary artery disease (odds ratio = 1.478, SE = 0.045, p = 6.96E-18), alanine transaminase (beta = 0.062, SE = 0.004, p = 6.88E-67), and systolic (beta = 0.134, SE = 0.022, p = 7.81E-10) and diastolic blood pressure (beta = 0.162, SE = 0.026, p = 5.38E-10). Adjustment for the mediators attenuated WHR's effects, but the associations remained significant with concordant results in females. In males, a similar pattern was seen, except after adjusting for the effect of the ratio of monounsaturated fatty acid to total free fatty acid, the potential causal effect of WHR was no longer significant: high-density lipoprotein (beta = -0.117, SE = 0.069, p = .09) and triglyceride (beta = 0.051, SE = 0.068, p = .459). CONCLUSIONS: MR suggests WHR increases the risk of CMD independent of these mediators, with the exception of dyslipidaemia in males, which is largely driven by the monounsaturated fatty acid to total free fatty acid ratio.

Factors associated with longer survival among older medicare patients after diagnosis of supratentorial primary brain malignancies: a retrospective cohort study.

OBJECTIVES: Despite recent advances, the prognosis for primary malignant brain tumors (PMBTs) remains poor. Some commonly prescribed medications may exhibit anti-tumor properties in various cancers, and neurodegenerative diseases may activate pathways that counteract gliomagenesis. Our study is focused on determining if there is a correlation between the use of metformin, beta-blockers, angiotensin converting enzyme inhibitors (ACEIs), and angiotensin receptor blockers (ARBs), or the presence of Parkinson's disease (PD), and the survival rates following a diagnosis of a PMBT. METHODS: This analysis of the 100% Texas Medicare Database identified patients aged 66+ years diagnosed with a supratentorial PMBT from 2014-2017. Cox proportional hazards regression was employed to analyze survival following diagnosis and associations of survival with surgical intervention, radiation, PD diagnosis, and prescription of metformin, beta-blockers, ACEIs, or ARBs. RESULTS: There were 1,943 patients who met study criteria, and the median age was 74 years. When medication utilization was stratified by none, pre-diagnosis only, post-diagnosis only, or both pre- and post-diagnosis (continuous), continuous utilization of metformin, beta-blockers, ACEIs, or ARBs was associated with prolonged survival compared to no utilization (hazard ratio [HR]:0.45, 95% CI:0.33-0.62; HR:0.71. 95% CI:0.59-0.86; HR:0.59, 95% CI:0.48-0.72; and HR:0.45, 95% CI:0.35-0.58 respectively). PD was also associated with longer survival (HR:0.59-0.63 across the four models). DISCUSSION: Our study suggests that metformin, beta-blockers, ACEIs, ARBs, and comorbid PD are associated with a survival benefit among geriatric Medicare patients with supratentorial PMBTs.

Neurosurgery at Baylor Scott & White Health: Recent History and a Decade of Neurosurgery Residency Training.

Neurosurgery at Baylor Scott & White Memorial Hospital in Temple, Texas began as a division in the Department of Surgery many decades ago. The hospital has long served as the flagship tertiary referral center for the Baylor Scott & White healthcare system, which merged in 2013 with Baylor University Medical Center, a hospital system based in Dallas. It is now the largest non-profit hospital system as well as the most awarded hospital system by the US News and World Report within the state of Texas. The Department of Neurosurgery was established at Baylor Scott & White Memorial Hospital in the 2006-2007 academic year. Between then and 2014, four neurosurgeons served as department chair or interim chair: Dr. Robert Buchanan, Dr. Gerhard Friehs, Dr. Ibrahim El Nihum, and Dr. David Garrett Jr. In 2014, Dr. Jason Huang was appointed chairman after a national search and established the neurosurgery residency program in 2015. The department has undergone tremendous growth under the leadership of Dr. Huang, and the residency program is a priority of the department. Surgical excellence is honed at primarily three campuses: Baylor Scott & White Memorial Hospital, Baylor Scott & White McLane Children's Medical Center, and Baylor Scott & White Medical Center - Hillcrest. In this editorial, we provide a brief history of the institution, a recent history of the neurosurgical presence at Baylor Scott & White Memorial Hospital in Temple, Texas, and briefly describe the program's future directions under the continued leadership of Dr. Jason Huang.

Uncovering Variations in Clinical Notes for NLP Modeling.

Clinical text contains rich patient information and has attracted much research interest in applying Natural Language Processing (NLP) tools to model it. In this study, we quantified and analyzed the textual characteristics of five common clinical note types using multiple measurements, including lexical-level features, semantic content, and grammaticality. We found there exist significant linguistic variations in different clinical note types, while some types tend to be more similar than others.

Developing Robust Clinical Text Deep Learning Models - A "Painless" Approach.

The success of deep learning in natural language processing relies on ample labelled training data. However, models in the health domain often face data inadequacy due to the high cost and difficulty of acquiring training data. Developing such models thus requires robustness and performance on new data. A generalised incremental multiphase framework is proposed for developing robust and performant clinical text deep learning classifiers. It incorporates incremental multiphases for training data size assessments, cross-validation setup to avoid test data bias, and robustness testing through inter/intra-model significance analysis. The framework's effectiveness and generalisation were confirmed by the task of identifying patients presenting in 'pain' to the emergency department.

Leveraging Unlabeled Clinical Data to Boost Performance of Risk Stratification Models for Suspected Acute Coronary Syndrome.

The performance of deep learning models in the health domain is desperately limited by the scarcity of labeled data, especially for specific clinical-domain tasks. Conversely, there are vastly available clinical unlabeled data waiting to be exploited to improve deep learning models where their training labeled data are limited. This paper investigates the use of task-specific unlabeled data to boost the performance of classification models for the risk stratification of suspected acute coronary syndrome. By leveraging large numbers of unlabeled clinical notes in task-adaptive language model pretraining, valuable prior task-specific knowledge can be attained. Based on such pretrained models, task-specific fine-tuning with limited labeled data produces better performances. Extensive experiments demonstrate that the pretrained task-specific language models using task-specific unlabeled data can significantly improve the performance of the downstream models for specific classification tasks.

Clinical characteristics of hospitalized male adolescents and young adults with atypical anorexia nervosa.

OBJECTIVE: To describe the clinical characteristics of male adolescents and young adults hospitalized for medical complications of atypical anorexia nervosa (atypical AN) and to compare their clinical characteristics with females with atypical AN and males with anorexia nervosa (AN). METHOD: A retrospective review of electronic medical records for patients with atypical AN and AN aged 9-25 admitted to the UCSF Eating Disorders Program from May 2012 to August 2020 was conducted. RESULTS: Among 21 males with atypical AN (mean age 15.1 ± 2.7, mean %mBMI 102.0 ± 11.8), medical complications evidenced by admission laboratory values included anemia (52.9%), vitamin D insufficiency/deficiency (52.6%), and zinc deficiency (31.6%). Compared with females with atypical AN (n = 69), males with atypical AN had longer length of stay (11.4 vs 8.4 days, p = .004), higher prescribed kcal at discharge (4114 vs 3045 kcal, p < .001), lower heart rate nadir (40.0 vs 45.8, p = .038), higher aspartate transaminase (AST, 37.9 vs 26.2 U/L, p = .032), higher alanine transaminase (ALT, 30.6 vs 18.3 U/L, p = .005), and higher rates of anemia (52.9% vs 19.4%, p = .005), with no differences in vitamin D, zinc, and vital signs. Compared with males with AN (n = 40), males with atypical AN had no significant differences in vital signs or laboratory assessments during the hospitalization. DISCUSSION: Atypical AN in males leads to significant medical comorbidity, and males with atypical AN require longer hospital stays compared to females with atypical AN. Rates of abnormal vital signs and abnormal serum laboratory values during hospital admissions do not differ in males with atypical AN compared to AN. PUBLIC SIGNIFICANCE: Adolescent and young adult males with atypical anorexia nervosa experience significant medical complications. Males with atypical anorexia nervosa had longer hospitalizations and higher prescribed nutrition at discharge than females. Medical complications of atypical anorexia nervosa in male adolescents and young adults were generally equal to those of male adolescents and young adults with anorexia nervosa. Clinicians should be aware of unique medical complications of males with atypical anorexia nervosa.

Feasibility and acceptability of ChatGPT generated radiology report summaries for cancer patients.

Objective: Patients now have direct access to their radiology reports, which can include complex terminology and be difficult to understand. We assessed ChatGPT's ability to generate summarized MRI reports for patients with prostate cancer and evaluated physician satisfaction with the artificial intelligence (AI)-summarized report. Methods: We used ChatGPT to summarize five full MRI reports for patients with prostate cancer performed at a single institution from 2021 to 2022. Three summarized reports were generated for each full MRI report. Full MRI and summarized reports were assessed for readability using Flesch-Kincaid Grade Level (FK) score. Radiation oncologists were asked to evaluate the AI-summarized reports via an anonymous questionnaire. Qualitative responses were given on a 1-5 Likert-type scale. Fifty newly diagnosed prostate cancer patient MRIs performed at a single institution were additionally assessed for physician online portal response rates. Results: Fifteen summarized reports were generated from five full MRI reports using ChatGPT. The median FK score for the full MRI reports and summarized reports was 9.6 vs. 5.0, (p < 0.05), respectively. Twelve radiation oncologists responded to our questionnaire. The mean [SD] ratings for summarized reports were factual correctness (4.0 [0.6], understanding 4.0 [0.7]), completeness (4.1 [0.5]), potential for harm (3.5 [0.9]), overall quality (3.4 [0.9]), and likelihood to send to patient (3.1 [1.1]). Current physician online portal response rates were 14/50 (28%) at our institution. Conclusions: We demonstrate a novel application of ChatGPT to summarize MRI reports at a reading level appropriate for patients. Physicians were likely to be satisfied with the summarized reports with respect to factual correctness, ease of understanding, and completeness. Physicians were less likely to be satisfied with respect to potential for harm, overall quality, and likelihood to send to patients. Further research is needed to optimize ChatGPT's ability to summarize radiology reports and understand what factors influence physician trust in AI-summarized reports.

Exploring Spinal Subarachnoid Hemorrhage: A Neurosurgical Case Series.

Spinal subarachnoid hemorrhage (SSAH) is a rare condition that can cause spinal cord or nerve root compression and permanent neurologic damage. The reported etiologies include trauma, vascular malformations or aneurysms, coagulopathies, neoplasms, autoimmune disease, and spontaneous hemorrhage. If there is evidence of neurologic deterioration, it is commonly managed as a surgical emergency, but cases of conservative management have also been reported. In this case series, we present three patients who suffered from SSAH. The first was a spontaneous cervical SSAH that occurred following cardiac catheterization, the second was a spontaneous thoracolumbar SSAH in a patient with a known history of coagulopathy, and the third was a thoracolumbar SSAH that was caused by a dural arteriovenous fistula (dAVF). All three patients exhibited neurologic deficits and thus underwent emergent decompression and hematoma evacuation. The patient with the dAVF also required open ligation of the fistula. Following surgical intervention, all three patients regained at least partial neurologic function, but one patient developed symptomatic arachnoid cysts that required further intervention. The presented case series highlights the importance and time-sensitivity of surgical decompression in patients experiencing neurologic deficits from SSAH. These cases underscore the urgency of timely neurosurgical intervention to mitigate neurologic impairment and add insights to the existing literature on this rare condition.

Ring-Enhancing Progressive Multifocal Leukoencephalopathy Mimicking Glioma in a Presumed Immunocompetent Patient With a History of Multiple Sclerosis: A Case Report and Review of the Literature.

The differential diagnoses of ring-enhancing lesions of the brain parenchyma is broad, but complete ring-enhancing lesions often indicate a neoplastic or infectious process. We present a case of a 70-year-old female with a history of multiple sclerosis (MS) who was not on current disease-modifying therapy (DMT) and was found to have a ring-enhancing lesion that mimicked a high-grade glioma. The patient underwent gross total resection, and histopathologic and molecular analysis revealed a diagnosis of progressive multifocal leukoencephalopathy (PML). A subsequent medical workup on the patient was unrevealing aside from mild lymphopenia. This is a unique case that highlights both an unusual clinical presentation and radiographic appearance of PML. There is a known associated increased risk of PML with the use of some DMTs for MS. However, this case raises the question of the possibility of developing PML years after interferon beta-1a therapy in a patient without overt immunosuppression.

Sex differences in cholesterol and triglyceride levels among hospitalized adolescents and young adults with eating disorders.

OBJECTIVE: To determine sex differences in cholesterol and triglyceride levels among adolescents and young adults hospitalized for medical complications of eating disorders. METHODS: A retrospective electronic medical record review of patients aged 9-25 years admitted to the University of California, San Francisco Eating Disorders Program for medical stabilization, between 2012 and 2020, was conducted. Non-fasting total cholesterol and triglycerides were collected; however, LDL and HDL levels were not available. RESULTS: Among 83 males and 441 females, mean ± SD age was 15.5 ± 2.8 years, 64.1% had anorexia nervosa, and admission percent median body mass index was 87.3 ± 13.9. The proportion of males and females with high total cholesterol (13.3% vs. 18.1%, Cramer's V = 0.05, p = .28) and high triglyceride levels (9.6% vs. 8.1%, Cramer's V = 0.02, p = .63) did not differ. Mean total cholesterol levels were higher in females compared to males (F 169.6 ± 41.1 mg/dL vs. M 154.5 ± 45.1 mg/dL, Cohen's d = 0.36, p = .003), although a majority were within the normal range. In adjusted linear regression models, male (compared to female) sex (B = -14.40, 95% CI -24.54, -4.27) and higher percent median body mass index (B = -0.33, 95% CI -0.60, -0.06) were associated with lower total cholesterol levels in adjusted models (R2 = 0.04). DISCUSSION: Building on prior work showing equally severe complications of eating disorders in males compared to females, we did not find sex differences in those presenting with high total cholesterol or triglycerides. Future research is needed to understand the pathophysiology and role of dyslipidemia in acute malnutrition, and the impact of nutritional rehabilitation and weight restoration. PUBLIC SIGNIFICANCE: We found that the proportion of male and female adolescents and young adults hospitalized for medical complications of an eating disorder with high total cholesterol did not significantly differ. Although average total cholesterol levels were higher in female compared to male patients with eating disorders, a majority of these levels remained within the normal range. Patients with more severe malnutrition had a higher risk of elevated total cholesterol levels. Clinicians should consider monitoring cholesterol levels in young people hospitalized for restrictive eating disorders.

Polypharmacy in chronic kidney disease: Health outcomes & pharmacy-based strategies to mitigate inappropriate polypharmacy.

The rising prevalence of comorbidities in an increasingly aging population has sparked a reciprocal rise in polypharmacy. Patients with chronic kidney disease (CKD) have a greater burden of polypharmacy due to the comorbidities and complications associated with their disease. Polypharmacy in CKD patients has been linked to myriad direct and indirect costs for patients and the society at large. Pharmacists are uniquely positioned within the healthcare team to streamline polypharmacy management in the setting of CKD. In this article, we review the landscape of polypharmacy and examine its impacts through the lens of the ECHO model of Economic, Clinical, and Humanistic Outcomes. We also present strategies for healthcare teams to improve polypharmacy care through comprehensive medication management process that includes medication reconciliation during transitions of care, medication therapy management, and deprescribing. These pharmacist-led interventions have the potential to mitigate adverse outcomes associated with polypharmacy in CKD.

Automated ICD coding using extreme multi-label long text transformer-based models.

Encouraged by the success of pretrained Transformer models in many natural language processing tasks, their use for International Classification of Diseases (ICD) coding tasks is now actively being explored. In this study, we investigated two existing Transformer-based models (PLM-ICD and XR-Transformer) and proposed a novel Transformer-based model (XR-LAT), aiming to address the extreme label set and long text classification challenges that are posed by automated ICD coding tasks. The Transformer-based model PLM-ICD, which currently holds the state-of-the-art (SOTA) performance on the ICD coding benchmark datasets MIMIC-III and MIMIC-II, was selected as our baseline model for further optimisation on both datasets. In addition, we extended the capabilities of the leading model in the general extreme multi-label text classification domain, XR-Transformer, to support longer sequences and trained it on both datasets. Moreover, we proposed a novel model, XR-LAT, which was also trained on both datasets. XR-LAT is a recursively trained model chain on a predefined hierarchical code tree with label-wise attention, knowledge transferring and dynamic negative sampling mechanisms. Our optimised PLM-ICD models, which were trained with longer total and chunk sequence lengths, significantly outperformed the current SOTA PLM-ICD models, and achieved the highest micro-F1 scores of 60.8 % and 50.9 % on MIMIC-III and MIMIC-II, respectively. The XR-Transformer model, although SOTA in the general domain, did not perform well across all metrics. The best XR-LAT based models obtained results that were competitive with the current SOTA PLM-ICD models, including improving the macro-AUC by 2.1 % and 5.1 % on MIMIC-III and MIMIC-II, respectively. Our optimised PLM-ICD models are the new SOTA models for automated ICD coding on both datasets, while our novel XR-LAT models perform competitively with the previous SOTA PLM-ICD models.

Orai3 Calcium Channel Contributes to Oral/Oropharyngeal Cancer Stemness through the Elevation of ID1 Expression.

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.

Indirect Bypass With Pericranial Transposition for Moyamoya Syndrome in an Infant.

Moyamoya syndrome (MMS) is a progressive disease that can result in debilitating strokes. Surgical revascularization is the mainstay of treatment. Selection of the proper bypass technique depends on the vascular anatomy and location of the hypoperfused cerebral territory. We describe here a case of successful indirect bypass utilizing a pericranial flap as well as dural inversion. A seven-month-old female was transferred from an outside facility to our institution for further evaluation and surgical treatment of MMS. She presented with bilateral brain infarcts worse on the left, with right-sided body weakness. After medical stabilization and hyperhydration, she was taken to the operating room for a left-sided indirect bypass. The superficial temporal artery (STA) was traced utilizing doppler but was determined to be too diminutive for transposition, so the decision was made to proceed with encephalo-duro-pericranio-synangiosis (EDPS). A pericranial graft was successfully affixed to the cortical surface in the hypoperfused middle cerebral artery (MCA) territory, and the dura was inverted. Postoperatively, the patient developed a pseudomeningocele, so a revision surgery was performed. She was discharged shortly after this and returned for encephalo-duro-arterio-synangiosis (EDAS) of the contralateral side. She followed up three months after her initial bypass surgery at age 10 months and was crawling without any focal deficits. She was lost to follow-up thereafter. EDPS is a safe technique for infants with MMS whose STA is too diminutive to be used for bypass surgery. This may be an effective method for indirect bypass in these patients.

Endothelial Cell APOE3 Regulates Neurovascular, Neuronal, and Behavioral Function.

BACKGROUND: Specialized brain endothelial cells and human APOE3 are independently important for neurovascular function, yet whether APOE3 expression by endothelial cells contributes to brain function is currently unknown. In the present study, we determined whether the loss of endothelial cell APOE3 impacts brain vascular and neural function. METHODS: We developed APOE3fl/fl/Cdh5(PAC)-CreERT2+/- (APOE3Cre+/-) and APOE3fl/fl/Cdh5(PAC)-CreERT2-/- (APOE3Cre-/-, control) mice and induced endothelial cell APOE3 knockdown with tamoxifen at ≈4 to 5 weeks of age. Neurovascular and neuronal function were evaluated by biochemistry, immunohistochemistry, behavioral testing, and electrophysiology at 9 months of age. RESULTS: We found that the loss of endothelial APOE3 expression was sufficient to cause neurovascular dysfunction including higher permeability and lower vessel coverage in tandem with deficits in spatial memory and fear memory extinction and a disruption of cortical excitatory/inhibitory balance. CONCLUSIONS: Our data collectively support the novel concept that endothelial APOE3 plays a critical role in the regulation of the neurovasculature, neural circuit function, and behavior.

Web-Based Application Based on Human-in-the-Loop Deep Learning for Deidentifying Free-Text Data in Electronic Medical Records: Development and Usability Study.

BACKGROUND: The 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. OBJECTIVE: We 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. METHODS: DEFT 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. RESULTS: DEFT 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. CONCLUSIONS: DEFT 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.

Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture.

BACKGROUND: The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function. RESULTS: We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection. CONCLUSIONS: We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.