Automated single-cell omics end-to-end framework with data-driven batch inference.

To facilitate single cell multi-omics analysis and improve reproducibility, we present SPEEDI (Single-cell Pipeline for End to End Data Integration), a fully automated end-to-end framework for batch inference, data integration, and cell type labeling. SPEEDI introduces data-driven batch inference and transforms the often heterogeneous data matrices obtained from different samples into a uniformly annotated and integrated dataset. Without requiring user input, it automatically selects parameters and executes pre-processing, sample integration, and cell type mapping. It can also perform downstream analyses of differential signals between treatment conditions and gene functional modules. SPEEDI's data-driven batch inference method works with widely used integration and cell-typing tools. By developing data-driven batch inference, providing full end-to-end automation, and eliminating parameter selection, SPEEDI improves reproducibility and lowers the barrier to obtaining biological insight from these valuable single-cell datasets. The SPEEDI interactive web application can be accessed at https://speedi.princeton.edu/.

exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling.

Small RNA sequencing has been widely adopted to study the diversity of extracellular RNAs (exRNAs) in biofluids; however, the analysis of exRNA samples can be challenging: they are vulnerable to contamination and artifacts from different isolation techniques, present in lower concentrations than cellular RNA, and occasionally of exogenous origin. To address these challenges, we present exceRpt, the exRNA-processing toolkit of the NIH Extracellular RNA Communication Consortium (ERCC). exceRpt is structured as a cascade of filters and quantifications prioritized based on one's confidence in a given set of annotated RNAs. It generates quality control reports and abundance estimates for RNA biotypes. It is also capable of characterizing mappings to exogenous genomes, which, in turn, can be used to generate phylogenetic trees. exceRpt has been used to uniformly process all ∼3,500 exRNA-seq datasets in the public exRNA Atlas and is available from genboree.org and github.gersteinlab.org/exceRpt.

exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids.

To develop a map of cell-cell communication mediated by extracellular RNA (exRNA), the NIH Extracellular RNA Communication Consortium created the exRNA Atlas resource (https://exrna-atlas.org). The Atlas version 4P1 hosts 5,309 exRNA-seq and exRNA qPCR profiles from 19 studies and a suite of analysis and visualization tools. To analyze variation between profiles, we apply computational deconvolution. The analysis leads to a model with six exRNA cargo types (CT1, CT2, CT3A, CT3B, CT3C, CT4), each detectable in multiple biofluids (serum, plasma, CSF, saliva, urine). Five of the cargo types associate with known vesicular and non-vesicular (lipoprotein and ribonucleoprotein) exRNA carriers. To validate utility of this model, we re-analyze an exercise response study by deconvolution to identify physiologically relevant response pathways that were not detected previously. To enable wide application of this model, as part of the exRNA Atlas resource, we provide tools for deconvolution and analysis of user-provided case-control studies.

Treatment of Non-ST Elevation Myocardial Infarction: A Process Analysis of Patient and Program Factors in a Teaching Hospital.

As part of a quality improvement project, we performed a process analysis to evaluate how patients presenting with type 1 non-ST elevation myocardial infarction (STEMI) are diagnosed and managed early after the diagnosis has been made. We performed a retrospective chart review and collected detailed information regarding the timing of the first 12-lead electrocardiogram, troponin order entry and first positive troponin result, administration of anticoagulation and antiplatelet medications, and referral for coronary angiography to identify areas of treatment variability and delay. A total of 242 patients with type 1 non-STEMI were included. The majority of patients received aspirin early after presentation to the emergency department; however, there was significant variability in the time from presentation to administration of other medications, including anticoagulation and P2Y12 therapy, even after an elevated troponin level was documented in the chart. Lack of a standardized non-STEMI admission order set, inconsistency regarding whether the emergency department physician or the cardiology admitting team order these medications after the diagnosis is made, and per current protocol, the initial call regarding the patient made to the cardiology fellow, not the admitting house staff, were identified as possible contributors to the delay. Patients who presented during "nighttime" hours had higher rates of atypical symptoms (P = 0.036) and longer delays to coronary angiography (46.5 versus 24 hours, P < 0.001) even in those deemed intermediate to high risk. A process analysis revealed considerable variation in non-STEMI treatment in our teaching hospital and identified specific areas for quality improvement measures.

Effect of clinical vignettes on senior medical students' opinions of climate change.

OBJECTIVES: The consequences of climate change directly threaten human health. Some have argued that, as such, doctors have a special duty to solve climate change. Despite such recommendations, to our knowledge, there has been no previous work documenting physician attitudes on climate change, or the stability of those opinions. METHODS: We invited 523 fourth-year medical students to a survey asking their opinion on climate change and their opinion regarding one of two fictional medical vignettes. In the vignettes, which are analogous to the climate change issue, students decide whether to discontinue a drug that may be adversely affecting laboratory values. In the climate change question, students are asked whether the United States should take efforts to discontinue the use of fossil fuels. Students are randomized to the order in which they receive the questions. RESULTS: Ninety-five percent (95% CI 89.1%-100%) of students initially asked about climate change feel the United States should take steps to curb carbon dioxide emissions, while only 73% (95% CI 57.5%-89.2%) of students respond similarly if first given an analogous patient vignette. Conversely, in all cases where a fictional medical vignette follows the climate change question, students are more likely to cease using a potentially harmful agent (66% CI 53.5%-71.8% vs. 52% CI 43.3%-67.1%). CONCLUSION: Our results suggest that student physician attitudes to climate change are mutable. Priming students into "medical mode" may alter their opinions on the scientific merit of nonmedical issues, and may be a vestige of a hidden medical curriculum. Further studies should explore the interrelationship between other sociopolitical beliefs and medical decision making.

Diagnosis and treatment of atypical presentations of hiatal hernia following bariatric surgery.

Bariatric surgery dramatically alters the normal stomach anatomy resulting in a significant incidence of hiatal hernia and gastroesophageal reflux disease. Although the majority of patients remain asymptomatic, many complain of severe heartburn refractory to medical management and additional highly atypical symptoms. Here, we describe the diagnosis and treatment regarding four cases of symptomatic hiatal hernia following bariatric surgery presenting with atypical symptoms in the University Hospital, USA. Four patients presented following laparoscopic Roux-en-Y gastric bypass or duodenal switch/pancreaticobiliary bypass (DS) with disabling and intractable midepigastric abdominal pain characterized as severe and radiating to the jaw, left shoulder, and midscapular area. The pain in all cases was described as paroxysmal and not necessarily associated with eating. All four patients also experienced nausea, vomiting, and failure to thrive at various intervals following laparoscopic bariatric surgery. Routine workup failed to produce any clear mechanical cause of these symptoms. However, complimentary use of multidetector CT and upper gastrointestinal contrast studies eventually revealed the diagnosis of hiatal hernia. Exploration identified the presence of a type I hiatal hernia in all four patients, with the stomach staple lines densely adherent to the diaphragm and parietal peritoneum. Operative intervention led to immediate and complete resolution of symptoms. The presence of a hiatal hernia following bariatric surgery can present with highly atypical symptoms that do not resolve without operative intervention. Recognition of this problem should lead to the consideration of surgery in cases where patients are dependent on artificial nutritional support and whose symptoms are poorly controlled with medication alone.

Bariatric surgery: a history of empiricism, a future in science.

BACKGROUND: The observation that obesity can be successfully treated by gastrointestinal surgery is a tribute to the innovative efforts by determined surgeons and the ever improving safety of general anesthesia. Yet as the body of knowledge and discovery on the root causes of human obesity accumulate, surgical approaches to treat morbid obesity are likely to change dramatically. While there is little doubt that dramatic weight loss can be achieved by surgically creating volume and absorption limitation to the reservoir and digestive functions of the gastrointestinal tract, human progress to more processed foods, less physical activity, and the pervasive public opinion that obesity is self-imposed are major obstacles to more widespread application of this approach. DISCUSSION: Here we provide a mechanico-physiologic analysis of current operations, their rationale and limitations, as well as a glimpse of how future interventions might develop as a result of current knowledge in the field. The future of bariatric surgery is discussed in the context of these emerging technologies and in the context of the politics of obesity.

Rapid genotyping of common MeCP2 mutations with an electronic DNA microchip using serial differential hybridization.

Rett syndrome is a neurodevelopmental disorder that affects females almost exclusively, and in which eight common point mutations on the X-linked MeCP2 gene are knows to cause over 70% of mutation-positive cases. We explored the use of a novel platform to detect the eight common mutations in Rett syndrome patients to expedite and simplify the process of identification of known genotypes. The Nanogen workstation consists of a two-color assay based on electric hybridization and thermal discrimination, all performed on an electronically active NanoChip. This genotyping platform was tested on 362 samples of a pre-determined genotype, which had been previously identified by a combination of DHPLC (denaturing high performance liquid chromatography) and direct sequencing. This genotyping technique proved to be rapid, facile, and displayed a specificity of 100% with 3% ambiguity. In addition, we present consecutive testing of seven mutations on a single pad of the NanoChip. This was accomplished by tagging down two amplimers together and serially hybridizing for seven different loci, allowing us to genotype samples for seven of the eight common Rett mutations on a single pad. This novel method displayed the same level of specificity and accuracy as the single amplimer reactions, and proved to be faster and more economical.