The Effect of Language on the Decision to Image in the Evaluation of Atraumatic Headache.

BACKGROUND: Patients with limited English proficiency seen in the emergency department (ED) experience lower quality of care and higher diagnostic resource utilization unless they are evaluated in their own language. Despite a low rate of serious pathology identified and the availability of guidelines to direct its use, computed tomography (CT) is commonly used to evaluate atraumatic headache in the ED. OBJECTIVE: Our aim was to determine whether Spanish-speaking patients with atraumatic headache were more likely than their English-speaking counterparts to undergo head CT, and whether evaluation by a clinician who passed a Spanish proficiency test mitigated this difference. METHODS: This retrospective observational study used electronic health record data of adult patients presenting with atraumatic headache to a level I trauma center during a 2-year period. Spanish-language testing of clinicians consisted of a brief, unvalidated, in-person, nonmedical verbal test administered by human resources staff. RESULTS: A total of 3030 patients with atraumatic headache were identified; 1437 were English speaking and 1593 were Spanish speaking. Spanish-speaking patients were older (48.3 vs. 41.9 years), more likely to be women (68.8% vs. 60.5%), and more likely to undergo head CT (31.8% vs. 26.4%). Evaluation by a clinician who passed the Spanish proficiency test had no significant influence on the likelihood of head CT for Spanish-speaking patients after controlling for confounding variables (adjusted odds ratio 0.95; 95% CI 0.75-1.20). CONCLUSIONS: Spanish-speaking patients are more likely to undergo head CT when evaluated for atraumatic headache than English-speaking patients. Evaluation by a clinician who passed a brief Spanish proficiency test did not mitigate this disparity.

Codependency of H2B monoubiquitination and nucleosome reassembly on Chd1.

Monoubiquitination of histone H2B on Lys 123 (H2BK123ub) is a transient histone modification considered to be essential for establishing H3K4 and H3K79 trimethylation by Set1/COMPASS and Dot1, respectively. Here, we identified Chd1 as a factor that is required for the maintenance of high levels of H2B monoubiquitination, but not for H3K4 and H3K79 trimethylation. Loss of Chd1 results in a substantial loss of H2BK123ub levels with little to no effect on the genome-wide pattern of H3K4 and H3K79 trimethylation. Our data show that nucleosomal occupancy is reduced in gene bodies in both chd1Δ and, as has been shown, K123A mutant backgrounds. We also demonstrated that Chd1's function in maintaining H2BK123ub levels is conserved from yeast to humans. Our study provides evidence that only small levels of H2BK123ub are necessary for full levels of H3K4 and H3K79 trimethylation in vivo and points to a possible role for Chd1 in positively regulating gene expression through promoting nucleosome reassembly coupled with H2B monoubiquitination.

The little elongation complex regulates small nuclear RNA transcription.

Eleven-nineteen lysine-rich leukemia (ELL) participates in the super elongation complex (SEC) with the RNA polymerase II (Pol II) CTD kinase P-TEFb. SEC is a key regulator in the expression of HOX genes in mixed lineage leukemia (MLL)-based hematological malignancies, in the control of induced gene expression early in development, and in immediate early gene transcription. Here, we identify an SEC-like complex in Drosophila, as well as a distinct ELL-containing complex that lacks P-TEFb and other components of SEC named the "little elongation complex" (LEC). LEC subunits are highly enriched at RNA Pol II-transcribed small nuclear RNA (snRNA) genes, and the loss of LEC results in decreased snRNA expression in both flies and mammals. The specialization of the SEC and LEC complexes for mRNA and snRNA-containing genes, respectively, suggests the presence of specific classes of elongation factors for each class of genes transcribed by RNA polymerase II.

Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC).

Transcriptional regulation of developmentally controlled genes is at the heart of differentiation and organogenesis. In this study, we performed global genomic analyses in murine embryonic stem (ES) cells and in human cells in response to activation signals. We identified an essential role for the ELL (eleven-nineteen lysine-rich leukemia gene)/P-TEFb (positive transcription elongation factor)-containing super elongation complex (SEC) in the regulation of gene expression, including several genes bearing paused RNA polymerase II (Pol II). Paused Pol II has been proposed to be associated with loci that respond rapidly to environmental stimuli. However, our studies in ES cells also identified a requirement for SEC at genes without paused Pol II, which also respond dynamically to differentiation signals. Our findings suggest that SEC is a major class of active P-TEFb-containing complexes required for transcriptional activation in response to environmental cues such as differentiation signals.

Cohesin proteins promote ribosomal RNA production and protein translation in yeast and human cells.

Cohesin is a protein complex known for its essential role in chromosome segregation. However, cohesin and associated factors have additional functions in transcription, DNA damage repair, and chromosome condensation. The human cohesinopathy diseases are thought to stem not from defects in chromosome segregation but from gene expression. The role of cohesin in gene expression is not well understood. We used budding yeast strains bearing mutations analogous to the human cohesinopathy disease alleles under control of their native promoter to study gene expression. These mutations do not significantly affect chromosome segregation. Transcriptional profiling reveals that many targets of the transcriptional activator Gcn4 are induced in the eco1-W216G mutant background. The upregulation of Gcn4 was observed in many cohesin mutants, and this observation suggested protein translation was reduced. We demonstrate that the cohesinopathy mutations eco1-W216G and smc1-Q843Δ are associated with defects in ribosome biogenesis and a reduction in the actively translating fraction of ribosomes, eiF2α-phosphorylation, and (35)S-methionine incorporation, all of which indicate a deficit in protein translation. Metabolic labeling shows that the eco1-W216G and smc1-Q843Δ mutants produce less ribosomal RNA, which is expected to constrain ribosome biogenesis. Further analysis shows that the production of rRNA from an individual repeat is reduced while copy number remains unchanged. Similar defects in rRNA production and protein translation are observed in a human Roberts syndrome cell line. In addition, cohesion is defective specifically at the rDNA locus in the eco1-W216G mutant, as has been previously reported for Roberts syndrome. Collectively, our data suggest that cohesin proteins normally facilitate production of ribosomal RNA and protein translation, and this is one way they can influence gene expression. Reduced translational capacity could contribute to the human cohesinopathies.

Making goals count: A theory-informed approach to on-shift learning goals.

Supervisors often ask emergency medicine trainees for their learning goals at the start of a clinical shift, though they may do so without considering the reasons for this practice. Recognizing the underlying rationale for voicing on-shift learning goals and proactively considering solutions for some of the associated challenges can help learners and supervisors employ this practice to its full potential. Goal articulation is rooted in educational principles such as self-regulated learning, targeted performance feedback, and collaborative relationships between learner and supervisor. Despite the potential for on-shift learning goals to augment learning, there are numerous barriers that make it challenging for learners and supervisors alike to create or follow up on meaningful goals. Learner-related challenges include uncertainty about how to develop goals within an unpredictable clinical environment and creating goals too narrow or broad in scope. Supervisor-related challenges include difficulties integrating direct observation into the clinical workflow and a desire to avoid negative feedback. The learning environment also presents inherent challenges, such as lack of longitudinal supervisor-learner relationships, time constraints, space limitations, and incentives for learners to conceal their knowledge gaps. The authors discuss these challenges to effective on-shift learning goals and propose solutions that target the learner's approach, the supervisor's approach, and the learning environment itself.

Case Report: Differential Diagnosis of Lower Extremity Weakness in a Young Male - Consider Foix Alajouanine Syndrome.

INTRODUCTION: There is a limited list of emergent spinal cord pathology that must be considered in patients with focal neurological deficits in the emergency department. Identification of these conditions requires a detailed history and neurological exam and may also require advanced testing and imaging. CASE REPORT: Here we present the case of a patient with a rare arteriovenous malformation of the spinal cord vessels causing congestive myelopathy (Foix-Alajouanine syndrome) that presented as a clinical mimic of spinal cord compression. CONCLUSION: Emergency physicians should be aware of Foix-Alajouanine syndrome, as its workup and management differ from more common pathologies that may present similarly.

Genomic and biochemical approaches in the discovery of mechanisms for selective neuronal vulnerability to oxidative stress.

BACKGROUND: Oxidative stress (OS) is an important factor in brain aging and neurodegenerative diseases. Certain neurons in different brain regions exhibit selective vulnerability to OS. Currently little is known about the underlying mechanisms of this selective neuronal vulnerability. The purpose of this study was to identify endogenous factors that predispose vulnerable neurons to OS by employing genomic and biochemical approaches. RESULTS: In this report, using in vitro neuronal cultures, ex vivo organotypic brain slice cultures and acute brain slice preparations, we established that cerebellar granule (CbG) and hippocampal CA1 neurons were significantly more sensitive to OS (induced by paraquat) than cerebral cortical and hippocampal CA3 neurons. To probe for intrinsic differences between in vivo vulnerable (CA1 and CbG) and resistant (CA3 and cerebral cortex) neurons under basal conditions, these neurons were collected by laser capture microdissection from freshly excised brain sections (no OS treatment), and then subjected to oligonucleotide microarray analysis. GeneChip-based transcriptomic analyses revealed that vulnerable neurons had higher expression of genes related to stress and immune response, and lower expression of energy generation and signal transduction genes in comparison with resistant neurons. Subsequent targeted biochemical analyses confirmed the lower energy levels (in the form of ATP) in primary CbG neurons compared with cortical neurons. CONCLUSION: Low energy reserves and high intrinsic stress levels are two underlying factors for neuronal selective vulnerability to OS. These mechanisms can be targeted in the future for the protection of vulnerable neurons.

Man With Bilateral Leg Swelling.

A 52-year-old man without known medical history presented with painful, progressive, bilateral lower extremity edema over a two-week period. An abdominal exam noted a firm left upper quadrant mass. Emergency department (ED) point-of-care ultrasound (POCUS) revealed a hyperechoic, heterogeneous structure in the inferior vena cava that was determined to represent a tumor thrombus extending from a primary renal cell carcinoma. This case demonstrates how POCUS was valuable in rapidly diagnosing this rare cause of lower extremity edema and its usefulness in directing the initial ED management of this patient.

Sequelae of Index Complications following Inpatient Head and Neck Surgery: Characterizing Secondary Complications.

Objective To characterize patterns of secondary complications after inpatient head and neck surgery. Study Design Retrospective cohort study. Setting National Surgical Quality Improvement Program (2005-2015). Subjects and Methods We identified 18,584 patients who underwent inpatient otolaryngologic surgery. Four index complications were studied: pneumonia, bleeding or transfusion event (BTE), deep/organ space surgical site infection (SSI), and myocardial infarction (MI). Each patient with an index complication was matched to a control patient based on propensity for the index event and event-free days. Rates of 30-day secondary complications and mortality were compared. Results Index pneumonia (n = 254) was associated with several complications, including reintubation (odds ratio [OR], 11.7; 95% confidence interval [CI], 5.2-26.4), sepsis (OR, 8.8; 95% CI, 4.5-17.2), and death (OR, 5.3; 95% CI, 1.9-14.9). Index MI (n = 50) was associated with increased odds of reintubation (OR, 17.2; 95% CI, 3.5-84.1), ventilatory failure (OR, 5.8; 95% CI, 1.8-19.1), and death (OR, 24.8; 95% CI, 2.9-211.4). Index deep/organ space SSI (n = 271) was associated with dehiscence (OR, 7.2; 95% CI, 3.6-14.2) and sepsis (OR, 38.3; 95% CI, 11.6-126.4). Index BTE (n = 1009) increased the odds of cardiac arrest (OR, 3.9; 95% CI, 1.8-8.5) and death (OR, 2.9; 95% CI, 1.6-5.1). Conclusions Our study is the first to quantify the effect of index complications on the risk of specific secondary complications following inpatient head and neck surgery. These associations may be used to identify patients most at risk postoperatively and target specific interventions aimed to prevent or interrupt further complications.

Minor Salivary Gland Carcinoma of the Oropharynx: A Population-Based Analysis of 1426 Patients.

Objective We sought to describe the patient, tumor, and survival characteristics of minor salivary gland carcinoma (MSGC) of the oropharynx using a large, population-based database. Study Design Cross-sectional analysis of the National Cancer Institute's SEER database (Surveillance, Epidemiology. and End Results). Subjects and Methods We reviewed the SEER database for all cases of MSGC of the oropharynx from 1988 to 2013. Relevant demographic, clinicopathologic, and survival variables were extracted and analyzed. Cox multivariate regression was performed to identify prognostic factors. Results We identified 1426 cases of MSGC of the oropharynx (mean age, 58 years; 51% female). The soft palate (39.2%) and base of tongue (38.6%) were the most commonly involved sites. The most common histologic subtypes were mucoepidermoid carcinoma (32.1%), adenocarcinoma (25.9%), and adenoid cystic carcinoma (23.3%). Five- and 10-year rates of disease-specific survival were 75.1% and 61.6%, respectively. Independent prognostic factors included tumor grade, T stage, N stage, and age >70 years. Conclusions This study represents the largest multivariate survival analysis of MSGC of the oropharynx to date. Independent prognosticators include tumor grade, T stage, N stage, and age.

Mimecan/osteoglycin-deficient mice have collagen fibril abnormalities.

PURPOSE: To study the role of mimecan, a member of the small leucine-rich proteoglycans (SLRPs) gene family and one of the major components of the cornea and other connective tissues, mice that lack a functional mimecan gene were generated and characterized. METHODS: Mimecan-deficient mice were generated by gene-targeting using standard techniques. Mice were genotyped by Southern blot analysis. The absence of mimecan transcripts was confirmed by Northern blot analysis. Corneal clarity was examined by slit lamp biomicroscopy. The strength of the skin was evaluated using a biomechanical skin fragility test. Collagen morphology in cornea and skin preparations from mimecan-null and control wild-type mice was analyzed by transmission electron microscopy. The diameter of collagen fibrils in these tissues was determined by morphometric analysis. RESULTS: Mice lacking mimecan appear to develop normally, are viable and fertile. In a controlled laboratory environment they do not display an evident pathological phenotype compared to wild type mice. Examination of corneal clarity and measurements of corneal thickness show no significant changes in the cornea. However, a skin fragility test revealed a moderate reduction in the tensile strength of skin from mutant mice. Ultrastructural analyses show, on average, thicker collagen fibrils in both corneal and skin preparations from mimecan-null mice. Collagen fibrils from the cornea of mutant mice show an average diameter of 31.84+/-0.322 nm, versus 22.40+/-0.296 nm in their wild type litter-mates. The most pronounced increase in collagen fibril diameter was found in the skin of mimecan-null mice, who demonstrated an average diameter of 130.33+/-1.769 nm, versus 78.82+/-1.157 nm in the wild type mice. In addition, size variability and altered collagen morphology was detected in dorsal and tail skin preparations from the mutant mice. CONCLUSIONS: The results of the present study demonstrate that mimecan, similar to other members of the SLRP gene family, has a role in regulating collagen fibrillogenesis in vivo. Further studies, such as functional challenges, an evaluation of potential compensation by other proteins (including members of the SLRP family), and generation of double-knockouts will be necessary to fully uncover physiological functions of mimecan in mice.

The super elongation complex family of RNA polymerase II elongation factors: gene target specificity and transcriptional output.

The elongation stage of transcription is highly regulated in metazoans. We previously purified the AFF1- and AFF4-containing super elongation complex (SEC) as a major regulator of development and cancer pathogenesis. Here, we report the biochemical isolation of SEC-like 2 (SEC-L2) and SEC-like 3 (SEC-L3) containing AFF2 and AFF3 in association with P-TEFb, ENL/MLLT1, and AF9/MLLT3. The SEC family members demonstrate high levels of polymerase II (Pol II) C-terminal domain kinase activity; however, only SEC is required for the proper induction of the HSP70 gene upon stress. Genome-wide mRNA-Seq analyses demonstrated that SEC-L2 and SEC-L3 control the expression of different subsets of genes, while AFF4/SEC plays a more dominant role in rapid transcriptional induction in cells. MYC is one of the direct targets of AFF4/SEC, and SEC recruitment to the MYC gene regulates its expression in different cancer cells, including those in acute myeloid or lymphoid leukemia. These findings suggest that AFF4/SEC could be a potential therapeutic target for the treatment of leukemia or other cancers associated with MYC overexpression.

Polycomb repressive complex 2-dependent and -independent functions of Jarid2 in transcriptional regulation in Drosophila.

Jarid2 was recently identified as an important component of the mammalian Polycomb repressive complex 2 (PRC2), where it has a major effect on PRC2 recruitment in mouse embryonic stem cells. Although Jarid2 is conserved in Drosophila, it has not previously been implicated in Polycomb (Pc) regulation. Therefore, we purified Drosophila Jarid2 and its associated proteins and found that Jarid2 associates with all of the known canonical PRC2 components, demonstrating a conserved physical interaction with PRC2 in flies and mammals. Furthermore, in vivo studies with Jarid2 mutants in flies demonstrate that among several histone modifications tested, only methylation of histone 3 at K27 (H3K27), the mark implemented by PRC2, was affected. Genome-wide profiling of Jarid2, Su(z)12 (Suppressor of zeste 12), and H3K27me3 occupancy by chromatin immunoprecipitation with sequencing (ChIP-seq) indicates that Jarid2 and Su(z)12 have very similar distribution patterns on chromatin. However, Jarid2 and Su(z)12 occupancy levels at some genes are significantly different, with Jarid2 being present at relatively low levels at many Pc response elements (PREs) of certain Homeobox (Hox) genes, providing a rationale for why Jarid2 was never identified in Pc screens. Gene expression analyses show that Jarid2 and E(z) (Enhancer of zeste, a canonical PRC2 component) are not only required for transcriptional repression but might also function in active transcription. Identification of Jarid2 as a conserved PRC2 interactor in flies provides an opportunity to begin to probe some of its novel functions in Drosophila development.

Bioinformatics process management: information flow via a computational journal.

This paper presents the Bioinformatics Computational Journal (BCJ), a framework for conducting and managing computational experiments in bioinformatics and computational biology. These experiments often involve series of computations, data searches, filters, and annotations which can benefit from a structured environment. Systems to manage computational experiments exist, ranging from libraries with standard data models to elaborate schemes to chain together input and output between applications. Yet, although such frameworks are available, their use is not widespread-ad hoc scripts are often required to bind applications together. The BCJ explores another solution to this problem through a computer based environment suitable for on-site use, which builds on the traditional laboratory notebook paradigm. It provides an intuitive, extensible paradigm designed for expressive composition of applications. Extensive features facilitate sharing data, computational methods, and entire experiments. By focusing on the bioinformatics and computational biology domain, the scope of the computational framework was narrowed, permitting us to implement a capable set of features for this domain. This report discusses the features determined critical by our system and other projects, along with design issues. We illustrate the use of our implementation of the BCJ on two domain-specific examples.