Measurements of All-Particle Energy Spectrum and Mean Logarithmic Mass of Cosmic Rays from 0.3 to 30 PeV with LHAASO-KM2A

We present the measurements of all-particle energy spectrum and mean logarithmic mass of cosmic rays in the energy range of 0.3-30 PeV using data collected from LHAASO-KM2A between September 2021 and December 2022, which is based on a nearly composition-independent energy reconstruction method, achieving unprecedented accuracy. Our analysis reveals the position of the knee at 3.67±0.05±0.15  PeV. Below the knee, the spectral index is found to be -2.7413±0.0004±0.0050, while above the knee, it is -3.128±0.005±0.027, with the sharpness of the transition measured with a statistical error of 2%. The mean logarithmic mass of cosmic rays is almost heavier than helium in the whole measured energy range. It decreases from 1.7 at 0.3 PeV to 1.3 at 3 PeV, representing a 24% decline following a power law with an index of -0.1200±0.0003±0.0341. This is equivalent to an increase in abundance of light components. Above the knee, the mean logarithmic mass exhibits a power law trend towards heavier components, which is reversal to the behavior observed in the all-particle energy spectrum. Additionally, the knee position and the change in power-law index are approximately the same. These findings suggest that the knee observed in the all-particle spectrum corresponds to the knee of the light component, rather than the medium-heavy components.

Measurement of Ultra-High-Energy Diffuse Gamma-Ray Emission of the Galactic Plane from 10 TeV to 1 PeV with LHAASO-KM2A

The diffuse Galactic γ-ray emission, mainly produced via interactions between cosmic rays and the interstellar medium and/or radiation field, is a very important probe of the distribution, propagation, and interaction of cosmic rays in the Milky Way. In this Letter, we report the measurements of diffuse γ rays from the Galactic plane between 10 TeV and 1 PeV energies, with the square kilometer array of the Large High Altitude Air Shower Observatory (LHAASO). Diffuse emissions from the inner (15°10  TeV). The energy spectrum in the inner Galaxy regions can be described by a power-law function with an index of -2.99±0.04, which is different from the curved spectrum as expected from hadronic interactions between locally measured cosmic rays and the line-of-sight integrated gas content. Furthermore, the measured flux is higher by a factor of ∼3 than the prediction. A similar spectrum with an index of -2.99±0.07 is found in the outer Galaxy region, and the absolute flux for 10≲E≲60  TeV is again higher than the prediction for hadronic cosmic ray interactions. The latitude distributions of the diffuse emission are consistent with the gas distribution, while the longitude distributions show clear deviation from the gas distribution. The LHAASO measurements imply that either additional emission sources exist or cosmic ray intensities have spatial variations.

Sex and Race Differences in Cardiac Sarcoidosis Presentation, Treatment and Outcomes

BACKGROUND

Although sex- and race-based patterns have been described in the extracardiac organ involvement of sarcoidosis, cardiac sarcoidosis (CS)-specific studies are lacking.

METHODS

We studied CS presentation, treatment and outcomes based on sex and race in a tertiary-center cohort. Multivariable adjusted Cox proportional hazards and survival analyses were performed for primary composite outcomes (left ventricular assist device, heart transplantation, all-cause death) and for secondary outcomes (ventricular arrhythmia and all-cause death.

RESULTS

We identified 252 patients with CS (108 female, 109 Black). At presentation with CS, females vs males (P = 0.001) and Black vs White individuals (P = 0.001) more commonly had symptomatic heart failure (HF), with HF most common in Black females (ANOVA P < 0.001). Treatment differences included more corticosteroid use (90% vs 79%; P = 0.020), higher 1-year prednisone dosage (13 vs 10 mg; P = 0.003) and less frequent early steroid-sparing agent use in males (29% vs 40%; P = 0.05). Black participants more frequently received a steroid-sparing agent (75% vs 60%; P = 0.023). Composite outcome-free survival did not differ by sex or race. Male sex had an adjusted hazard ratio of 2.34 (95% CI 1.13, 4.80; P = 0.021) for ventricular arrhythmia.

CONCLUSION

CS course may differ by sex and race and may contribute to distinct clinical CS phenotypes.

Considerations and clinical management of infections in sarcoidosis

PURPOSE OF REVIEW

To summarize data from recent reports about risks and outcomes of the infections most often reported in patients with sarcoidosis.

RECENT FINDINGS

Rates of fungal infections and other severe infections are higher in patients with sarcoidosis compared to controls. Immunosuppression further increases the risk for an infection requiring hospitalization. In contrast, outcomes of coronavirus disease 2019 (COVID-19) are not worse unless lung impairment or other comorbidities are present.

SUMMARY

Tuberculosis, fungal infections, and other severe infections requiring hospital admission are, fortunately, relatively rare in patients with sarcoidosis who live in nonendemic regions. However, ongoing vigilance is required when the course of sarcoidosis is atypical or inexplicably progressive, as costs are high when these infections are missed. In contrast, COVID-19 and other respiratory viral illnesses are common, including among patients with sarcoidosis. When organ impairment is minimal, an underlying diagnosis of sarcoidosis does not appear to increase the risk of severe COVID-19, but patients may have higher risks due to comorbidities, which are important factors to address in routine sarcoidosis care. The burden from respiratory viral events, including impacts on quality of life and life functionality including work capacity, is unknown and is important to measure.

A tera-electron volt afterglow from a narrow jet in an extremely bright gamma-ray burst

Some gamma-ray bursts (GRBs) have a tera-electron volt (TeV) afterglow, but the early onset of this has not been observed. We report observations with the Large High Altitude Air Shower Observatory of the bright GRB 221009A, which serendipitously occurred within the instrument field of view. More than 64,000 photons >0.2 TeV were detected within the first 3000 seconds. The TeV flux began several minutes after the GRB trigger, then rose to a peak about 10 seconds later. This was followed by a decay phase, which became more rapid ~650 seconds after the peak. We interpret the emission using a model of a relativistic jet with half-opening angle ~0.8°. This is consistent with the core of a structured jet and could explain the high isotropic energy of this GRB.

Standardization of flow cytometry and cell sorting to enable a transcriptomic analysis in a multi-site sarcoidosis study

The contribution and regulation of various CD4+ T cell lineages that occur with remitting vs progressive courses in sarcoidosis are poorly understood. We developed a multiparameter flow cytometry panel to sort these CD4+ T cell lineages followed by measurement of their functional potential using RNA-sequencing analysis at six-month intervals across multiple study sites. To obtain good quality RNA for sequencing, we relied on chemokine receptor expression to identify and sort lineages. To minimize gene expression changes induced by perturbations of T cells and avoid protein denaturation caused by freeze/thaw cycles, we optimized our protocols using freshly isolated samples at each study site. To accomplish this study, we had to overcome significant standardization challenges across multiple sites. Here, we detail standardization considerations for cell processing, flow staining, data acquisition, sorting parameters, and RNA quality control analysis that were performed as part of the NIH-sponsored, multi-center study, BRonchoscopy at Initial sarcoidosis diagnosis Targeting longitudinal Endpoints (BRITE). After several rounds of iterative optimization, we identified the following aspects as critical for successful standardization: 1) alignment of PMT voltages across sites using CS&T/rainbow bead technology; 2) a single template created in the cytometer program that was used by all sites to gate cell populations during data acquisition and cell sorting; 3) use of standardized lyophilized flow cytometry staining cocktails to reduce technical error during processing; 4) development and implementation of a standardized Manual of Procedures. After standardization of cell sorting, we were able to determine the minimum number of sorted cells necessary for next generation sequencing through analysis of RNA quality and quantity from sorted T cell populations. Overall, we found that implementing a multi-parameter cell sorting with RNA-seq analysis clinical study across multiple study sites requires iteratively tested standardized procedures to ensure comparable and high-quality results.

Heterogeneity of Lung Function Phenotypes in Sarcoidosis: Role of Race and Sex Differences

Rationale: Historically, sarcoidosis was described as a restrictive lung disease, but several alternative phenotypes of pulmonary function have been observed. Pulmonary function phenotypes in sarcoidosis may represent different clinical and/or molecular phenotypes. Objectives: To characterize the prevalence of different pulmonary function phenotypes in a large and diverse sarcoidosis cohort from a tertiary care referral center. Methods: We identified individuals seen between 2005-2015 with a confirmed diagnosis of sarcoidosis. Data were collected from the first pulmonary function test (PFT) performed at our institution which included spirometry and diffusing capacity of the lung for carbon monoxide (DlCO). Demographics and clinical data were collected. Chi-squared analyses and multiple linear regressions were done to assess statistical differences and associations. Global Lung Function Initiative equations were used to calculate percent predicted measurements for spirometry and DlCO. Results: Of 602 individuals with sarcoidosis, 93% (562) had pulmonary involvement, 64% (385) were female, and 57% (341) were Black. Of those with pulmonary involvement, 56% had abnormal pulmonary function. Lung function impairment phenotypes included: 47% restriction, 22% obstruction, 15% isolated reduction in DlCO, and 16% combined obstructive restrictive phenotype. Restriction was the most common PFT phenotype among Black individuals (41%), while no lung impairment was most common among White individuals (66%) (P < 0.001). Males more frequently had obstruction (19%) compared with females (9%) P = 0.001, and females had more restriction (30%) compared with males (21%) P = 0.031. Conclusions: Among individuals with sarcoidosis and pulmonary function impairment, less than half demonstrated a restrictive phenotype. There were significant differences in pulmonary function phenotypes by race and sex.

Constraints on Heavy Decaying Dark Matter from 570 Days of LHAASO Observations

The kilometer square array (KM2A) of the large high altitude air shower observatory (LHAASO) aims at surveying the northern γ-ray sky at energies above 10 TeV with unprecedented sensitivity. γ-ray observations have long been one of the most powerful tools for dark matter searches, as, e.g., high-energy γ rays could be produced by the decays of heavy dark matter particles. In this Letter, we present the first dark matter analysis with LHAASO-KM2A, using the first 340 days of data from 1/2-KM2A and 230 days of data from 3/4-KM2A. Several regions of interest are used to search for a signal and account for the residual cosmic-ray background after γ/hadron separation. We find no excess of dark matter signals, and thus place some of the strongest γ-ray constraints on the lifetime of heavy dark matter particles with mass between 10^{5} and 10^{9}  GeV. Our results with LHAASO are robust, and have important implications for dark matter interpretations of the diffuse astrophysical high-energy neutrino emission.

Prospective, multi-site study of patient outcomes after implementation of the TREWS machine learning-based early warning system for sepsis

Early recognition and treatment of sepsis are linked to improved patient outcomes. Machine learning-based early warning systems may reduce the time to recognition, but few systems have undergone clinical evaluation. In this prospective, multi-site cohort study, we examined the association between patient outcomes and provider interaction with a deployed sepsis alert system called the Targeted Real-time Early Warning System (TREWS). During the study, 590,736 patients were monitored by TREWS across five hospitals. We focused our analysis on 6,877 patients with sepsis who were identified by the alert before initiation of antibiotic therapy. Adjusting for patient presentation and severity, patients in this group whose alert was confirmed by a provider within 3 h of the alert had a reduced in-hospital mortality rate (3.3%, confidence interval (CI) 1.7, 5.1%, adjusted absolute reduction, and 18.7%, CI 9.4, 27.0%, adjusted relative reduction), organ failure and length of stay compared with patients whose alert was not confirmed by a provider within 3 h. Improvements in mortality rate (4.5%, CI 0.8, 8.3%, adjusted absolute reduction) and organ failure were larger among those patients who were additionally flagged as high risk. Our findings indicate that early warning systems have the potential to identify sepsis patients early and improve patient outcomes and that sepsis patients who would benefit the most from early treatment can be identified and prioritized at the time of the alert.

Effect of Corticosteroids on Left Ventricular Function in Patients With Cardiac Sarcoidosis

Cardiac sarcoidosis (CS) is an important cause of cardiomyopathy. The trajectory of left ventricular ejection fraction (LVEF) in patients with CS undergoing treatment remains unclear. Patients with CS who were treated with corticosteroids and who underwent transthoracic echocardiography were studied. Baseline characteristics, treatment, echocardiographic data (including baseline to follow-up change in LVEF), and outcomes were retrospectively evaluated. Among 100 patients, 55 had baseline reduced LVEF (<50%), and 45 had preserved LVEF (≥50%). At follow-up, 82% of patients demonstrated stable or improved LVEF. Change in LVEF was significantly higher in the baseline reduced than in the preserved LVEF group (5% [interquartile range 0 to 15] vs 0% [interquartile range -10% to 5%], p = 0.001). There was no difference in corticosteroid exposure or use of heart failure guideline-directed medical therapy between patients who did experience improvement in LVEF and those who did not experience improvement in LVEF. On multivariable analysis, baseline reduced LVEF (Odds ratio 54.89, 95% confidence interval 3.84 to 785.09, p = 0.003) and complete heart block (Odds ratio 28.88, 95% confidence interval 2.17 to 383.74, p = 0.011) at presentation were significantly associated with reduced LVEF after treatment. In conclusion, most patients with CS treated with corticosteroids maintain or improve LV systolic function. Cardiac characteristics at presentation impact prognosis in CS, despite treatment.

Risk Factors for Infection and Health Impacts of the Coronavirus Disease 2019 (COVID-19) Pandemic in People With Autoimmune Diseases

BACKGROUND

People with autoimmune or inflammatory conditions taking immunomodulatory/suppressive medications may have higher risk of novel coronavirus disease 2019 (COVID-19). Chronic disease care has also changed for many patients, with uncertain downstream consequences.

METHODS

We included participants with autoimmune or inflammatory conditions followed by specialists at Johns Hopkins. Participants completed periodic surveys querying comorbidities, disease-modifying medications, exposures, COVID-19 testing and outcomes, social behaviors, and disruptions to healthcare. We assessed whether COVID-19 risk is higher among those on immunomodulating or suppressive agents and characterized pandemic-associated changes to care and mental health.

RESULTS

In total, 265 (5.6%) developed COVID-19 over 9 months of follow-up (April-December 2020). Patient characteristics (age, race, comorbidity, medications) were associated with differences in social distancing behaviors during the pandemic. Glucocorticoid exposure was associated with higher odds of COVID-19 in models incorporating behavior and other potential confounders (odds ratio [OR]: 1.43; 95% confidence interval [CI]: 1.08, 1.89). Other medication classes were not associated with COVID-19 risk. Diabetes (OR: 1.72; 95% CI: 1.08, 2.73), cardiovascular disease (OR: 1.68; 95% CI: 1.24, 2.28), and kidney disease (OR: 1.76; 95% CI: 1.04, 2.97) were associated with higher odds of COVID-19. Of the 2156 reporting pre-pandemic utilization of infusion, mental health or rehabilitative services, 975 (45.2%) reported disruptions therein, which disproportionately affected individuals experiencing changes to employment or income.

CONCLUSIONS

Glucocorticoid exposure may increase risk of COVID-19 in people with autoimmune or inflammatory conditions. Disruption to healthcare and related services was common. Those with pandemic-related reduced income may be most vulnerable to care disruptions.

Exploring Lorentz Invariance Violation from Ultrahigh-Energy γ Rays Observed by LHAASO

Recently, the LHAASO Collaboration published the detection of 12 ultrahigh-energy γ-ray sources above 100 TeV, with the highest energy photon reaching 1.4 PeV. The first detection of PeV γ rays from astrophysical sources may provide a very sensitive probe of the effect of the Lorentz invariance violation (LIV), which results in decay of high-energy γ rays in the superluminal scenario and hence a sharp cutoff of the energy spectrum. Two highest energy sources are studied in this work. No signature of the existence of the LIV is found in their energy spectra, and the lower limits on the LIV energy scale are derived. Our results show that the first-order LIV energy scale should be higher than about 10^{5} times the Planck scale M_{Pl} and that the second-order LIV scale is >10^{-3}M_{Pl}. Both limits improve by at least one order of magnitude the previous results.

Transcriptomics of bronchoalveolar lavage cells identifies new molecular endotypes of sarcoidosis

BACKGROUND

Sarcoidosis is a multisystem granulomatous disease of unknown origin with a variable and often unpredictable course and pattern of organ involvement. In this study we sought to identify specific bronchoalveolar lavage (BAL) cell gene expression patterns indicative of distinct disease phenotypic traits.

METHODS

RNA sequencing by Ion Torrent Proton was performed on BAL cells obtained from 215 well-characterised patients with pulmonary sarcoidosis enrolled in the multicentre Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) study. Weighted gene co-expression network analysis and nonparametric statistics were used to analyse genome-wide BAL transcriptome. Validation of results was performed using a microarray expression dataset of an independent sarcoidosis cohort (Freiburg, Germany; n=50).

RESULTS

Our supervised analysis found associations between distinct transcriptional programmes and major pulmonary phenotypic manifestations of sarcoidosis including T-helper type 1 (Th1) and Th17 pathways associated with hilar lymphadenopathy, transforming growth factor-β1 (TGFB1) and mechanistic target of rapamycin (MTOR) signalling with parenchymal involvement, and interleukin (IL)-7 and IL-2 with airway involvement. Our unsupervised analysis revealed gene modules that uncovered four potential sarcoidosis endotypes including hilar lymphadenopathy with increased acute T-cell immune response; extraocular organ involvement with PI3K activation pathways; chronic and multiorgan disease with increased immune response pathways; and multiorgan involvement, with increased IL-1 and IL-18 immune and inflammatory responses. We validated the occurrence of these endotypes using gene expression, pulmonary function tests and cell differentials from Freiburg.

CONCLUSION

Taken together, our results identify BAL gene expression programmes that characterise major pulmonary sarcoidosis phenotypes and suggest the presence of distinct disease molecular endotypes.

Defining CD4 T helper and T regulatory cell endotypes of progressive and remitting pulmonary sarcoidosis (BRITE): protocol for a US-based, multicentre, longitudinal observational bronchoscopy study

INTRODUCTION

Sarcoidosis is a multiorgan granulomatous disorder thought to be triggered and influenced by gene-environment interactions. Sarcoidosis affects 45-300/100 000 individuals in the USA and has an increasing mortality rate. The greatest gap in knowledge about sarcoidosis pathobiology is a lack of understanding about the underlying immunological mechanisms driving progressive pulmonary disease. The objective of this study is to define the lung-specific and blood-specific longitudinal changes in the adaptive immune response and their relationship to progressive and non-progressive pulmonary outcomes in patients with recently diagnosed sarcoidosis.

METHODS AND ANALYSIS

The BRonchoscopy at Initial sarcoidosis diagnosis Targeting longitudinal Endpoints study is a US-based, NIH-sponsored longitudinal blood and bronchoscopy study. Enrolment will occur over four centres with a target sample size of 80 eligible participants within 18 months of tissue diagnosis. Participants will undergo six study visits over 18 months. In addition to serial measurement of lung function, symptom surveys and chest X-rays, participants will undergo collection of blood and two bronchoscopies with bronchoalveolar lavage separated by 6 months. Freshly processed samples will be stained and flow-sorted for isolation of CD4 +T helper (Th1, Th17.0 and Th17.1) and T regulatory cell immune populations, followed by next-generation RNA sequencing. We will construct bioinformatic tools using this gene expression to define sarcoidosis endotypes that associate with progressive and non-progressive pulmonary disease outcomes and validate the tools using an independent cohort.

ETHICS AND DISSEMINATION

The study protocol has been approved by the Institutional Review Boards at National Jewish Hospital (IRB# HS-3118), University of Iowa (IRB# 201801750), Johns Hopkins University (IRB# 00149513) and University of California, San Francisco (IRB# 17-23432). All participants will be required to provide written informed consent. Findings will be disseminated via journal publications, scientific conferences, patient advocacy group online content and social media platforms.

Sarcoidosis-Related Cardiomyopathy: Current Knowledge, Challenges, and Future Perspectives State-of-the-Art Review

The prevalence of sarcoidosis-related cardiomyopathy is increasing. Sarcoidosis impacts cardiac function through granulomatous infiltration of the heart, resulting in conduction disease, arrhythmia, and/or heart failure. The diagnosis of cardiac sarcoidosis (CS) can be challenging and requires clinician awareness as well as differentiation from overlapping diagnostic phenotypes, such as other forms of myocarditis and arrhythmogenic cardiomyopathy. Clinical manifestations, extracardiac involvement, histopathology, and advanced cardiac imaging can all lend support to a diagnosis of CS. The mainstay of therapy for CS is immunosuppression; however, no prospective clinical trials exist to guide management. Patients may progress to developing advanced heart failure or ventricular arrhythmia, for which ventricular assist device therapies or heart transplantation may be considered. The existing knowledge gaps in CS call for an interdisciplinary approach to both patient care and future investigation to improve mechanistic understanding and therapeutic strategies.

Peta-electron volt gamma-ray emission from the Crab Nebula

The Crab Nebula is a bright source of gamma rays powered by the Crab Pulsar's rotational energy through the formation and termination of a relativistic electron-positron wind. We report the detection of gamma rays from this source with energies from 5 × 10^-4 to 1.1 peta-electron volts with a spectrum showing gradual steepening over three energy decades. The ultrahigh-energy photons imply the presence of a peta-electron volt electron accelerator (a pevatron) in the nebula, with an acceleration rate exceeding 15% of the theoretical limit. We constrain the pevatron's size between 0.025 and 0.1 parsecs and the magnetic field to ≈110 microgauss. The production rate of peta-electron volt electrons, 2.5 × 10³⁶ ergs per second, constitutes 0.5% of the pulsar spin-down luminosity, although we cannot exclude a contribution of peta-electron volt protons to the production of the highest-energy gamma rays.

Management of Cardiac Sarcoidosis Using Mycophenolate Mofetil as a Steroid-Sparing Agent

BACKGROUND

Cardiac sarcoidosis (CS) is a major cause of morbidity and mortality in patients with systemic sarcoidosis. Steroid-sparing agents are increasingly used, despite a lack of randomized trials or published guidelines to direct treatment.

METHODS AND RESULTS

This retrospective study included 77 patients with CS treated with prednisone monotherapy (n = 32) or a combination with mycophenolate mofetil (n = 45) between 2003 and 2018. Baseline characteristics and clinical outcomes were evaluated. The mean patient age was 53 ± 11 years at CS diagnosis, 66.2% were male, and 35.1% were Black. The total exposure to maximum prednisone dose (initial prednisone dose × days at dose) was lower in the combination therapy group (1440 mg [interquartile range (IQR), 1200-2760 mg] vs 2710 mg [IQR, 1200-5080 mg]; P = .06). On ¹⁸F-fluorodeoxyglucose positron emission tomography scans, both groups demonstrated a significant decrease in the cardiac maximum standardized uptake value after treatment: a median decrease of 3.9 (IQR 2.7-9.0, P = .002) and 2.9 (IQR 0-5.0, P = .001) for prednisone monotherapy and combination therapy, respectively. Most patients experienced improvement or complete resolution in qualitative cardiac ¹⁸F-fluorodeoxyglucose uptake (92.3% and 70.4% for the prednisone and combination therapy groups, respectively). Mycophenolate mofetil was well tolerated.

CONCLUSIONS

Mycophenolate mofetil in combination with prednisone for the treatment of CS may minimize corticosteroid exposure and decrease cardiac inflammation without significant adverse effects.

Comparing Critical Care Admissions Among Urban Populations Before and During the COVID-19 Pandemic

In the context of the COVID-19 pandemic, reassessing intensive care unit (ICU) use by population should be a priority for hospitals planning for critical care resource allocation. In our study, we reviewed the impact of COVID-19 on a community hospital serving an urban region, comparing the sociodemographic distribution of ICU admissions before and during the pandemic. We executed a time-sensitive analysis to see if COVID-19 ICU admissions reflect the regional sociodemographic populations and ICU admission trends before the pandemic. Sociodemographic variables included sex, race, ethnicity, and age of adult patients (ages 18 years and older) admitted to the hospital's medical and cardiac ICUs, which were converted to COVID-19 ICUs. The time period selected was 18 months, which was then dichotomized into pre-COVID-19 admissions (December 1, 2018 to March 13, 2020) and COVID-19 ICU admissions (March 14 to May 31, 2020). Variables were compared using Fisher's exact tests and Wilcoxon tests when appropriate. During the 18-month period, 1,861 patients were admitted to the aforementioned ICUs. The mean age of the patients was 62.75 (SD 15.57), with the majority of these patients being male (52.23%), White (64.43%), and non-Hispanic/Latinx (95.75%). Differences were found in racial and ethnic distribution comparing pre-COVID-19 admissions to COVID-19 admissions. Compared with pre-COVID-19 ICU admissions, we found an increase in African American versus White admissions (P = .01) and an increase in Hispanic/Latinx versus non-Hispanic/Latinx admissions (P < .01), during the COVID-19 pandemic. During the first 3 months of admissions to COVID-19 ICUs, the number of admissions among Hispanic/Latinx and African American patients increased while the number of admissions among non-Hispanic/Latinx and White patient decreased, compared with the pre-COVID-19 period. These findings support development of strategies to enhance allocation of resources to bolster novel, equitable strategies to mitigate the incidence of COVID-19 in urban populations.

RISK FACTORS FOR INFECTION AND HEALTH IMPACTS OF THE COVID-19 PANDEMIC IN PEOPLE WITH AUTOIMMUNE DISEASES

Background

People with autoimmune or inflammatory conditions who take immunomodulatory/suppressive medications may have a higher risk of novel coronavirus disease 2019 (COVID-19). Chronic disease care has also changed for many patients, with uncertain downstream consequences.

Objective

Assess whether COVID-19 risk is higher among those on immunomodulating or suppressive agents and characterize pandemic-associated changes to care.

Design

Longitudinal registry study.

Participants

4666 individuals with autoimmune or inflammatory conditions followed by specialists in neurology, rheumatology, cardiology, pulmonology or gastroenterology at Johns Hopkins.

Measurements

Periodic surveys querying comorbidities, disease-modifying medications, exposures, COVID-19 testing and outcomes, social behaviors, and disruptions to healthcare.

Results

A total of 265 (5.6%) developed COVID-19 over 9 months of follow-up (April-December 2020). Patient characteristics (age, race, comorbidity, medication exposure) were associated with differences in social distancing behaviors during the pandemic. Glucocorticoid exposure was associated with higher odds of COVID-19 in multivariable models incorporating behavior and other potential confounders (OR: 1.43; 95%CI: 1.08, 1.89). Other medication classes were not associated with COVID-19 risk. Diabetes (OR: 1.72; 95%CI: 1.08, 2.73), cardiovascular disease (OR: 1.68; 95%CI: 1.24, 2.28), and chronic kidney disease (OR: 1.76; 95%CI: 1.04, 2.97) were each associated with higher odds of COVID-19. Pandemic-related disruption to care was common. Of the 2156 reporting pre-pandemic utilization of infusion, mental health or rehabilitative services, 975 (45.2%) reported disruptions. Individuals experiencing changes to employment or income were at highest odds of care disruption.

Limitations

Results may not be generalizable to all patients with autoimmune or inflammatory conditions. Information was self-reported.

Conclusions

Exposure to glucocorticoids may increase risk of COVID-19 in people with autoimmune or inflammatory conditions. Disruption to healthcare and related services was common. Those with pandemic-related reduced income may be most vulnerable to care disruptions.

Gene coexpression networks reveal novel molecular endotypes in alpha-1 antitrypsin deficiency

BACKGROUND

Alpha-1 antitrypsin deficiency (AATD) is a genetic condition that causes early onset pulmonary emphysema and airways obstruction. The complete mechanisms via which AATD causes lung disease are not fully understood. To improve our understanding of the pathogenesis of AATD, we investigated gene expression profiles of bronchoalveolar lavage (BAL) and peripheral blood mononuclear cells (PBMCs) in AATD individuals.

METHODS

We performed RNA-Seq on RNA extracted from matched BAL and PBMC samples isolated from 89 subjects enrolled in the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) study. Subjects were stratified by genotype and augmentation therapy. Supervised and unsupervised differential gene expression analyses were performed using Weighted Gene Co-expression Network Analysis (WGCNA) to identify gene profiles associated with subjects' clinical variables. The genes in the most significant WGCNA module were used to cluster AATD individuals. Gene validation was performed by NanoString nCounter Gene Expression Assay.

RESULT

We observed modest effects of AATD genotype and augmentation therapy on gene expression. When WGCNA was applied to BAL transcriptome, one gene module, ME31 (2312 genes), correlated with the highest number of clinical variables and was functionally enriched with numerous immune T-lymphocyte related pathways. This gene module identified two distinct clusters of AATD individuals with different disease severity and distinct PBMC gene expression patterns.

CONCLUSIONS

We successfully identified novel clusters of AATD individuals where severity correlated with increased immune response independent of individuals' genotype and augmentation therapy. These findings may suggest the presence of previously unrecognised disease endotypes in AATD that associate with T-lymphocyte immunity and disease severity.

Clinical and Imaging Response to Tumor Necrosis Factor Alpha Inhibitors in Treatment of Cardiac Sarcoidosis: A Multicenter Experience

BACKGROUND

Cardiac sarcoidosis (CS) is an increasingly recognized cause of cardiomyopathy; however, data on immunosuppressive strategies are limited. Treatment with tumor necrosis factor (TNF) alpha inhibitors is not well described; moreover, there may be heart failure-related safety concerns.

METHODS

Retrospective multicenter study of patients with CS treated with TNF alpha inhibitors. Baseline characteristics, treatments, and outcomes were adjudicated.

RESULTS

Thirty-eight patients with CS (mean age 49.9 years, 42% women, 53% African American) were treated with TNF alpha inhibitor (30 infliximab, 8 adalimumab). Prednisone dose decreased from time of TNF alpha inhibitor initiation (21.7 ± 17.5 mg) to 6 months (10.4 ± 6.1 mg, P = .001) and 12 months (7.3 ± 7.3 mg, P = .002) after treatment. On pre-TNF alpha inhibitor treatment positron emission tomography with 18-flourodoxyglucose (FDG-PET), 84% of patients had cardiac FDG uptake. After treatment, there was a significant decrease in number of segments involved (3.5 ± 3.8 to 1.0 ± 2.5, P = .008) and maximum standardized uptake value (3.59 ± 3.70 to 0.57 ± 1.60, P = .0005), with 73% of patients demonstrating complete resolution or improvement of cardiac FDG uptake. The left ventricular ejection fraction remained stable (45.0 ± 16.5% to 47.0 ± 15.0%, P = .10). Four patients required inpatient heart failure treatment, and 8 had infections; 2 required treatment cessation.

CONCLUSIONS

TNF alpha inhibitor treatment guided by FDG-PET imaging may minimize corticosteroid use and effectively reduce cardiac inflammation without significant adverse effect on cardiac function. However, infections were common, some of which were serious, and therefore patients require close monitoring for both infection and cardiac symptoms.

Implementation of a Protocol Using the 5-Item Brief Alcohol Withdrawal Scale for Treatment of Severe Alcohol Withdrawal in Intensive Care Units

BACKGROUND

There is variation in the treatment of patients with severe alcohol withdrawal and a need for effective protocols. The purpose of this study was to evaluate the implementation of a symptom-triggered benzodiazepine protocol using the 5-item Brief Alcohol Withdrawal Scale (BAWS) for treatment of alcohol withdrawal in intensive care units (ICUs).

METHODS

This retrospective study included admissions to ICUs of 2 hospitals over 6 months who had an alcohol withdrawal protocol ordered and experienced severe withdrawal. Records were reviewed to collect demographic data, benzodiazepine exposure, duration of treatment, and withdrawal severity.

RESULTS

The protocol was ordered and implemented in 279 admissions; 48 (17.9%) had severe withdrawal defined as a BAWS of 6 or more. The majority of the 48 patients were from the emergency department (79.2%); mean hospital length of stay was 11.2 days and mean ICU stay 6.6 days; 31.3% required mechanical ventilation. A little more than half were treated only with the protocol (53.2%); 25.0% received additional benzodiazepines, 20.8% dexmedetomidine, 10.4% propofol, 25.0% antipsychotics and 2.0% phenobarbital.

CONCLUSION

Among ICU patients treated for alcohol withdrawal with a symptom-triggered benzodiazepine protocol using a novel 5-item scale, most did not develop severe withdrawal, and of those who did, approximately half were treated with the protocol alone.

Clinical and MRI phenotypes of sarcoidosis-associated myelopathy

OBJECTIVE

To determine the characteristic clinical and spinal MRI phenotypes of sarcoidosis-associated myelopathy (SAM), we analyzed a large cohort of patients with this disorder.

METHODS

Patients diagnosed with SAM at a single center between 2000 and 2018 who met the established criteria for definite and probable neurosarcoidosis were included in a retrospective analysis to identify clinical profiles, CSF characteristics, and MRI lesion morphology.

RESULTS

Of 62 included patients, 33 (53%) were male, and 30 (48%) were African American. SAM was the first clinical presentation of sarcoidosis in 49 patients (79%). Temporal profile of symptom evolution was chronic in 81%, with sensory symptoms most frequently reported (87%). CSF studies showed pleocytosis in 79% and CSF-restricted oligoclonal bands in 23% of samples tested. Four discrete patterns of lesion morphology were identified on spine MRI: longitudinally extensive myelitis (n = 28, 45%), short tumefactive myelitis (n = 14, 23%), spinal meningitis/meningoradiculitis (n = 14, 23%), and anterior myelitis associated with areas of disc degeneration (n = 6, 10%). Postgadolinium enhancement was seen in all but 1 patient during the acute phase. The most frequent enhancement pattern was dorsal subpial enhancement (n = 40), followed by meningeal/radicular enhancement (n = 23) and ventral subpial enhancement (n = 12). In 26 cases (42%), enhancement occurred at locations with coexisting structural changes (e.g., spondylosis).

CONCLUSIONS

Recognition of the clinical features (chronically evolving myelopathy) and distinct MRI phenotypes (with enhancement in a subpial and/or meningeal pattern) seen in SAM can aid diagnosis of this disorder. Enhancement patterns suggest that SAM may have a predilection for areas of the spinal cord susceptible to mechanical stress.

Diagnosis and Detection of Sarcoidosis. An Official American Thoracic Society Clinical Practice Guideline

Background: The diagnosis of sarcoidosis is not standardized but is based on three major criteria: a compatible clinical presentation, finding nonnecrotizing granulomatous inflammation in one or more tissue samples, and the exclusion of alternative causes of granulomatous disease. There are no universally accepted measures to determine if each diagnostic criterion has been satisfied; therefore, the diagnosis of sarcoidosis is never fully secure.

Methods: Systematic reviews and, when appropriate, meta-analyses were performed to summarize the best available evidence. The evidence was appraised using the Grading of Recommendations, Assessment, Development, and Evaluation approach and then discussed by a multidisciplinary panel. Recommendations for or against various diagnostic tests were formulated and graded after the expert panel weighed desirable and undesirable consequences, certainty of estimates, feasibility, and acceptability.

Results: The clinical presentation, histopathology, and exclusion of alternative diagnoses were summarized. On the basis of the available evidence, the expert committee made 1 strong recommendation for baseline serum calcium testing, 13 conditional recommendations, and 1 best practice statement. All evidence was very low quality.

Conclusions: The panel used systematic reviews of the evidence to inform clinical recommendations in favor of or against various diagnostic tests in patients with suspected or known sarcoidosis. The evidence and recommendations should be revisited as new evidence becomes available.

Association of Medication Adherence and Clinical Outcomes in Sarcoidosis

BACKGROUND

Sarcoidosis, one of the most common interstitial lung diseases, has significant health disparities. Approximately 50% of individuals affected with sarcoidosis will undergo spontaneous remission, but those who do not undergo remission often require long-term or lifelong treatment to prevent disease progression. We sought to assess the association between medication adherence and clinical outcomes in sarcoidosis.

METHODS

Adult patients in the Johns Hopkins Sarcoidosis Clinic diagnosed with pulmonary sarcoidosis on treatment were eligible for enrollment. Questionnaires were administered to assess medication adherence, health-related quality of life (HRQoL), health-care utilization, and sociodemographic information. Clinical information was abstracted from medical charts including lung function, disease duration, comorbidities, and sarcoidosis organ involvement.

RESULTS

A total of 117 participants were enrolled (57% women; 55% black; median age, 57 years). Within the cohort, 66% of individuals reported at least one nonadherent behavior. Higher medication adherence was associated with better HRQoL (P < .05). There was no association between medication adherence and the odds of health-care utilization, FVC % predicted, FEV₁ % predicted, or diffusion capacity of the lungs for carbon monoxide % predicted. Black participants reported lower medication adherence than white participants (P < .05).

CONCLUSIONS

This is the first observational study of medication adherence in sarcoidosis. We found that higher medication adherence was associated with better HRQoL, with blacks more likely to report nonadherence. Medication adherence may be an important target to improve patient-reported outcomes and health disparities in sarcoidosis.

Design tools for MPRA experiments

Motivation

Genetic reporter assays are a convenient, relatively inexpensive method for studying the regulation of gene expression. Massively Parallel Reporter Assays (MPRA) are high-throughput functionalization assays that interrogate the transcriptional activity of many genetic variants at once using a library of synthetic barcoded constructs. Despite growing interest in this area, there are few computational tools to design and execute MPRA studies.

Results

We designed an online web-tool and R package that allows for interactive MPRA experimental design encompassing both power analysis and design of constructs. Our tool is tuned using data from real MPRA studies. Users can adjust experimental parameters to examine the predicted effect on assay power as well as upload VCFs for automated construct sequence generation.

Availability and implementation

The MPRA Design Tools web application is available here: https://andrewghazi.shinyapps.io/designmpra/, https://github.com/andrewGhazi/designMPRA and https://github.com/andrewGhazi/mpradesigntools.

Supplementary information

Supplementary data are available at Bioinformatics online.

A clinical survey of mosaic single nucleotide variants in disease-causing genes detected by exome sequencing

Background

Although mosaic variation has been known to cause disease for decades, high-throughput sequencing technologies with the analytical sensitivity to consistently detect variants at reduced allelic fractions have only recently emerged as routine clinical diagnostic tests. To date, few systematic analyses of mosaic variants detected by diagnostic exome sequencing for diverse clinical indications have been performed.

Methods

To investigate the frequency, type, allelic fraction, and phenotypic consequences of clinically relevant somatic mosaic single nucleotide variants (SNVs) and characteristics of the corresponding genes, we retrospectively queried reported mosaic variants from a cohort of ~ 12,000 samples submitted for clinical exome sequencing (ES) at Baylor Genetics.

Results

We found 120 mosaic variants involving 107 genes, including 80 mosaic SNVs in proband samples and 40 in parental/grandparental samples. Average mosaic alternate allele fraction (AAF) detected in autosomes and in X-linked disease genes in females was 18.2% compared with 34.8% in X-linked disease genes in males. Of these mosaic variants, 74 variants (61.7%) were classified as pathogenic or likely pathogenic and 46 (38.3%) as variants of uncertain significance. Mosaic variants occurred in disease genes associated with autosomal dominant (AD) or AD/autosomal recessive (AR) (67/120, 55.8%), X-linked (33/120, 27.5%), AD/somatic (10/120, 8.3%), and AR (8/120, 6.7%) inheritance. Of note, 1.7% (2/120) of variants were found in genes in which only somatic events have been described. Nine genes had recurrent mosaic events in unrelated individuals which accounted for 18.3% (22/120) of all detected mosaic variants in this study. The proband group was enriched for mosaicism affecting Ras signaling pathway genes.

Conclusions

In sum, an estimated 1.5% of all molecular diagnoses made in this cohort could be attributed to a mosaic variant detected in the proband, while parental mosaicism was identified in 0.3% of families analyzed. As ES design favors breadth over depth of coverage, this estimate of the prevalence of mosaic variants likely represents an underestimate of the total number of clinically relevant mosaic variants in our cohort.

Electronic supplementary material

The online version of this article (10.1186/s13073-019-0658-2) contains supplementary material, which is available to authorized users.

Functionalization of CD36 cardiovascular disease and expression associated variants by interdisciplinary high throughput analysis

CD36 is a platelet membrane glycoprotein whose engagement with oxidized low-density lipoprotein (oxLDL) results in platelet activation. The CD36 gene has been associated with platelet count, platelet volume, as well as lipid levels and CVD risk by genome-wide association studies. Platelet CD36 expression levels have been shown to be associated with both the platelet oxLDL response and an elevated risk of thrombo-embolism. Several genomic variants have been identified as associated with platelet CD36 levels, however none have been conclusively demonstrated to be causative. We screened 81 expression quantitative trait loci (eQTL) single nucleotide polymorphisms (SNPs) associated with platelet CD36 expression by a Massively Parallel Reporter Assay (MPRA) and analyzed the results with a novel Bayesian statistical method. Ten eQTLs located 13kb to 55kb upstream of the CD36 transcriptional start site of transcript ENST00000309881 and 49kb to 92kb upstream of transcript ENST00000447544, demonstrated significant transcription shifts between their minor and major allele in the MPRA assay. Of these, rs2366739 and rs1194196, separated by only 20bp, were confirmed by luciferase assay to alter transcriptional regulation. In addition, electromobility shift assays demonstrated differential DNA:protein complex formation between the two alleles of this locus. Furthermore, deletion of the genomic locus by CRISPR/Cas9 in K562 and Meg-01 cells results in upregulation of CD36 transcription. These data indicate that we have identified a variant that regulates expression of CD36, which in turn affects platelet function. To assess the clinical relevance of our findings we used the PhenoScanner tool, which aggregates large scale GWAS findings; the results reinforce the clinical relevance of our variants and the utility of the MPRA assay. The study demonstrates a generalizable paradigm for functional testing of genetic variants to inform mechanistic studies, support patient management and develop precision therapies.

Platelets are anucleate cells that are best known as regulators of vascular hemostasis and thrombosis but also play important roles in cancer, angiogenesis, and inflammation. CD36 is a platelet surface marker that can activate platelet in response to oxidized low density lipoprotein (oxLDL). CD36 has been associated with numerous cardiovascular traits in human including blood lipid levels, platelet count, and cardiovascular disease prevalence in human genetic studies. Human variability in platelet CD36 levels are associated with the platelet response to oxLDL. However, the genetic mechanisms responsible for the variability of CD36 levels are unknown. We examined 81 genetic variants associated with CD36 levels for functionality using a high-throughput assay. Of the ten variants that were identified in that assay, one doublet, rs2366739 and rs1194196, were confirmed using additional molecular and cellular assays. Deletion of the genomic region containing rs2366739 and rs1194196 resulted in overexpression of CD36 in a cell culture system. This finding indicates a control locus which can serve as a potential target in modulating CD36 expression and altering platelet function in cardiovascular disease.

Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2

DNA rearrangements resulting in human genome structural variants (SVs) are caused by diverse mutational mechanisms. We used long- and short-read sequencing technologies to investigate end products of de novo chromosome 17p11.2 rearrangements and query the molecular mechanisms underlying both recurrent and non-recurrent events. Evidence for an increased rate of clustered single-nucleotide variant (SNV) mutation in cis with non-recurrent rearrangements was found. Indel and SNV formation are associated with both copy-number gains and losses of 17p11.2, occur up to ∼1 Mb away from the breakpoint junctions, and favor C > G transversion substitutions; results suggest that single-stranded DNA is formed during the genesis of the SV and provide compelling support for a microhomology-mediated break-induced replication (MMBIR) mechanism for SV formation. Our data show an additional mutational burden of MMBIR consisting of hypermutation confined to the locus and manifesting as SNVs and indels predominantly within genes.

Electron affinities from gas chromatography electron capture detector and negative ion mass spectrometry responses and complementary methods

The use of the electron-capture detector, ECD, to measure molecular electron affinities and kinetic parameters for reactions of thermal electrons with molecules at atmospheric pressure separated by chromatography and the sensitive and selective quantitative analysis of certain classes molecules are reviewed. The evaluated ground state electron affinities of the main group elements and diatomic molecules from slightly positive, 0+, to 3.6 eV are summarized. The electron affinities of twenty-seven superoxide states determined from pulsed discharge ECD and other methods are used to calculate one dimensional potential energy curves in agreement with theory. Advances in literature searches have uncovered ECD data in dissertations and theses and in the Russian and Japanese literature. These data, unpublished radioactive and pulsed discharge ECD thermal data from the University of Houston laboratories are used to report and evaluate electron affinities. The accuracy and precision of ECD electron affinities of organic molecules are identified and tabulated so that they can be added to compilations. A procedure for calculating the temperature dependence of electron molecule reactions is presented using kinetic and thermodynamic data. These are used toselect the most appropriate equipment and conditions for ECD analyses and physical determinations.

Comment on: Negative ions, molecular electron affinity and orbital structure of cata-condensed polycyclic aromatic hydrocarbons by Rustem V. Khatymov, Mars V. Muftakhov and Pavel V. Shchukin

RATIONALE

The anion mass spectral lifetimes for several aromatic hydrocarbons reported in the subject article were related to significantly different electron affinities. The different values are rationalized using negative ion mass spectral data.

METHODS

Electron affinities for polycyclic aromatic hydrocarbons are reported from the temperature dependence of unpublished electron capture detector data. These are compared with published values and the largest values are assigned to the ground state.

RESULTS

The ground state adiabatic electron affinities: (eV) pentacene, 1.41 (3); tetracene, 1.058 (5); benz(a)pyrene, 0.82 (4); benz(a) anthracene, 0.69 (2) anthracene, 0.68 (2); and pyrene, 0.59 (1) are used to assign excited state adiabatic electron affinities: (eV) tetracene: 0.88 (4); anthracene 0.53 (1); pyrene, 0.41 (1); benz(a)anthracene, 0.39 (10); chrysene, 0.32 (1); and phenanthrene, 0.12 (2) and ground state adiabatic electron affinities: (eV) dibenz(a,j)anthracene, 0.69 (3); dibenz(a,h)anthracene, 0.68 (3); benz(e)pyrene, 0.60 (3); and picene, 0.59 (3) from experimental data. The lifetime of benz(a)pyrene is predicted to be larger than 150 μs and for benzo(c)phenanthrene and picene about 40 μs, from ground state adiabatic electron affinities.

CONCLUSIONS

The assignments of adiabatic electron affinities of aromatic hydrocarbons determined from electron capture detector and mass spectrometric data to ground and excited states are supported by constant electronegativities. A set of consistent ground state adiabatic electron affinities for 15 polycyclic aromatic hydrocarbons is related to lifetimes from the subject article.

The effect of community socioeconomic status on sepsis-attributable mortality

PURPOSE

Community factors may play a role in determining individual risk for sepsis, as well as sepsis-related morbidity and mortality. We sought to define the relationship between community socioeconomic status and mortality due to sepsis in an urban locale.

METHODS

Using community statistical areas of Baltimore City, we dichotomized neighborhoods at median household income, and compared distribution of outcomes of interest within the two income categories. We performed multivariable regression analyses to determine the relationship between socioeconomic variables and sepsis-attributable mortality.

RESULTS

The collective median household income was $38,660 (IQR $32,530, 54,480), family poverty rate was 28.4% (IQR 13.5, 38.8%), and rate of death from sepsis was 3.1 per 10,000 persons (IQR 2.60, 4.10). Lower household income communities demonstrated higher rates of death from sepsis (3.65 (IQR 2.78, 4.40)) than higher household income communities (2.80 (IQR 2.05, 3.55)) (p = .02). In regression models, household income (β = -8.42, p = .006) and percentage of poverty in communities (β = 2.71, p = .01) demonstrated associations with sepsis-attributable mortality.

DISCUSSION

Our findings suggest that socioeconomic variables play significant role in sepsis-attributable mortality. Such confirmation of regional disparities in mortality due to sepsis warrants further consideration, as well as integration, for future national sepsis policies.

Genetic, Immunologic, and Environmental Basis of Sarcoidosis

Sarcoidosis is a multisystem disease with tremendous heterogeneity in disease manifestations, severity, and clinical course that varies among different ethnic and racial groups. To better understand this disease and to improve the outcomes of patients, a National Heart, Lung, and Blood Institute workshop was convened to assess the current state of knowledge, gaps, and research needs across the clinical, genetic, environmental, and immunologic arenas. We also explored to what extent the interplay of the genetic, environmental, and immunologic factors could explain the different phenotypes and outcomes of patients with sarcoidosis, including the chronic phenotypes that have the greatest healthcare burden. The potential use of current genetic, epigenetic, and immunologic tools along with study approaches that integrate environmental exposures and precise clinical phenotyping were also explored. Finally, we made expert panel-based consensus recommendations for research approaches and priorities to improve our understanding of the effect of these factors on the health outcomes in sarcoidosis.

HER2 Reactivation through Acquisition of the HER2 L755S Mutation as a Mechanism of Acquired Resistance to HER2-targeted Therapy in HER2+ Breast Cancer

Purpose: Resistance to anti-HER2 therapies in HER2+ breast cancer can occur through activation of alternative survival pathways or reactivation of the HER signaling network. Here we employed BT474 parental and treatment-resistant cell line models to investigate a mechanism by which HER2+ breast cancer can reactivate the HER network under potent HER2-targeted therapies.Experimental Design: Resistant derivatives to lapatinib (L), trastuzumab (T), or the combination (LR/TR/LTR) were developed independently from two independent estrogen receptor ER+/HER2+ BT474 cell lines (AZ/ATCC). Two derivatives resistant to the lapatinib-containing regimens (BT474/AZ-LR and BT474/ATCC-LTR lines) that showed HER2 reactivation at the time of resistance were subjected to massive parallel sequencing and compared with parental lines. Ectopic expression and mutant-specific siRNA interference were applied to analyze the mutation functionally. In vitro and in vivo experiments were performed to test alternative therapies for mutant HER2 inhibition.Results: Genomic analyses revealed that the HER2L755S mutation was the only common somatic mutation gained in the BT474/AZ-LR and BT474/ATCC-LTR lines. Ectopic expression of HER2L755S induced acquired lapatinib resistance in the BT474/AZ, SK-BR-3, and AU565 parental cell lines. HER2L755S-specific siRNA knockdown reversed the resistance in BT474/AZ-LR and BT474/ATCC-LTR lines. The HER1/2-irreversible inhibitors afatinib and neratinib substantially inhibited both resistant cell growth and the HER2 and downstream AKT/MAPK signaling driven by HER2L755S in vitro and in vivoConclusions: HER2 reactivation through acquisition of the HER2L755S mutation was identified as a mechanism of acquired resistance to lapatinib-containing HER2-targeted therapy in preclinical HER2-amplified breast cancer models, which can be overcome by irreversible HER1/2 inhibitors. Clin Cancer Res; 23(17); 5123-34. ©2017 AACR.

Development and implementation of an alcohol withdrawal protocol using a 5-item scale, the Brief Alcohol Withdrawal Scale (BAWS)

BACKGROUND

The standard of care for management of alcohol withdrawal is symptom-triggered treatment using the Clinical Institute Withdrawal Assessment for Alcohol (CIWA-Ar). Many items of this 10-question scale rely on subjective assessments of withdrawal symptoms, making it time-consuming and cumbersome to use. Therefore, there is interest in shorter and more objective methods to assess alcohol withdrawal symptoms.

METHODS

A 6-item withdrawal scale developed at another institution was piloted. Based on comparison with the CIWA-Ar, this was adapted into a 5-item scale named the Brief Alcohol Withdrawal Scale (BAWS). The BAWS was compared with the CIWA-Ar and a withdrawal protocol utilizing the BAWS was developed. The new protocol was implemented on an inpatient unit dedicated to treating substance withdrawal. Data was collected on the first 3 months of implementation and compared with the 3 months prior to that.

RESULTS

A BAWS score of 3 or more predicted CIWA-Ar score ≥8 with a sensitivity of 85.3% and specificity of 65.8%. The demographics of the patients in the 2 time periods were similar: the mean age was 45.9; 70.6% were male; 30.9% received concurrent treatment for opioid withdrawal; and 14.2% were receiving methadone maintenance. During the BAWS phase, patients received significantly less diazepam (mean dose 81.4 vs. 60.3 mg, P < .001). There was no significant difference in length of stay. No patients experienced a seizure, delirium, or required transfer to a higher level of care during any of the 664 admissions in either phase.

CONCLUSIONS

This simple protocol utilizing a 5-item withdrawal scale performed well in this setting. Its use in other settings, particularly with patients with concurrent medical illnesses or more severe withdrawal, needs to be explored further.

Identification of a RAI1-associated disease network through integration of exome sequencing, transcriptomics, and 3D genomics

Background

Smith-Magenis syndrome (SMS) is a developmental disability/multiple congenital anomaly disorder resulting from haploinsufficiency of RAI1. It is characterized by distinctive facial features, brachydactyly, sleep disturbances, and stereotypic behaviors.

Methods

We investigated a cohort of 15 individuals with a clinical suspicion of SMS who showed neither deletion in the SMS critical region nor damaging variants in RAI1 using whole exome sequencing. A combination of network analysis (co-expression and biomedical text mining), transcriptomics, and circularized chromatin conformation capture (4C-seq) was applied to verify whether modified genes are part of the same disease network as known SMS-causing genes.

Results

Potentially deleterious variants were identified in nine of these individuals using whole-exome sequencing. Eight of these changes affect KMT2D, ZEB2, MAP2K2, GLDC, CASK, MECP2, KDM5C, and POGZ, known to be associated with Kabuki syndrome 1, Mowat-Wilson syndrome, cardiofaciocutaneous syndrome, glycine encephalopathy, mental retardation and microcephaly with pontine and cerebellar hypoplasia, X-linked mental retardation 13, X-linked mental retardation Claes-Jensen type, and White-Sutton syndrome, respectively. The ninth individual carries a de novo variant in JAKMIP1, a regulator of neuronal translation that was recently found deleted in a patient with autism spectrum disorder. Analyses of co-expression and biomedical text mining suggest that these pathologies and SMS are part of the same disease network. Further support for this hypothesis was obtained from transcriptome profiling that showed that the expression levels of both Zeb2 and Map2k2 are perturbed in Rai1^–/– mice. As an orthogonal approach to potentially contributory disease gene variants, we used chromatin conformation capture to reveal chromatin contacts between RAI1 and the loci flanking ZEB2 and GLDC, as well as between RAI1 and human orthologs of the genes that show perturbed expression in our Rai1^–/– mouse model.

Conclusions

These holistic studies of RAI1 and its interactions allow insights into SMS and other disorders associated with intellectual disability and behavioral abnormalities. Our findings support a pan-genomic approach to the molecular diagnosis of a distinctive disorder.

Electronic supplementary material

The online version of this article (doi:10.1186/s13073-016-0359-z) contains supplementary material, which is available to authorized users.

Mass spectrometric determination of Morse parameters for the fifty-four superoxide states dissociating to the lowest limit

RATIONALE

Superoxide is the most significant homonuclear diatomic anion in biochemistry. Theory predicts 12 doublet (X, A-K) and 12 quartet (a-l) electronic states split by spin orbital coupling into 54 states dissociating to the (3) P(O) + (2) P(O(-) ) limit. Dissociation energies for the 27 bonding states with positive electron affinities have been determined from mass spectrometric data. However, the 27 antibonding states with negative electron affinities have not been experimentally characterized.

METHODS

The electron affinity of the hydrogen atom per electron, the Hylleraas, is the fundamental measure of electron correlation. It has been used to assign and evaluate experimental electron affinities of atoms and diatomic molecules. The 27 negative electron affinities of oxygen are estimated from the 27 positive values and the Hylleraas. These values are used to determine frequencies and internuclear separations by fitting theoretical electron impact distributions to the gas-phase mass spectrometric atomic oxygen anion distribution peaking at about 6.5 eV.

RESULTS

The dissociation energies, internuclear distances and frequencies giving the first complete set of Morse potential energy curves for the 54 superoxide states dissociating to the lowest limit are reported from mass spectrometric data. The potentials are compared to theoretical and empirical literature curves.

CONCLUSIONS

The existence of the 27 bonding and 27 antibonding spin orbital coupling superoxide states dissociating to (3) P(O) + (2) P(O(-) ) is established from mass analyzed thermal, photon, and electron ionization data. There are electron affinities from 0 to 0.15 eV, and onsets and peaks for dissociative electron attachment that cannot be explained by the 54 states. These support the existence of the 36 superoxide spin states dissociating to [(1) D(O) + (2) P(O(-) )] and [(1) S(O) + (2) P(O(-) )] predicted by quantum mechanics. Copyright © 2016 John Wiley & Sons, Ltd.

Etiologies of Sarcoidosis

Since sarcoidosis was first described more than a century ago, the etiologic determinants causing this disease remain uncertain. Studies suggest that genetic, host immunologic, and environmental factors interact together to cause sarcoidosis. Immunologic characteristics of sarcoidosis include non-caseating granulomas, enhanced local expression of T helper-1 (and often Th17) cytokines and chemokines, dysfunctional regulatory T-cell responses, dysregulated Toll-like receptor signaling, and oligoclonal expansion of CD4+ T cells consistent with chronic antigenic stimulation. Multiple environmental agents have been suggested to cause sarcoidosis. Studies from several groups implicate mycobacterial or propionibacterial organisms in the etiology of sarcoidosis based on tissue analyses and immunologic responses in sarcoidosis patients. Despite these studies, there is no consensus on the nature of a microbial pathogenesis of sarcoidosis. Some groups postulate sarcoidosis is caused by an active viable replicating infection while other groups contend there is no clinical, pathologic, or microbiologic evidence for such a pathogenic mechanism. The authors posit a novel hypothesis that proposes that sarcoidosis is triggered by a hyperimmune Th1 response to pathogenic microbial and tissue antigens associated with the aberrant aggregation of serum amyloid A within granulomas, which promotes progressive chronic granulomatous inflammation in the absence of ongoing infection.

A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics

Background

Genome-wide data are increasingly important in the clinical evaluation of human disease. However, the large number of variants observed in individual patients challenges the efficiency and accuracy of diagnostic review. Recent work has shown that systematic integration of clinical phenotype data with genotype information can improve diagnostic workflows and prioritization of filtered rare variants. We have developed visually interactive, analytically transparent analysis software that leverages existing disease catalogs, such as the Online Mendelian Inheritance in Man database (OMIM) and the Human Phenotype Ontology (HPO), to integrate patient phenotype and variant data into ranked diagnostic alternatives.

Methods

Our tool, “OMIM Explorer” (http://www.omimexplorer.com), extends the biomedical application of semantic similarity methods beyond those reported in previous studies. The tool also provides a simple interface for translating free-text clinical notes into HPO terms, enabling clinical providers and geneticists to contribute phenotypes to the diagnostic process. The visual approach uses semantic similarity with multidimensional scaling to collapse high-dimensional phenotype and genotype data from an individual into a graphical format that contextualizes the patient within a low-dimensional disease map. The map proposes a differential diagnosis and algorithmically suggests potential alternatives for phenotype queries—in essence, generating a computationally assisted differential diagnosis informed by the individual’s personal genome. Visual interactivity allows the user to filter and update variant rankings by interacting with intermediate results. The tool also implements an adaptive approach for disease gene discovery based on patient phenotypes.

Results

We retrospectively analyzed pilot cohort data from the Baylor Miraca Genetics Laboratory, demonstrating performance of the tool and workflow in the re-analysis of clinical exomes. Our tool assigned to clinically reported variants a median rank of 2, placing causal variants in the top 1 % of filtered candidates across the 47 cohort cases with reported molecular diagnoses of exome variants in OMIM Morbidmap genes. Our tool outperformed Phen-Gen, eXtasy, PhenIX, PHIVE, and hiPHIVE in the prioritization of these clinically reported variants.

Conclusions

Our integrative paradigm can improve efficiency and, potentially, the quality of genomic medicine by more effectively utilizing available phenotype information, catalog data, and genomic knowledge.

Electronic supplementary material

The online version of this article (doi:10.1186/s13073-016-0261-8) contains supplementary material, which is available to authorized users.

Atmospheric pressure anion mass spectrometry: electron affinities and activation energies of thermal electron attachment - perfluoromethylcyclohexane, C7F14

RATIONALE

Perfluorocarbons such as perfluoromethylcyclohexane (c-C6 F11 -CF3 ) are important man-made chemicals that have many uses including plasma processing, blood substitutes and atmospheric tracers. It is important to know the kinetics and thermodynamics of the reactions of thermal electrons with these molecules since they are potentially harmful greenhouse gases that can accumulate in the atmosphere.

METHODS

The least-squares fits of the temperature dependence of electron-capture detection and atmospheric pressure negative ion mass spectrometry to a kinetic model are used to determine the electron affinities of c-C6 F11 -CF3 , activation energies for the formation of c-C6 F10 -CF3 , and c-C6 F11 anions and single bond dissociation energies. These are supported by semi-empirical quantum mechanical calculations. These techniques were previously used to characterize superoxide, NO and SF6 anions.

RESULTS

The literature electron affinities: (eV) c-C6 F11 -CF3 , 1.06, c-C6 F10 -CF3 , 3.9, c-C6 F11 , 3.5 and D(R1-CF3 ), 3.8; D(R-F), 4.3 are supported. Additional electron affinities for c-C6 F11 -CF3 , from 0.5 to 1.5 eV are assigned to excited states. The ground state electron affinity is 3.0(2) eV from the photodetachment threshold. Pseudo one-dimensional anionic Morse potentials illustrating the mechanism for the reaction of thermal electrons with c-C6 F11 -CF3 are presented. The major anion peaks in perfluorokerosene-L are identified. An experimental setup for studying thermal electron capture reactions at variable temperatures, pressures and concentrations proposed by Herder in 2004 is presented.

CONCLUSIONS

There are multiple anions of c-C6 F11 -CF3 more stable than the neutral. Electron-capture detection and atmospheric pressure negative ion mass spectrometry are effective general methods for determining multiple electron affinities similar to the photodetachment, flowing afterglow, magnetron, negative surface ionization, swarm and beam procedures. Semi-empirical theoretical calculations support experimental results. Additional mass analysis studies of reactions of c-C6 F11 -CF3 with electrons over a wide range of temperatures, pressures and electron energies are desirable.