Within-host genetic diversity of SARS-CoV-2 in the context of large-scale hospital-associated genomic surveillance.

The COVID-19 pandemic has resulted in extensive surveillance of the genomic diversity of SARS-CoV-2. Sequencing data generated as part of these efforts can also capture the diversity of the SARS-CoV-2 virus populations replicating within infected individuals. To assess this within-host diversity of SARS-CoV-2 we quantified low frequency (minor) variants from deep sequence data of thousands of clinical samples collected by a large urban hospital system over the course of a year. Using a robust analytical pipeline to control for technical artefacts, we observe that at comparable viral loads, specimens from patients hospitalized due to COVID-19 had a greater number of minor variants than samples from outpatients. Since individuals with highly diverse viral populations could be disproportionate drivers of new viral lineages in the patient population, these results suggest that transmission control should pay special attention to patients with severe or protracted disease to prevent the spread of novel variants.

Implementing flowDensity for Automated Analysis of Bone Marrow Lymphocyte Population.

INTRODUCTION: Manual gating of flow cytometry (FCM) data for marrow cell analysis is a standard approach in current practice, although it is time- and labor-consuming. Recent advances in cytometry technology have led to significant efforts in developing partially or fully automated analysis methods. Although multiple supervised and unsupervised FCM data analysis algorithms have been developed, they have not been widely adopted by the clinical and research laboratories. In this study, we evaluated flowDensity, an open source freely available algorithm, as an automated analysis tool for classification of lymphocyte subsets in the bone marrow biopsy specimens. MATERIALS AND METHODS: FlowDensity-based gating was applied to 102 normal bone marrow samples and compared with the manual analysis. Independent expression of each cell marker was assessed for comprehensive expression analysis and visualization. RESULTS: Our findings showed a correlation between the manual and flowDensity-based gating in the lymphocyte subsets. However, flowDensity-based gating in the populations with a small number of cells in each cluster showed a low degree of correlation. Comprehensive expression analysis successfully identified and visualized the lymphocyte subsets. DISCUSSION: Our study found that although flowDensity might be a promising method for FCM data analysis, more optimization is required before implementing this algorithm into day-to-day workflow.

Carbapenems drive the collateral resistance to ceftaroline in cystic fibrosis patients with MRSA.

Chronic airways infection with methicillin-resistant Staphylococcus aureus (MRSA) is associated with worse respiratory disease cystic fibrosis (CF) patients. Ceftaroline is a cephalosporin that inhibits the penicillin-binding protein (PBP2a) uniquely produced by MRSA. We analyzed 335 S. aureus isolates from CF sputum samples collected at three US centers between 2015-2018. Molecular relationships demonstrated that high-level resistance of preceding isolates to carbapenems were associated with subsequent isolation of ceftaroline resistant CF MRSA. In vitro evolution experiments showed that pre-exposure of CF MRSA to meropenem with further selection with ceftaroline implied mutations in mecA and additional mutations in pbp1 and pbp2, targets of carbapenems; no effects were achieved by other ß-lactams. An in vivo pneumonia mouse model showed the potential therapeutic efficacy of ceftaroline/meropenem combination against ceftaroline-resistant CF MRSA infections. Thus, the present findings highlight risk factors and potential therapeutic strategies offering an opportunity to both prevent and address antibiotic resistance in this patient population.

Pathology Trainee Redeployment and Education During the COVID-19 Pandemic: An Institutional Experience.

Pathology training programs throughout the United States have endured unprecedented challenges dealing with the ongoing coronavirus disease 2019 pandemic. At Houston Methodist Hospital, the Department of Pathology and Genomic Medicine planned and executed a trainee-oriented, stepwise emergency response. The focus was on optimizing workflows among areas of both clinical and anatomic pathology, maintaining an excellent educational experience, and minimizing trainee exposure to coronavirus disease 2019. During the first phase of the response, trainees were divided into 2 groups: one working on-site and the other working remotely. With the progression of the pandemic, all trainees were called back on-site and further redeployed within our department to meet the significantly increased workload demands of our clinical laboratory services. Adjustments to trainee educational activities included, among others, the organization of a daily coronavirus disease 2019 virtual seminar series. This series served to facilitate communication between faculty, laboratory managers, and trainees. Moreover, it became a forum for trainees to provide updates on individual service workflows and volumes, ongoing projects and research, as well as literature reviews on coronavirus disease 2019-related topics. From our program's experience, redeploying pathology trainees within our department during the coronavirus disease 2019 pandemic resulted in optimization of patient care while ensuring trainee safety, and importantly, helped to maintain continuous high-quality education through active involvement in unique learning opportunities.

Forty-One Million RADPEER Reviews Later: What We Have Learned and Are Still Learning.

ACR RADPEER® is the leading method of radiologic peer review in the United States. The program has evolved since its inception in 2002 and was most recently updated in 2016. In 2018, a survey was sent to RADPEER participants to gauge the current state of the program and explore opportunities for continued improvement. A total of 26 questions were included, and more than 300 practices responded. In this report, the ACR RADPEER Committee authors summarize the survey results and discuss opportunities for future iterations of the RADPEER program.

Discovery of 3-Cyano- N-(3-(1-isobutyrylpiperidin-4-yl)-1-methyl-4-(trifluoromethyl)-1 H-pyrrolo[2,3- b]pyridin-5-yl)benzamide: A Potent, Selective, and Orally Bioavailable Retinoic Acid Receptor-Related Orphan Receptor C2 Inverse Agonist.

The nuclear hormone receptor retinoic acid receptor-related orphan C2 (RORC2, also known as RORγt) is a promising target for the treatment of autoimmune diseases. A small molecule, inverse agonist of the receptor is anticipated to reduce production of IL-17, a key proinflammatory cytokine. Through a high-throughput screening approach, we identified a molecule displaying promising binding affinity for RORC2, inhibition of IL-17 production in Th17 cells, and selectivity against the related RORA and RORB receptor isoforms. Lead optimization to improve the potency and metabolic stability of this hit focused on two key design strategies, namely, iterative optimization driven by increasing lipophilic efficiency and structure-guided conformational restriction to achieve optimal ground state energetics and maximize receptor residence time. This approach successfully identified 3-cyano- N-(3-(1-isobutyrylpiperidin-4-yl)-1-methyl-4-(trifluoromethyl)-1 H-pyrrolo[2,3- b]pyridin-5-yl)benzamide as a potent and selective RORC2 inverse agonist, demonstrating good metabolic stability, oral bioavailability, and the ability to reduce IL-17 levels and skin inflammation in a preclinical in vivo animal model upon oral administration.

Chlorhexidine bathing and Clostridium difficile infection in a surgical intensive care unit.

BACKGROUND: Clostridium difficile is the most common causative pathogen for hospital-acquired infections in the intensive care unit. This study evaluated the effect of chlorhexidine bathing every other day in preventing hospital-acquired C. difficile infection (CDI) using data from the CHlorhexidine Gluconate BATHing (CHG-BATH) randomized trial. METHODS: The primary endpoint was the proportion of patients acquiring CDIs among patients at risk for incident CDIs. Infections detected >48 h after randomization were classified as incident CDIs. Infections detected before or within 48 h of randomization were classified as prevalent CDIs. RESULTS: Of 38 patients (11.7%) who met criteria for potential CDI and underwent adjudication, 24 (7.4%) received oral or enema vancomycin, 18 (5.5%) had a positive C. difficile molecular assay, 14 (4.3%) received an International Classification of Diseases, Ninth Revision, Clinical Modification code for CDI, and 2 (0.6%) had possible pseudomembranous colitis on histopathology reports. The prevalence of CDI was 3.7% (6 of 164) in the soap and water arm and 4.3% (7 of 161) in the chlorhexidine arm. Compared with daily soap and water bathing, 2% chlorhexidine bathing every other day was not associated with the prevention of hospital-acquired CDI (1.3% [2 of 152] soap and water versus 2.0% [3 of 148] chlorhexidine, P = 0.68). CONCLUSIONS: It is inconclusive if there was an association between chlorhexidine bathing and incidence of CDI among surgical intensive care unit patients in this study as statistical power was limited. There are limited published data evaluating the association between chlorhexidine bathing and CDI, and this study provides data for future systematic reviews and meta-analyses.

ACR RADPEER Committee White Paper with 2016 Updates: Revised Scoring System, New Classifications, Self-Review, and Subspecialized Reports.

The ACR's RADPEER program is currently the leading method for peer review in the United States. To date, more than 18,000 radiologists and more than 1,100 groups participate in the program. The ABR accepted RADPEER as a practice quality improvement in 2009, which can be applied toward maintenance of certification; there are currently over 2,200 practice quality improvement participants. There have been ongoing deliberations regarding the utility of RADPEER, its goals, and its scoring system since the preceding 2009 white paper. This white paper reviews the history and evolution of RADPEER and eRADPEER, the 2016 ACR Peer Review Committee's discussions, the updated recommended scoring system and lexicon for RADPEER, and updates to eRADPEER including the study type, age, and discrepancy classifications. The central goal of RADPEER to aid in nonpunitive peer learning is discussed.

Discovery of novel spirocyclic inhibitors of fatty acid amide hydrolase (FAAH). Part 2. Discovery of 7-azaspiro[3.5]nonane urea PF-04862853, an orally efficacious inhibitor of fatty acid amide hydrolase (FAAH) for pain.

Fatty acid amide hydrolase (FAAH) is an integral membrane serine hydrolase responsible for the degradation of fatty acid amide signaling molecules such as endocannabinoid anandamide (AEA), which has been shown to possess cannabinoid-like analgesic properties. Herein we report the optimization of spirocyclic 7-azaspiro[3.5]nonane and 1-oxa-8-azaspiro[4.5]decane urea covalent inhibitors of FAAH. Using an iterative design and optimization strategy, lead compounds were identified with a remarkable reduction in molecular weight and favorable CNS drug like properties. 3,4-Dimethylisoxazole and 1-methyltetrazole were identified as superior urea moieties for this inhibitor class. A dual purpose in vivo efficacy and pharmacokinetic screen was designed to be the key decision enabling experiment affording the ability to move quickly from compound synthesis to selection of preclinical candidates. On the basis of the remarkable potency, selectivity, pharmacokinetic properties and in vivo efficacy, PF-04862853 (15p) was advanced as a clinical candidate.

Discovery of novel spirocyclic inhibitors of fatty acid amide hydrolase (FAAH). Part 1: identification of 7-azaspiro[3.5]nonane and 1-oxa-8-azaspiro[4.5]decane as lead scaffolds.

Herein we report the identification of two new fatty acid amide hydrolase (FAAH) inhibitor lead series with FAAH k(inact)/K(i) potency values greater than 1500M(-1)s(-1). The two novel spirocyclic cores, 7-azaspiro[3.5]nonane and 1-oxa-8-azaspiro[4.5]decane, clearly distinguished themselves from the other spirocyclic cores on the basis of their superior potency for FAAH. Lead compounds from these two series have suitable FAAH potency and selectivity for additional medicinal chemistry optimization.

Good manufacturing practice production of self-complementary serotype 8 adeno-associated viral vector for a hemophilia B clinical trial.

To generate sufficient clinical-grade vector to support a phase I/II clinical trial of adeno-associated virus serotype 8 (AAV8)-mediated factor IX (FIX) gene transfer for hemophilia B, we have developed a large-scale, good manufacturing practice (GMP)-compatible method for vector production and purification. We used a 293T-based two-plasmid transient transfection system coupled with a three-column chromatography purification process to produce high-quality self-complementary AAV2/8 FIX clinical-grade vector. Two consecutive production campaigns using a total of 432 independent 10-stack culture chambers produced a total of ∼2 × 10(15) vector genomes (VG) by dot-blot hybridization. Benzonase-treated microfluidized lysates generated from pellets of transfected cells were purified by group separation on Sepharose beads followed by anion-exchange chromatography. The virus-containing fractions were further processed by gel filtration and ultrafiltration, using a 100-kDa membrane. The vector was formulated in phosphate-buffered saline plus 0.25% human serum albumin. Spectrophotometric analysis suggested ∼20% full particles, with only low quantities of nonviral proteins were visible on silver-stained sodium dodecyl sulfate-polyacrylamide gels. A sensitive assay for the detection of replication-competent AAV was developed, which did reveal trace quantities of such contaminants in the final product. Additional studies have confirmed the long-term stability of the vector at -80°C for at least 24 months and for at least 24 hr formulated in the clinical diluent and stored at room temperature within intravenous bags. This material has been approved for use in clinical trials in the United States and the United Kingdom.

Can individuals who are specialists in death, dying, and bereavement contribute to the prevention and/or mitigation of armed conflicts and cycles of violence?

Specialists in death, dying, and bereavement and their consequences for individuals, families, and communities have experience and research findings that are relevant to an understanding of the reactions of individuals faced by deadly violence. At such times, powerful emotions and ingrained patterns of thought and behavior can given rise to disproportionate responses that may feed into cycles of violence. An extended table shows how professionals helping individuals and families faced with violent death share common aims with those aiming to help larger social units faced with armed attacks. It follows that these professionals should work together to improve death education, to prepare people for possible deadly violence and, where possible, to suggest alternatives, to create secure places and relationships in which communication becomes possible, bad news can be broken and understood, feelings examined, differences reconciled, and people can redirect anger into the prevention of escalation rather than its perpetuation. All of these activities hold out hope that cycles of deadly violence can be broken as well as mitigating the consequences when they are not. The undoubted success of the worldwide palliative care movement resulted from the recognition of serious deficiencies in existing services, the provision of an inclusive, holistic, program that extends across medical, social psychological, and spiritual realms of discourse, providing care for patients and their families, irrespective of wealth, race, religion, and political persuasion, by dedicated leaders and teams backed by education and information services and organized across geographical boundaries. It is argued here that the time is ripe for a similar commitment to bring to an end the scandal of armed conflict by a similarly multidisciplinary, multicultural effort to relieve the suffering that both causes and results from armed conflict. This must remain independent of race, religion, political persuasion, and opposing sides and could build upon the leadership, educational models, information services, and international organizations that already exist for the provision of palliative and bereavement care.

Discovery of (3S,3aR)-2-(3-chloro-4-cyanophenyl)-3-cyclopentyl-3,3a,4,5-tetrahydro-2H-benzo[g]indazole-7-carboxylic acid (PF-3882845), an orally efficacious mineralocorticoid receptor (MR) antagonist for hypertension and nephropathy.

We have discovered a novel class of nonsteroidal pyrazoline antagonists of the mineralocorticoid receptor (MR) that show excellent potency and selectivity against other nuclear receptors. Early analogues were poorly soluble and had a propensity to inhibit the hERG channel. Remarkably, both of these challenges were overcome by incorporation of a single carboxylate moiety. Structural modification of carboxylate-containing lead R-4g with a wide range of substituents at each position of the pyrazoline ring resulted in R-12o, which shows excellent activity against MR and reasonable pharmacokinetic profile. Introduction of conformational restriction led to a novel series characterized by exquisite potency and favorable steroid receptor selectivity and pharmacokinetic profile. Oral dosing of 3S,3aR-27d (PF-3882845) in the Dahl salt sensitive preclinical model of salt-induced hypertension and nephropathy showed blood pressure attenuation significantly greater than that with eplerenone, reduction in urinary albumin, and renal protection. As a result of these findings, 3S,3aR-27d was advanced to clinical studies.

Structure-based drug design enables conversion of a DFG-in binding CSF-1R kinase inhibitor to a DFG-out binding mode.

The work described herein demonstrates the utility of structure-based drug design (SBDD) in shifting the binding mode of an HTS hit from a DFG-in to a DFG-out binding mode resulting in a class of novel potent CSF-1R kinase inhibitors suitable for lead development.

Benzothiophene inhibitors of MK2. Part 2: improvements in kinase selectivity and cell potency.

Optimization of kinase selectivity for a set of benzothiophene MK2 inhibitors provided analogs with potencies of less than 500 nM in a cell based assay. The selectivity of the inhibitors can be rationalized by examination of X-ray crystal structures of inhibitors bound to MK2.

Benzothiophene inhibitors of MK2. Part 1: structure-activity relationships, assessments of selectivity and cellular potency.

Identification of potent benzothiophene inhibitors of mitogen activated protein kinase-activated protein kinase 2 (MK2), structure-activity relationship (SAR) studies, selectivity assessments against CDK2, cellular potency and mechanism of action are presented. Crystallographic data provide a rationale for the observed MK2 potency as well as selectivity over CDK2 for this class of inhibitors.

MRI and US findings of subcutaneous fat necrosis of the newborn.

Subcutaneous fat necrosis of the newborn (SCFN) is an uncommon, benign disorder found in full-term or post-mature neonates. It usually presents in neonates who have experienced perinatal difficulty such as asphyxia, peripheral hypoxemia, hypothermia, meconium aspiration or trauma. We present a newborn with abnormal findings on MRI and US within the axilla, neck, and abdominal walls that were pathologically proved via biopsy to be subcutaneous fat necrosis.

Secretin-receptor and secretin-receptor-variant expression in gastrinomas: correlation with clinical and tumoral features and secretin and calcium provocative test results.

CONTEXT/OBJECTIVES: The diagnosis of Zollinger-Ellison syndrome requires secretin testing in 60% of patients. Even with secretin, the diagnosis may be difficult because variable responses occur, and 6-30% have negative testing. The basis for variability or negative responses is unclear. It is unknown whether the tumor density of secretin receptors or the presence of a secretin-receptor-variant, which can act as a dominant negative, is important. The aim of this study was to investigate these possibilities. PATIENTS/METHODS: Secretin-receptor and variant mRNA expression was determined in gastrinomas using real-time PCR from 54 Zollinger-Ellison syndrome patients. Results were correlated with Western blotting, secretin-receptor immunohistochemistry, with gastrin-provocative test results and tumoral/clinical/laboratory features. RESULTS: Secretin-receptor mRNA was detectible in all gastrinomas but varied 132-fold with a mean of 0.89 +/- 0.12 molecules per beta-actin. Secretin-receptor PCR results correlated closely with Western blotting (r = 0.95; P < 0.0001) and receptor immunohistochemistry (P = 0.0015; r = 0.71). The variant was detected in all gastrinomas, but levels varied 102-fold and were 72-fold lower than the total. Secretin-receptor levels correlated with variant levels, Deltasecretin, but not Deltacalcium and with tumor location, but not growth, extent, or clinical responses. Variant levels did not correlate with the Deltasecretin. Detailed analysis provides no evidence that variant expression modified the secretin-receptor response or accounted for negative tests. CONCLUSIONS: Secretin-receptor and secretin-receptor-variant expressions occur in all gastrinomas. Because the expression of the total, but not variant, correlated with the secretin results and no evidence for dominant negative activity of the variant was found, our results suggest that the total secretin-receptor density is an important determinant of the secretin test response.

EBV-associated diseases in the AIDS patient.

EBV-associated malignancies remain a considerable problem in HIV-infected individuals, even in the era of HAART. Although EBV is a common factor, each disease has a unique pathogenesis. Study of these diseases reveals the viral proteins expressed in the malignancies that might contribute to the development of the disease as well as the molecular basis for pathogenesis. It is likely that this knowledge will contribute to the development of novel therapeutics that will result in more favorable outcomes in the future.