MISC: missing imputation for single-cell RNA sequencing data.

Background: Single-cell RNA sequencing (scRNA-seq) technology provides an effective way to study cell heterogeneity. However, due to the low capture efficiency and stochastic gene expression, scRNA-seq data often contains a high percentage of missing values. It has been showed that the missing rate can reach approximately 30% even after noise reduction.

Non-insidious Large Joint Manifestation of Severe Cachectic Rheumatoid Arthritis.

Rheumatoid arthritis (RA) is an autoimmune disorder in which constitutional symptoms typically occur before joint swelling becomes a true clinical phenomenon. Weight loss, although common, is generally mild in nature and occurs after long standing inflammation. While large joints do become inflamed, RA has a much stronger predilection for the small joints.

Who Wants to Switch? Gauging Patient Interest in Novel Antiretroviral Therapies.

Study participants were asked about their interest in switching to novel drug delivery systems that reduce the dosing frequency of antiretroviral regimens. Across a diverse, treatment-experienced cohort, we describe greatest interest in switching to an oral regimen taken once weekly, followed by injections taken every other month and twice-annual implants.

A Rare Presentation of Epstein-Barr Virus-induced Hepatitis With an Interesting Twist: A Case Report Involving a Clinical Pearl.

An Epstein-Barr Virus (EBV) infection generally presents with the classic infectious mononucleosis symptomatology-sore throat, lymph node enlargement, and fatigue. However, there are cases in which induced hepatitis does occur. The liver enzymes leaked during the acute damage would be apparent in the serum as an elevation of transaminases and alkaline phosphatase.

Photoelectron spectra of copper oxide cluster anions from first principles methods.

We present results and analyses for the photoelectron spectra of small copper oxide cluster anions (CuO, Cu , Cu , and CuO). The spectra are computed using various techniques, including density functional theory (DFT) with semi-local, global hybrid, and optimally tuned range-separated hybrid functionals, as well as many-body perturbation theory within the approximation based on various DFT starting points. The results are compared with each other and with the available experimental data.

Rapid and Extensive Expansion in the United States of a New Multidrug-resistant Escherichia coli Clonal Group, Sequence Type 1193.

We describe the rapid and ongoing emergence across multiple US cities of a new multidrug-resistant Escherichia coli clone-sequence type (ST) 1193-resistant to fluoroquinolones (100%), trimethoprim-sulfamethoxazole (55%), and tetracycline (53%). ST1193 is associated with younger adults (age <40 years) and currently comprises a quarter of fluoroquinolone-resistant clinical E. coli urine isolates.

Missed Opportunities to Prescribe Preexposure Prophylaxis in South Carolina, 2013-2016.

Background: Expanding use of preexposure prophylaxis (PrEP) in ways that address current racial/ethnic disparities is an important human immunodeficiency virus (HIV) prevention goal. We investigated missed opportunities to provide PrEP during healthcare visits that occur prior to HIV infection.

Methods: This retrospective cohort study linked South Carolina HIV case surveillance data to 3 statewide healthcare databases.

The dawn of consumer-directed testing.

As the public's interest in genetics and genomics has increased, there has been corresponding and unprecedented growth in direct-to-consumer genetic testing (DTC-GT). Although regulatory concerns have limited true DTC-GT available without a physician order, the paradigm has shifted to a model of consumer-directed genetic testing (CD-GT) in which patients are researching testing options and requesting specific genetic testing from their health-care providers. However, many nongenetics health-care providers do not have the background, education, interest, or time to order and/or interpret typical clinical genetic testing, let alone DTC-GT.

Continued in vitro cefazolin susceptibility in methicillin-susceptible Staphylococcus aureus.

Objectives: In vitro trends of cefazolin and ceftriaxone susceptibilities from pediatric clinical isolates of methicillin-susceptible Staphylococcus aureus (MSSA) between 2011 and 2016 were analyzed for surveillance.

Methods: Our laboratory continues to use agar disk diffusion for staphylococcal susceptibilities applying Clinical Laboratory Standard Institute's 2012 breakpoints.

Results: A total of 3992 MSSA clinical isolates in the last 6 years were analyzed for their in vitro cefazolin and ceftriaxone susceptibilities.

Improving Antibiotic Prescribing for Children With Urinary Tract Infection in Emergency and Urgent Care Settings.

Objectives: Children with urinary tract infection (UTI) are often diagnosed in emergency and urgent care settings and increasingly are unnecessarily treated with broad-spectrum antibiotics. This study evaluated the effect of a quality improvement intervention on empiric antibiotic prescribing for the treatment of uncomplicated UTI in children.

Methods: A local clinical pathway for uncomplicated UTI, introduced in June 2010, recommended empiric treatment with cephalexin, a narrow-spectrum (first-generation) cephalosporin antibiotic.

Implementing a Virtual Health Telemedicine Program in a Community Setting.

Aurora Health Care in eastern Wisconsin has a clinical genetics program driven by genetic counselors in the cancer/adult and prenatal genetics settings. In 2015, the workforce shortage of genetic counselors left us with 4 open positions for genetic counselors that we were unable to fill. We explored many models of alternative service delivery, and determined virtual health (VH) via telemedicine to be the best option for our system.

Epidemiology and Antimicrobial Resistance Characteristics of the Sequence Type 131-H30 Subclone Among Extraintestinal Escherichia coli Collected From US Children.

Background: Escherichia coli sequence type (ST) 131-H30 is a globally important pathogen implicated in rising rates of multidrug resistance among E. coli causing extraintestinal infections. Previous studies have focused on adults, leaving the epidemiology of H30 among children undefined.

Accuracy of Administrative Data for Antimicrobial Administration in Hospitalized Children.

Administrative data are often used as a proxy for medication-administration record (MAR) data. Multicenter MAR data were compared retrospectively with administrative data from January 2010 through June 2013 from the Pediatric Health Information Systems database. We found that administrative data were more concordant with bill-upon-administration than bill-upon-dispense data.

Ritornello: high fidelity control-free chromatin immunoprecipitation peak calling.

With the advent of next generation high-throughput DNA sequencing technologies, omics experiments have become the mainstay for studying diverse biological effects on a genome wide scale. Chromatin immunoprecipitation (ChIP-seq) is the omics technique that enables genome wide localization of transcription factor (TF) binding or epigenetic modification events. Since the inception of ChIP-seq in 2007, many methods have been developed to infer ChIP-target binding loci from the resultant reads after mapping them to a reference genome.

FDA Approval of PARP Inhibitors and the Impact on Genetic Counseling and Genetic Testing Practices.

In December 2014, the FDA approved olaparib, a poly(ADP-ribose) polymerase inhibitor (PARPi) for ovarian cancer patients who have failed three or more lines of chemotherapy and have a germline BRCA1/2 mutation identified through a companion diagnostic test (BRACAnalysis CDx™ (CDx™)) offered exclusively by Myriad Genetic Laboratories. This study explored the impact of PARPi/CDx™ on genetic counselors' (GCs) counseling and testing practices. One hundred twenty three GCs responded to an online survey regarding pre- and post-FDA approval referral patterns, testing strategies/influences, and anecdotal experiences with insurance coverage of PARPi for BRCA1/2 positive patients through a non-CDx™ platform.

Fusion of Regionally Specified hPSC-Derived Organoids Models Human Brain Development and Interneuron Migration.

Organoid techniques provide unique platforms to model brain development and neurological disorders. Whereas several methods for recapitulating corticogenesis have been described, a system modeling human medial ganglionic eminence (MGE) development, a critical ventral brain domain producing cortical interneurons and related lineages, has been lacking until recently. Here, we describe the generation of MGE and cortex-specific organoids from human pluripotent stem cells that recapitulate the development of MGE and cortex domains, respectively.

The HIV continuum of care in the Bahamas in 2014.

Objective: The HIV cascade of care describes the spectrum of engagement in HIV care from diagnosis to viral suppression (VS). The study objective was to develop a baseline HIV cascade of care for new HIV diagnoses in the Bahamas in 2014.

Methods: Individuals who were newly diagnosed with HIV in 2014 and known to be alive within a year of that diagnosis were included in the cascade of care (n = 250).

New Delhi metallo-β-lactamase-1 (NDM-1) isolated from household vacuum cleaner-Oregon, 2013.

The first Oregon case of New Delhi metallo-β-lactamase-1 (NDM-1)-producing was reported during November 2013. Epidemiologic investigation revealed only local outpatient medical care and no travel outside Oregon for both the patient and his household contact. Environmental sampling discovered a matching isolate from the patient's household vacuum cleaner, suggesting environmental persistence.

Management of Viral Central Nervous System Infections: A Primer for Clinicians.

Viruses are a common cause of central nervous system (CNS) infections with many host, agent, and environmental factors influencing the expression of viral diseases. Viruses can be responsible for CNS disease through a variety of mechanisms including direct infection and replication within the CNS resulting in encephalitis, infection limited to the meninges, or immune-related processes such as acute disseminated encephalomyelitis. Common pathogens including herpes simplex virus, varicella zoster, and enterovirus are responsible for the greatest number of cases in immunocompetent hosts.

Bacterial clonal diagnostics as a tool for evidence-based empiric antibiotic selection.

Despite the known clonal distribution of antibiotic resistance in many bacteria, empiric (pre-culture) antibiotic selection still relies heavily on species-level cumulative antibiograms, resulting in overuse of broad-spectrum agents and excessive antibiotic/pathogen mismatch. Urinary tract infections (UTIs), which account for a large share of antibiotic use, are caused predominantly by Escherichia coli, a highly clonal pathogen. In an observational clinical cohort study of urgent care patients with suspected UTI, we assessed the potential for E.