Cytomegalovirus (CMV) is a significant cause of morbidity and mortality among immunocompromised hosts, including transplant recipients. Antiviral prophylaxis or treatment is used to reduce the incidence of CMV disease in this patient population; however, there is concern about increasing antiviral resistance. Detection of antiviral resistance in CMV was traditionally accomplished using Sanger sequencing of UL54 and UL97 genes, in which specific mutations may result in reduced antiviral activity. In this study, a novel next-generation sequencing (NGS) method was developed and validated to detect mutations in UL54/UL97 associated with antiviral resistance. Plasma samples (n = 27) submitted for antiviral resistance testing by Sanger sequencing were also analyzed using the NGS method. When compared to Sanger sequencing, the NGS assay demonstrated 100% (27/27) overall agreement for determining antiviral resistance/susceptibility and 88% (22/25) agreement at the level of resistance-associated mutations. The limit of detection of the NGS method was determined to be 500 IU/mL, and the lower threshold for detecting mutations associated with resistance was established at 15%. The NGS assay represents a novel laboratory tool that assists healthcare providers in treating patients who are infected with CMV harboring resistance-associated mutations and who may benefit from tailored antiviral therapy.

In this work, we present a new analysis method applied to revitalize permanent magnet Compton spectrometers used to measure photon energy spectra in the MeV range. The inversion of the measured electron distribution to determine the original photon distribution is achieved via a method of consistent coupled radiation transport and magnetic field mapping of the input photon spectra to the measured electron distribution. The method of linear least squares was used to perform the unfolding of the electron distribution to the initial photon spectra, without any assumptions made regarding the electron distribution. We present an application of this method to data from a nominal 19.4 MeV flash radiographic source (the first axis of the Dual Axis Radiographic Hydro-Test Facility) capable of generating 500 R @ 1 m in ∼60 ns and a medical therapy source (a Scanditronix M22, Microtron) capable of variable energies with nominal endpoints of 6, 10, 15, and 20 MeV and an output of ∼1000-2000 R/min @ 1 m. The results provide agreement between the modeled and unfolded experimentally measured photon spectra as quantified by statistical tests, from 1.5 to 20 MeV. Experimental results are presented as well as a discussion of the novel MCNP6-based simulations and methods for reconstruction of the spectra.

A pre- and post-collimation scheme has been applied to high energy proton radiography to establish a dark field condition, which defaults to a state of no transmission until a scatterer is placed at the object plane. This technique, dark field proton radiography, provides two additional capabilities to a standard proton radiography setup. First, protons with a high degree of angular dispersion are removed from the beam, reducing the effects of chromatic aberrations and decreasing noise. Second, protons below the same threshold are removed from the beam downstream of the objects, effectively making the transmission highly sensitive to small amounts of scatter at the object plane. Initial results indicate that the system is highly sensitive to the presence of thinner materials and improves sensitivity to subtle areal density variations in thick objects.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of coronavirus disease-19 (COVID-19), has caused a global pandemic since being discovered in late 2019.…

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has caused a global pandemic since being discovered in late 2019. In response, clinical microbiology and public health laboratories have worked to develop, validate, and implement molecular assays to detect SARS-CoV-2 from respiratory samples. The preferred and most commonly collected specimen is a nasopharyngeal (NP) swab placed in viral transport media (VTM). As testing demand has increased, specimen collection and transportation supplies, including VTM, are decreasing nationwide. Due to these shortages of collection supplies and transport media, we assessed the feasibility of placing NP swabs in sterile 0.9% saline (Baxter, Deerfield, IL), sterile phosphate-buffered saline without calcium and magnesium (PBS), or minimum essential medium (MEM) (Corning, Corning, NY) prior to testing for SARS-CoV-2 by a commercially available (emergency use authorized [EUA]) FDA platform (cobas SARS-CoV-2; Roche Diagnostics, Indianapolis, IN) and a SARS-CoV-2 laboratory-developed test (LDT) that has been validated and submitted to the Food and Drug Administration for EUA approval. The Roche cobas SARS-CoV-2 test is performed on the cobas 6800 platform (Roche) per the manufacturer’s protocol. The SARS-CoV-2 LDT is performed as described in the supplemental material, targeting the nucleocapsid (NUC) and open reading frame (ORF) regions of the virus.

Recent experiments on the Mercury pulsed power accelerator were performed with a large-area bremsstrahlung diode operated at 5 MV. Extensive measurements of the x-ray dose distribution were made using TLDs, both in the near field and far field of the x-ray beam. In order to understand the operation of the diode and the properties of the x-ray beam, numerical simulations of the diode and beam were performed. Particle-in-cell simulations of the diode were driven using the measured currents from the experiment in order to simulate the electron beam produced by the accelerator. These beam electrons were then used as a source in Monte Carlo simulations of the bremsstrahlung converter to compute the generated x-ray beam. The photons from this simulation were then transported to the near- and far-field TLD locations and doses were computed. The dose predictions were compared to measurements, showing reasonably good agreement.

Although U.S. Food and Drug Administration-approved and CLIA-waived point-of-care (POC) molecular systems are being implemented in routine clinical practice, instrument reliability, test performance in the hands of end users, and the potential for environmental contamination resulting from use of POC molecular systems have not been extensively evaluated. We performed a prospective evaluation of the Roche cobas Liat group A streptococcus (GAS) assay compared to routine real-time PCR. We evaluated test accuracy, instrument failure rate, and monitored for environmental contamination when testing was performed by minimally trained end users in an Express Care Clinic environment. The overall concordance of the Liat GAS assay with routine testing was 97.2% (455/468). The average Liat failure rate across three analyzers was 6.6% (33/501) (range, 3.7 to 11.6%), and no environmental contamination was detected during the course of the study. The cobas Liat platform and GAS assay demonstrated reliable performance in the end user setting and may serve as a rapid, POC option for routine diagnostic testing for certain infectious diseases, including GAS.

Background: Recently, automated platforms have been developed that can perform processing, extraction and testing for herpes simplex virus (HSV) nucleic acid on a single instrument.Objectives: In this study, we compared three commercially-available systems; Aptima (R)/Panther (Hologic, San Diego, CA), ARIES (R) (Luminex Corporation, Austin, TX), and cobas (R) 4800 (Roche Molecular Systems Inc, Pleasanton, CA) for the qualitative detection of HSV-1/2 in clinical samples.Study design: Two-hundred seventy-seven specimens (genital [n = 193], dermal [n = 84]) were submitted for routine HSV-1/2 real-time PCR by a laboratory developed test. Following routine testing, samples were also tested by the Aptima, ARIES, and cobas HSV-1/2 assays per the manufacturer's recommendations. Results were compared to a "consensus standard" defined as the result obtained from >= 3 of the 4 assays.Results: Following testing of 277 specimens, the cobas and ARIES assays demonstrated a sensitivity of 100% for HSV-1 (61/61) and HSV-2 (55/55). The Aptima assays showed a sensitivity of 91.8% (56/61) for HSV-1 and 90.9% (50/55) for HSV-2. Percent specificities for HSV-1 were 96.2% (202/210) by cobas, 99.5% (209/210) by ARIES and 100% (236/236) by Aptima. For HSV-2, the specificities were 98.1% (211/215) by cobas, 99.5% (215/216) by ARIES and 100% (216/216) by Aptima. The turnaround time for testing 24 samples was 2.5 h by the cobas 4800, 3.1 h by Aptima/Panther, and 3.9 h by ARIES.Conclusions: The three commercial systems can perform all current functions on a single platform, thereby improving workflow and potentially reducing errors associated with manual processing of samples. (C) 2017 Elsevier B.V. All rights reserved.

Our team at Los Alamos National Laboratory has successfully employed Compton spectrometers to measure the x-ray spectra of intense radiographic sources, both continuous and flash. In this method, a collimated beam of x-rays incident on a convertor foil ejects Compton electrons. A collimator may be inserted into the entrance of the spectrometer to select the angular acceptance of the forward-scattered electrons, which then enter the magnetic field region of the spectrometer. The position of the electrons at the magnet's focal plane is proportional to the square root of their momentum, allowing the x-ray spectrum to be reconstructed. Two spectrometers have been fielded since 2013; a neodymium-iron-boron permanent magnet with an energy range of 500 keV to 20 MeV, and a new samarium-cobalt magnet with an energy range of 50 keV to 4 MeV. Measured spectra were produced by x-ray generating machines of various intensities (~5 rad at 1 m per 50 ns pulse to >2000 rad/min at 1 m) and different endpoints (range of 2.25 to 20 MeV). Preliminary analysis of the electron spectra produced at two different facilities with various beryllium converter foil thicknesses is presented in these proceedings.

OBJECTIVE:To determine the sensitivity and specificity of the AdenoPlus test compared with real-time polymerase chain reaction (PCR) and to determine whether there was a reduction in antibiotic prescriptions with the use of AdenoPlus compared with the previous year.PATIENTS AND METHODS:A total of 125 patients with suspected infectious conjunctivitis were accrued from June 4, 2015, through September 27, 2015. Forty-six participants from the prospective cohort completed both AdenoPlus and PCR testing. Two hundred fifty age-matched individuals were in the retrospective cohort.RESULTS:There was a significant reduction in the percentage of patients who received an antibiotic ophthalmic prescription in the prospective cohort vs the retrospective cohort (32% vs 45%; χ2P=.01). AdenoPlus test sensitivity was 50% (5 of 10) and specificity was 92% (33 of 36) compared with real-time PCR testing.CONCLUSION:The AdenoPlus test has high specificity for diagnosing adenoviral conjunctivitis but lower sensitivity than has been previously published. These data suggest that negative AdenoPlus results should be confirmed by real-time PCR owing to the low overall sensitivity of AdenoPlus observed.

A real-time RT-PCR assay was designed to detect and differentiate norovirus genogroups I (GI) and II (GII), with primers and probes targeting the nonstructural polyprotein gene. Stool samples (n = 100) submitted for routine testing by the BioFire FilmArray® GI panel were also tested by the norovirus GI/GII real-time PCR assays. When compared to the FilmArray GI panel, the norovirus real-time PCR assay demonstrated a sensitivity of 77.5% (62/80) and specificity of 95% (19/20). Specimens yielding discordant results (n = 19) were tested at two outside laboratories for adjudication. Following discordant resolution, the adjusted sensitivity and specificity of the norovirus real-time PCR assays were 96.9% (63/65) and 100% (35/35), respectively. These results suggest that the real-time PCR assays are able to accurately detect and differentiate norovirus GI/GII from clinical stool specimens. Furthermore, our report highlights a potential issue with the specificity of the BioFire FilmArray® norovirus assay, which warrants additional investigation.

Norovirus is an emerging pathogen causing gastroenteritis. We sought to identify factors associated with clinical outcomes in a cohort of patients with laboratory-confirmed norovirus infection. We performed a retrospective chart review of patients with positive norovirus polymerase chain reaction in stool between October 1, 2015, and May 31, 2016. 128 unique patients were identified during the study period, 64 of whom had immune deficiency, of which only 3 patients had a primary immune deficiency (common variable immune deficiency), while 61 patients had a secondary immune deficiency. 50% of patients with immune deficiency were hospitalized as compared to only 30% of the non-immune-deficient cohort (odds ratio: 2.1 (1.1-4.18, P=0.04). One-third (32.8%) of the patients had a polymicrobial stool infection, and 21.1% had concurrent Clostridium difficile infection. Initial mean total leukocyte count was higher in the hospitalized group at 8.40×109/L versus 6.31×109/L in the nonhospitalized group (P=0.049). All 13 patients presenting with fever had symptomatic resolution (P=0.002). The presence of C. difficile infection was correlated with persistent symptoms (OR 2.30 [0.95-5.58], P=0.067). The overall mortality rate among our cohort was 3.13% (4 patients). All deceased patients had secondary immune deficiency, and none had C. difficile coinfection. Presence of an immune deficiency increases the risk of hospitalization with norovirus infection. Absence of fever is associated with lower resolution and possibly may contribute to a persistent infectious state. Presence of concomitant C. difficile infection is correlated with a lower overall mortality rate.

pRINCIplEs OF MRI MRI is the tomographic implementation of the wellestablished technique of nuclear magnetic resonance (NMR), which is based on the principle that nuclear particles with spin precess around the direction of an applied magnetic field (B) when tipped away from their equilibrium alignment in the field. This precession occurs at a certain frequency, known as the Larmor frequency, ωL. For protons in water ωL/2π = 42.6 MHz/T (or 42.6 Hz/μT, which is more suitable for the ULF regime). The precession of the spins generates an oscillating magnetic field, which can be detected by a sensor. Tomography is obtained by encoding spatial locations by magnetic field gradients in all three dimensions. The gradients can be used to change the frequency of the spins, or the phase of them depending on how they are implemented in the pulse sequence. COMpARIsON OF ulF-MRI tO CONVENtIONAl MRI ULF-MRI provides the ability to switch all the fields and gradients on and off. The field-free state makes ULF-MRI uniquely compatible with magnetoencephalography (MEG), where miniscule magnetic fields generated by active neuronal clusters are detected by very sensitive magnetic field sensors. The requirement on field homogeneity for NMR linewidths scales with the absolute field and thus is greatly relaxed at ULF compared to the parts-permillion requirements at high fields. The lower homogeneities allow open designs with simple copper-wound air-core coils leading to less expensive field and gradient coil-systems. At ULF the fields and gradients are orders of magnitude smaller than in conventional systems and thus there is less concern about exciting nerves due to the switched fields and gradients through dB/dt. The specific absorption rate from resonant fields at the Larmor frequency is also less of a concern at these low frequencies as it scales as the square of the magnetic field, B2. The susceptibility of tissue, which describes the level of magnetization when exposed to a magnetic field, influences MR-images. The effect scales with the magnitude of the magnetic field and can cause strong artifacts in high-field systems especially at interfaces between volumes with very different susceptibilities, such as the paranasal sinuses [1] and metal implants [2]. Because the effect is dependenct on the magnitude of the magnetic field, it is negligible at ULF and it is possible to acquire satisfactory images in the vicinity of non-ferrous metals [3]. For the same reasons, susceptibility weighted imaging at ULF has not been demonstrated and would be challenging — if at all possible. Relaxation time dispersion is more enhanced at Conventional magnetic resonance imaging (MRI) is moving toward the use of stronger and stronger magnetic fields with 3T, and even 7 T systems being increasingly used in routine clinical applications. However there is another branch of MRI, namely Ultra Low Field MRI (ULF-MRI) where the magnetic fields during readout are several orders of magnitude smaller, namely 1–100 μT. While conventional high-field MRI remains the gold standard there are several situations such as in military emergencies or in developing countries where for cost and logistical reasons, conventional MRI is not practical. In such scenarios, ULF-MRI could provide a solution. This article describes the basic principles and the potential of ULF-MRI.