Deep Learning Denoising of Low-Dose Computed Tomography Chest Images: A Quantitative and Qualitative Image Analysis.

PURPOSE: To assess deep learning denoised (DLD) computed tomography (CT) chest images at various low doses by both quantitative and qualitative perceptual image analysis. METHODS: Simulated noise was inserted into sinogram data from 32 chest CTs acquired at 100 mAs, generating anatomically registered images at 40, 20, 10, and 5 mAs. A DLD model was developed, with 23 scans selected for training, 5 for validation, and 4 for test.Quantitative analysis of perceptual image quality was assessed with Structural SIMilarity Index (SSIM) and Fréchet Inception Distance (FID). Four thoracic radiologists graded overall diagnostic image quality, image artifact, visibility of small structures, and lesion conspicuity. Noise-simulated and denoised image series were evaluated in comparison with one another, and in comparison with standard 100 mAs acquisition at the 4 mAs levels. Statistical tests were conducted at the 2-sided 5% significance level, with multiple comparison correction. RESULTS: At the same mAs levels, SSIM and FID between noise-simulated and reconstructed DLD images indicated that images were closer to a perfect match with increasing mAs (closer to 1 for SSIM, and 0 for FID).In comparing noise-simulated and DLD images to standard-dose 100-mAs images, DLD improved SSIM and FID. Deep learning denoising improved SSIM of 40-, 20-, 10-, and 5-mAs simulations in comparison with standard-dose 100-mAs images, with change in SSIM from 0.91 to 0.94, 0.87 to 0.93, 0.67 to 0.87, and 0.54 to 0.84, respectively. Deep learning denoising improved FID of 40-, 20-, 10-, and 5-mAs simulations in comparison with standard-dose 100-mAs images, with change in FID from 20 to 13, 46 to 21, 104 to 41, and 148 to 69, respectively.Qualitative image analysis showed no significant difference in lesion conspicuity between DLD images at any mAs in comparison with 100-mAs images. Deep learning denoising images at 10 and 5 mAs were rated lower for overall diagnostic image quality ( P < 0.001), and at 5 mAs lower for overall image artifact and visibility of small structures ( P = 0.002), in comparison with 100 mAs. CONCLUSIONS: Deep learning denoising resulted in quantitative improvements in image quality. Qualitative assessment demonstrated DLD images at or less than 10 mAs to be rated inferior to standard-dose images.

SARS-CoV-2 reactive and neutralizing antibodies discovered by single-cell sequencing of plasma cells and mammalian display.

Characterization of COVID-19 antibodies has largely focused on memory B cells; however, it is the antibody-secreting plasma cells that are directly responsible for the production of serum antibodies, which play a critical role in resolving SARS-CoV-2 infection. Little is known about the specificity of plasma cells, largely because plasma cells lack surface antibody expression, thereby complicating their screening. Here, we describe a technology pipeline that integrates single-cell antibody repertoire sequencing and mammalian display to interrogate the specificity of plasma cells from 16 convalescent patients. Single-cell sequencing allows us to profile antibody repertoire features and identify expanded clonal lineages. Mammalian display screening is used to reveal that 43 antibodies (of 132 candidates) derived from expanded plasma cell lineages are specific to SARS-CoV-2 antigens, including antibodies with high affinity to the SARS-CoV-2 receptor-binding domain (RBD) that exhibit potent neutralization and broad binding to the RBD of SARS-CoV-2 variants (of concern/interest).

A Single-Cell Atlas of Lymphocyte Adaptive Immune Repertoires and Transcriptomes Reveals Age-Related Differences in Convalescent COVID-19 Patients.

COVID-19 disease outcome is highly dependent on adaptive immunity from T and B lymphocytes, which play a critical role in the control, clearance and long-term protection against SARS-CoV-2. To date, there is limited knowledge on the composition of the T and B cell immune receptor repertoires [T cell receptors (TCRs) and B cell receptors (BCRs)] and transcriptomes in convalescent COVID-19 patients of different age groups. Here, we utilize single-cell sequencing (scSeq) of lymphocyte immune repertoires and transcriptomes to quantitatively profile the adaptive immune response in COVID-19 patients of varying age. We discovered highly expanded T and B cells in multiple patients, with the most expanded clonotypes coming from the effector CD8+ T cell population. Highly expanded CD8+ and CD4+ T cell clones show elevated markers of cytotoxicity (CD8: PRF1, GZMH, GNLY; CD4: GZMA), whereas clonally expanded B cells show markers of transition into the plasma cell state and activation across patients. By comparing young and old convalescent COVID-19 patients (mean ages = 31 and 66.8 years, respectively), we found that clonally expanded B cells in young patients were predominantly of the IgA isotype and their BCRs had incurred higher levels of somatic hypermutation than elderly patients. In conclusion, our scSeq analysis defines the adaptive immune repertoire and transcriptome in convalescent COVID-19 patients and shows important age-related differences implicated in immunity against SARS-CoV-2.

Optimization of therapeutic antibodies by predicting antigen specificity from antibody sequence via deep learning.

The optimization of therapeutic antibodies is time-intensive and resource-demanding, largely because of the low-throughput screening of full-length antibodies (approximately 1 × 103 variants) expressed in mammalian cells, which typically results in few optimized leads. Here we show that optimized antibody variants can be identified by predicting antigen specificity via deep learning from a massively diverse space of antibody sequences. To produce data for training deep neural networks, we deep-sequenced libraries of the therapeutic antibody trastuzumab (about 1 × 104 variants), expressed in a mammalian cell line through site-directed mutagenesis via CRISPR-Cas9-mediated homology-directed repair, and screened the libraries for specificity to human epidermal growth factor receptor 2 (HER2). We then used the trained neural networks to screen a computational library of approximately 1 × 108 trastuzumab variants and predict the HER2-specific subset (approximately 1 × 106 variants), which can then be filtered for viscosity, clearance, solubility and immunogenicity to generate thousands of highly optimized lead candidates. Recombinant expression and experimental testing of 30 randomly selected variants from the unfiltered library showed that all 30 retained specificity for HER2. Deep learning may facilitate antibody engineering and optimization.

Increased Incidence of Barotrauma in Patients with COVID-19 on Invasive Mechanical Ventilation.

Background A high number of patients with coronavirus disease 2019 (COVID-19) pneumonia who had barotrauma related to invasive mechanical ventilation at the authors' institution were observed. Purpose To determine if the rate of barotrauma in patients with COVID-19 infection was greater than in other patients requiring invasive mechanical ventilation at the authors' institution. Materials and Methods In this retrospective study, clinical and imaging data of patients seen between March 1, 2020, and April 6, 2020, who tested positive for COVID-19 and experienced barotrauma associated with invasive mechanical ventilation, were compared with patients without COVID-19 infection during the same period. Historical comparison was made to barotrauma rates of patients with acute respiratory distress syndrome from February 1, 2016, to February 1, 2020, at the authors' institution. Comparison of patient groups was performed using categoric or continuous statistical testing as appropriate, with multivariable regression analysis. Patient survival was assessed using Kaplan-Meier curves analysis. Results A total of 601 patients with COVID-19 infection underwent invasive mechanical ventilation (mean age, 63 years ± 15 [standard deviation]; 71% men). Of the total, there were 89 (15%) patients with one or more barotrauma events for a total of 145 barotrauma events (24% overall events) (95% confidence interval [CI]: 21%, 28%). During the same period, 196 patients without COVID-19 infection (mean age, 64 years ± 19; 52% men) with invasive mechanical ventilation had one barotrauma event (0.5%; 95% CI: 0%, 3%; P < .001 vs the group with COVID-19 infection). Of 285 patients with acute respiratory distress syndrome on invasive mechanical ventilation during the previous 4 years (mean age, 68 years ± 17; 60% men), 28 patients (10%) had 31 barotrauma events, with an overall barotrauma rate of 11% (95% CI: 8%, 15%; P < .001 vs the group with COVID-19 infection). Barotrauma is an independent risk factor for death in COVID-19 (odds ratio = 2.2; P = .03) and is associated with a longer hospital stay (odds ratio = 0.92; P < .001). Conclusion Patients with coronavirus disease 2019 (COVID-19) infection and invasive mechanical ventilation had a higher rate of barotrauma than patients with acute respiratory distress syndrome and patients without COVID-19 infection. © RSNA, 2020 Online supplemental material is available for this article.

Antibody discovery and engineering by enhanced CRISPR-Cas9 integration of variable gene cassette libraries in mammalian cells.

Antibody engineering in mammalian cells offers the important advantage of expression and screening of libraries in their native conformation, increasing the likelihood of generating candidates with more favorable molecular properties. Major advances in cellular engineering enabled by CRISPR-Cas9 genome editing have made it possible to expand the use of mammalian cells in biotechnological applications. Here, we describe an antibody engineering and screening approach where complete variable light (VL) and heavy (VH) chain cassette libraries are stably integrated into the genome of hybridoma cells by enhanced Cas9-driven homology-directed repair (HDR), resulting in their surface display and secretion. By developing an improved HDR donor format that utilizes in situ linearization, we are able to achieve >15-fold improvement of genomic integration, resulting in a screening workflow that only requires a simple plasmid electroporation. This proved suitable for different applications in antibody discovery and engineering. By integrating and screening an immune library obtained from the variable gene repertoire of an immunized mouse, we could isolate a diverse panel of >40 unique antigen-binding variants. Additionally, we successfully performed affinity maturation by directed evolution screening of an antibody library based on random mutagenesis, leading to the isolation of several clones with affinities in the picomolar range.

Genome Engineering of Hybridomas to Generate Stable Cell Lines for Antibody Expression.

From the perspective of academic and small research laboratories, the most common and practical strategy for recombinant expression of full-length monoclonal antibodies is to perform transient plasmid transfection of mammalian cells, resulting in small-scale and limited protein production. The generation of stable antibody producing mammalian cell lines enables larger-scale and consistent expression, however this approach is rarely pursued due to the time-consuming and expensive process of single colony screening and characterization. In order to bridge the gap between the simplicity of transient transfection and consistent production by stable cell lines, we describe a method to stably integrate antibody genes into the endogenous immunogenomic loci of hybridoma cells using CRISPR/Cas9 genome editing. Initially, the antibody variable light (VL) chain is deleted by multiplexed Cas9 cleavage; subsequently, the variable heavy (VH) chain is replaced by a fluorescent reporter gene (mRuby) by Cas9-assisted homology-directed repair (HDR). This cell line is customized by replacing mRuby with a synthetic antibody (consisting of a VL, light constant region and VH) by once again using Cas9-assisted HDR. Due to hybridomas' inherent ability to surface display and secrete antibodies, they provide a suitable host for both the selection and the production process, substantially streamlining the process for stable cell line generation, and thus we refer to this platform as plug-and-(dis)play (PnP) hybridomas.

Congenital Coronary Artery Anomalies and Implications.

This pictorial essay presents cases of congenital coronary artery anomalies, including congenital anomalies of origin, course, and termination. Familiarity with atypical coronary anatomy and clinical presentation may facilitate appropriate diagnosis and management, particularly as cardiac and thoracic computed tomographic utilization increases.

High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis.

Antibody engineering is often performed to improve therapeutic properties by directed evolution, usually by high-throughput screening of phage or yeast display libraries. Engineering antibodies in mammalian cells offer advantages associated with expression in their final therapeutic format (full-length glycosylated IgG); however, the inability to express large and diverse libraries severely limits their potential throughput. To address this limitation, we have developed homology-directed mutagenesis (HDM), a novel method which extends the concept of CRISPR/Cas9-mediated homology-directed repair (HDR). HDM leverages oligonucleotides with degenerate codons to generate site-directed mutagenesis libraries in mammalian cells. By improving HDR to a robust efficiency of 15-35% and combining mammalian display screening with next-generation sequencing, we validated this approach can be used for key applications in antibody engineering at high-throughput: rational library construction, novel variant discovery, affinity maturation and deep mutational scanning (DMS). We anticipate that HDM will be a valuable tool for engineering and optimizing antibodies in mammalian cells, and eventually enable directed evolution of other complex proteins and cellular therapeutics.

Intracardiac Embolized Prostate Brachytherapy Seeds: Imaging Features in Patients Undergoing Electrocardiogram-Gated Cardiac Computed Tomography.

OBJECTIVE: This study aims to provide the first description of the computed tomographic (CT) appearances of intracardiac embolized brachytherapy seeds in patients undergoing electrocardiogram (ECG)-gated cardiac CT. METHODS: The institutional Picture Archive and Communication System was searched for male patients who underwent enhanced ECG-gated cardiac CT, and reports were searched for the key words "metallic," "prostate," "brachytherapy," "radiation," "embolized," and "radioactive." Each study was identified and examined for an intracardiac metallic object conforming to the size of a prostate seed. RESULTS: Between January 01, 2005, and June 30, 2014, a total of 3206 male patients underwent ECG-gated cardiac CT. Five patients (0.15%) had a history of prostate cancer and an intracardiac metallic object with CT imaging characteristics consistent with an embolized prostate seed. In all 5 patients, the seeds were embedded in the trabeculations of the inferior aspect of the basal right ventricular free wall. CONCLUSIONS: Intracardiac embolized brachytherapy seeds appear as small objects with surrounding metallic artifact characteristically embedded in the inferior aspect of the basal right ventricular free wall.

The Radiologist as Direct Public Educator: Impact of Sessions Demystifying Select Cancer Screening Imaging Examinations.

PURPOSE: The aim of this report is to describe our early experience with radiologist-led direct public education about imaging-based cancer screening examinations, with a focus on the level of satisfaction and the educational impact reported by session participants. METHODS: Subspecialty radiologists provided 1-hour educational sessions to small lay public audiences covering breast, prostate, and lung cancer screening, focusing on key radiologic screening tests. Subsequently, session participants completed a survey pertaining to their levels of satisfaction and the perceived impact of the sessions on knowledge of the diseases and relevant screening tests; results from all topic sessions were pooled for analysis. RESULTS: One hundred nineteen participants attended a total of 144 sessions. The large majority of respondents agreed or strongly agreed that the sessions increased their understanding (95.4%), they gained information not obtained from clinic visit (88.1%), seeing radiology images helped their understanding (92.6%), they felt more involved in their own care (85.8%), they felt more prepared to undergo screening tests (87.4%), they were satisfied with the sessions' format (93.3%) and content (96.2%), their main questions were answered (88.3%), they would be interested in similar future radiologist-led sessions (88.5%), and they would recommend the sessions to friends (93.9%). The provided information (43.1%) and images (34.7%) were identified as the most helpful aspects of the sessions. CONCLUSION: Radiologist-led direct public education sessions about imaging-based cancer screening examinations yield high levels of audience satisfaction and add value to the public's understanding of the role of radiology and radiologists. Our experience may provide an encouraging model for other radiology practices in pursuing similar endeavors.

Cultural and gender differences in coping strategies between Caucasian American and Korean American older people.

Coping strategies have significant effects on older people's health. This study examined whether gender and ethnic differences influence the coping strategies chosen by older adults when they encounter daily life stressors. Data were collected from 444 community-dwelling people over the age of 65, including 238 Caucasian Americans and 206 Korean Americans. Results showed significant differences between the two groups. Korean Americans had higher scores on problem and emotion-focused coping strategies as well as avoidant coping strategies than Caucasian Americans. Caucasian older women employed more active coping, planning, and positive reframing skills; relied more on religion; and sought emotional support more than Caucasian men. For Korean Americans, older women utilized religion and denial; whereas older men employed instrumental support and substance abuse. The results suggest that practitioners should develop ethnic, gender-specific programs to help older adults cope more effectively with their daily life stressors.

The experiences of homicide victims' families with the criminal justice system: an exploratory study.

Although the crime of homicide has received significant attention from scholars, little research exists that examines the impact of homicide on surviving family members. Because opportunities for victims and family members of victims to participate in the criminal justice system are increasing, it is important to understand the impact of these forms of participation on those who choose to participate. This study uses data from focus groups to examine the experiences of homicide survivors within the criminal justice system, including views about how system involvement and specific outcomes (i.e., sentencing) may help or hinder healing. Findings suggest that many families leave the criminal justice system feeling marginalized and revictimized. This study calls into question the current criminal justice system's ability to meet the needs of crime victim and their families.

The radiologist as direct public educator: impact of sessions demystifying select cancer screening imaging examinations.

PURPOSE: The aim of this report is to describe our early experience with radiologist-led direct public education about imaging-based cancer screening examinations, with a focus on the level of satisfaction and the educational impact reported by session participants. METHODS: Subspecialty radiologists provided 1-hour educational sessions to small lay public audiences covering breast, prostate, and lung cancer screening, focusing on key radiologic screening tests. Subsequently, session participants completed a survey pertaining to their levels of satisfaction and the perceived impact of the sessions on knowledge of the diseases and relevant screening tests; results from all topic sessions were pooled for analysis. RESULTS: One hundred nineteen participants attended a total of 144 sessions. The large majority of respondents agreed or strongly agreed that the sessions increased their understanding (95.4%), they gained information not obtained from clinic visit (88.1%), seeing radiology images helped their understanding (92.6%), they felt more involved in their own care (85.8%), they felt more prepared to undergo screening tests (87.4%), they were satisfied with the sessions' format (93.3%) and content (96.2%), their main questions were answered (88.3%), they would be interested in similar future radiologist-led sessions (88.5%), and they would recommend the sessions to friends (93.9%). The provided information (43.1%) and images (34.7%) were identified as the most helpful aspects of the sessions. CONCLUSION: Radiologist-led direct public education sessions about imaging-based cancer screening examinations yield high levels of audience satisfaction and add value to the public's understanding of the role of radiology and radiologists. Our experience may provide an encouraging model for other radiology practices in pursuing similar endeavors.

Optimism and coping strategies among Caucasian, Korean, and African American older women.

Coping strategies and optimism have significant effects on the health of older women. Culture affects coping behaviors used to deal with stress. We examined the relationship between optimism and coping strategies used to manage daily stress and health among community-dwelling Caucasian, Korean American, and African American women. Data were collected from 373 women over the age of 65. Results showed that each group used different coping strategies. The more optimistic used more problem-focused and adaptive copings, while the less optimistic employed more avoidant copings. Differences in cultural background and individual levels of optimism guided their coping strategies.

Impact of a computer-aided detection (CAD) system integrated into a picture archiving and communication system (PACS) on reader sensitivity and efficiency for the detection of lung nodules in thoracic CT exams.

The objective of this study is to assess the impact on nodule detection and efficiency using a computer-aided detection (CAD) device seamlessly integrated into a commercially available picture archiving and communication system (PACS). Forty-eight consecutive low-dose thoracic computed tomography studies were retrospectively included from an ongoing multi-institutional screening study. CAD results were sent to PACS as a separate image series for each study. Five fellowship-trained thoracic radiologists interpreted each case first on contiguous 5 mm sections, then evaluated the CAD output series (with CAD marks on corresponding axial sections). The standard of reference was based on three-reader agreement with expert adjudication. The time to interpret CAD marking was automatically recorded. A total of 134 true-positive nodules, measuring 3 mm and larger were included in our study; with 85 ≥ 4 and 50 ≥ 5 mm in size. Readers detection improved significantly in each size category when using CAD, respectively, from 44 to 57 % for ≥3 mm, 48 to 61 % for ≥4 mm, and 44 to 60 % for ≥5 mm. CAD stand-alone sensitivity was 65, 68, and 66 % for nodules ≥3, ≥4, and ≥5 mm, respectively, with CAD significantly increasing the false positives for two readers only. The average time to interpret and annotate a CAD mark was 15.1 s, after localizing it in the original image series. The integration of CAD into PACS increases reader sensitivity with minimal impact on interpretation time and supports such implementation into daily clinical practice.

Kinetic simulation of a centrifugal bioreactor for high population density hybridoma culture.

Demand for increasingly complex post-translationally modified proteins, such as monoclonal antibodies (mAbs), necessitates the use of mammalian hosts for production. The focus of this article is a continuous centrifugal bioreactor (CCBR) capable of increasing volumetric productivity for mAb production through high density hybridoma culture, exceeding 10(8) cells/mL. At these extreme densities, environmental conditions such as substrate and inhibitor concentrations rapidly change dramatically affecting the growth rate. The development of a kinetic model predicting glucose, mAb, lactate, and ammonium concentrations based on dilution rate and cell density is shown in this article. Additionally, it is found that pH affects both growth rate and viability, and a range of 6.9-7.4 is needed to maintain growth rate above 90% of the maximum. Modeling shows that operating an 11.4 mL CCBR inoculated with 2.0 x 10(7) cells/mL at a dilution rate of 1.3 h(-1), results in a predicted growth rate 82% of the maximum value. At the same dilution rate increasing density to 6.0 x 10(7) cells/mL decreases the predicted growth rate to 60% of the maximum; however, by increasing dilution rate to 6.1 h(-1) the growth rate can be increased to 86% of the maximum. Using the kinetic model developed in this research, the concentration of glucose, mAb, lactate, and ammonium are all predicted within 13% of experimental results. This model and an understanding of how RPM impacts cell retention serve as valuable tools for maintaining high density CCBR cultures, ensuring maximum growth associated mAb production rates.