Transient anti-interferon autoantibodies in the airways are associated with recovery from COVID-19.

Preexisting anti-interferon-α (anti-IFN-α) autoantibodies in blood are associated with susceptibility to life-threatening COVID-19. However, it is unclear whether anti-IFN-α autoantibodies in the airways, the initial site of infection, can also determine disease outcomes. In this study, we developed a multiparameter technology, FlowBEAT, to quantify and profile the isotypes of anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and anti-IFN-α antibodies in longitudinal samples collected over 20 months from the airways and blood of 129 donors spanning mild to severe COVID-19.

Predictive Validity of the HESI Radiography Exit Exam and Best Practices for ARRT Certification Exam Success.

Purpose: To determine the predictive validity of Health Education Systems Incorporated (HESI) Exit Exam scores for student first-time success on the American Registry of Radiologic Technologists (ARRT) certification exam and to analyze whether schools' policies on the HESI Exit Exam are associated with end-of-program student success.

Methods: Twenty-five radiography program directors provided retrospective data on ARRT certification exam student outcomes, and 24 program directors completed the HESI Exit Exam program policy survey. Data analysis was performed to examine the correlation between students' HESI Exit Exam scores and their first-time ARRT certification exam outcomes and to investigate the relationship between program policies and performance on both exams.

UK research priority setting for childhood neurological conditions.

Aim: To identify research priorities regarding the effectiveness of interventions for children and young people (CYP) with childhood neurological conditions (CNCs). These include common conditions such as epilepsies and cerebral palsy, as well as many rare conditions.

Method: The National Institute for Health and Care Research (NIHR) and the James Lind Alliance (JLA) champion and facilitate priority setting partnerships (PSPs) between patients, caregivers, and clinicians (stakeholders) to identify the most important unanswered questions for research (uncertainties).

HESI Admission Assessment, HESI Radiography Exit Exam, and ARRT Outcomes.

Purpose: To analyze a radiography program's use of the Health Education Systems Incorporated Admission Assessment (HESI A2) and the HESI Exit Exam for preparing graduates to take the American Registry of Radiologic Technologists (ARRT) certification and registration exam for radiography.

Methods: The program collected exam scores from the HESI Exit Exam for radiography and the ARRT radiography certification and registration exam for a 10-year period. The study included scores of 171 students who graduated from the radiography education program.

Hospitalized Infants With Medical Complexity Experience Slow Acquisition of Gross Motor Skills.

Objectives: The progression of infant gross motor development during an acute hospitalization is unknown. Understanding gross motor skill acquisition in hospitalized infants with complex medical conditions is necessary to develop and evaluate interventions that may lessen delays. Establishing a baseline of gross motor abilities and skill development for these infants will guide future research.

scRNA-seq for Microcephaly Research [III]: Computational Analysis of scRNA-seq Data.

Single-cell transcriptomic analysis (scRNA-seq) can enable researchers to explore the gene expression patterns of thousands of individual cells simultaneously. Processing the complex data generated by scRNA-seq requires specialized computational tools. This chapter focuses on the analytical aspect of scRNA-seq workflow, with a focus on resolving biological signals from large-scale scRNA-seq data produced by the Drop-Seq platform.

scRNA-seq for Microcephaly Research [II]: Preparation of Single-Cell cDNA Libraries.

Droplet-based single-cell RNA-seq (scRNA-seq) requires the addition of bar codes that mark the cell and transcript of origin. Cell-specific bar codes, typically added by cDNA elongation on beads, label each transcript derived from an individual cell. Transcript-specific bar codes serve as unique molecular identifiers and allow for the maintenance of transcript proportions after PCR-based amplification of cDNA.

scRNA-seq for Microcephaly Research [I]: Single-Cell Droplet Encapsulation, mRNA Capture, and cDNA Synthesis.

Single-cell RNA sequencing (scRNA-seq) allows for the transcriptomic profiling of a sample tissue with single-cell resolution. The concept of scRNA-seq builds on traditional, "bulk" RNA-seq by recording and preserving the cellular origin of each transcript throughout library preparation. Here we describe an adaptation of the Drop-Seq method (Macosko et al.

Comprehensive multi-omics single-cell data integration reveals greater heterogeneity in the human immune system.

Single-cell transcriptomics enables the definition of diverse human immune cell types across multiple tissues and disease contexts. Further deeper biological understanding requires comprehensive integration of multiple single-cell omics (transcriptomic, proteomic, and cell-receptor repertoire). To improve the identification of diverse cell types and the accuracy of cell-type classification in multi-omics single-cell datasets, we developed SuPERR, a novel analysis workflow to increase the resolution and accuracy of clustering and allow for the discovery of previously hidden cell subsets.

Noncanonical activation of GLI signaling in SOX2 cells drives medulloblastoma relapse.

SRY (sex determining region Y)-box 2 (SOX2)-labeled cells play key roles in chemoresistance and tumor relapse; thus, it is critical to elucidate the mechanisms propagating them. Single-cell transcriptomic analyses of the most common malignant pediatric brain tumor, medulloblastoma (MB), revealed the existence of astrocytic cells expressing sonic hedgehog (SHH) signaling biomarkers. Treatment with vismodegib, an SHH inhibitor that acts on Smoothened (Smo), led to increases in astrocyte-like cells.

Protracted yet Coordinated Differentiation of Long-Lived SARS-CoV-2-Specific CD8 T Cells during Convalescence.

CD8 T cells can potentiate long-lived immunity against COVID-19. We screened longitudinally-sampled convalescent human donors against SARS-CoV-2 tetramers and identified a participant with an immunodominant response against residues 322 to 311 of nucleocapsid (Nuc), a peptide conserved in all variants of concern reported to date. We conducted 38-parameter cytometry by time of flight on tetramer-identified Nuc-specific CD8 T cells and on CD4 and CD8 T cells recognizing the entire nucleocapsid and spike proteins, and took 32 serological measurements.

Cryptic developmental events determine medulloblastoma radiosensitivity and cellular heterogeneity without altering transcriptomic profile.

It is unclear why medulloblastoma patients receiving similar treatments experience different outcomes. Transcriptomic profiling identified subgroups with different prognoses, but in each subgroup, individuals remain at risk of incurable recurrence. To investigate why similar-appearing tumors produce variable outcomes, we analyzed medulloblastomas triggered in transgenic mice by a common driver mutation expressed at different points in brain development.

Protracted yet coordinated differentiation of long-lived SARS-CoV-2-specific CD8+ T cells during COVID-19 convalescence.

CD8+ T cells are important antiviral effectors that can potentiate long-lived immunity against COVID-19, but a detailed characterization of these cells has been hampered by technical challenges. We screened 21 well-characterized, longitudinally-sampled convalescent donors that recovered from mild COVID-19 against a collection of SARS-CoV-2 tetramers, and identified one participant with an immunodominant response against Nuc, a peptide that is conserved in all the SARS-CoV-2 variants-of-concern reported to date. We conducted 38-parameter CyTOF phenotyping on tetramer-identified Nuc-specific CD8+ T cells, and on CD4+ and CD8+ T cells recognizing the entire nucleocapsid and spike proteins from SARS-CoV-2, and took 32 serological measurements on longitudinal specimens from this participant.

Perceived Vulnerability and Propensity to Adopt Best Management Practices for Huanglongbing Disease of Citrus in California.

Huanglongbing (HLB) disease of citrus, which is associated with the bacterium ' Liberibacter asiaticus', has been confined to residential properties in Southern California 8 years after it was first detected in the state. To prevent the spread of HLB to commercial citrus groves, growers have been asked to adopt a portfolio of voluntary best management practices. This study evaluates the citrus industry's propensity to adopt these practices using surveys and a novel multivariate ordinal regression model.

Exam Performance of Reinstatement Candidates Pursuing ARRT Certification and Registration in Radiography.

Purpose: To investigate the exam performance of reinstatement candidates pursuing the American Registry of Radiologic Technologists (ARRT) certification and registration in radiography.

Methods: This study compared exam performance data from reinstatement candidates taking the ARRT radiography exam in 2017 and 2018 (N = 412) to the performance of 2017 and 2018 first-time exam candidates (N = 22 731) and the reinstatement candidates' past successful passing exam attempts.

Results: Scores on the reinstatement exam at the overall exam and the section levels were significantly lower (P < .

Molecular Targeting of H/MDM-2 Oncoprotein in Human Colon Cancer Cells and Stem-like Colonic Epithelial-derived Progenitor Cells.

Background/aim: We have tested whether the anticancer peptide, PNC-27, that kills cancer cells but not normal cells by binding to cancer cell membrane HDM-2 forming pores, kills CD44+ colon cancer stem cells.

Materials And Methods: Flow cytometry determined the CD44 and HDM-2 expression on six-colon cancer cell lines and one normal cell line (CCD-18Co). MTT, LDH release, annexin V binding and caspase 3 assays were used to assess PNC-27-induced cell death.

Antiapoptotic Bcl-2 family proteins BCL-xL and MCL-1 integrate neural progenitor survival and proliferation during postnatal cerebellar neurogenesis.

The tendency of brain cells to undergo apoptosis in response to exogenous events varies across neural development, with apoptotic threshold dependent on proliferation state. Proliferative neural progenitors show a low threshold for apoptosis, while terminally differentiated neurons are relatively refractory. To define the mechanisms linking proliferation and apoptotic threshold, we examined the effect of conditionally deleting Bcl2l1, the gene that codes the antiapoptotic protein BCL-xL, in cerebellar granule neuron progenitors (CGNPs), and of co-deleting Bcl2l1 homologs, antiapoptotic Mcl-1, or pro-apoptotic Bax.

Peritoneal carcinomatosis in gastric cancer: Are Hispanics at higher risk?

Background: A recent study from our group identified Hispanic race/ethnicity as an independent predictor of peritoneal carcinomatosis (PC) in gastric cancer. We sought to identify the tumor factors that might contribute to this strong association in Hispanics.

Methods: California Cancer Registry data were used to identify patients diagnosed with gastric adenocarcinoma from 2004 to 2014.

Rasch Versus Classical Equating in the Context of Small Sample Sizes.

Equating and scaling in the context of small sample exams, such as credentialing exams for highly specialized professions, has received increased attention in recent research. Investigators have proposed a variety of both classical and Rasch-based approaches to the problem. This study attempts to extend past research by (1) directly comparing classical and Rasch techniques of equating exam scores when sample sizes are small (≤ 100 per exam form) and (2) attempting to pool multiple forms' worth of data to improve estimation in the Rasch framework.

Projected t-SNE for batch correction.

Motivation: Low-dimensional representations of high-dimensional data are routinely employed in biomedical research to visualize, interpret and communicate results from different pipelines. In this article, we propose a novel procedure to directly estimate t-SNE embeddings that are not driven by batch effects. Without correction, interesting structure in the data can be obscured by batch effects.

The Equivalence of the Test Response Function to the Maximum Likelihood Ability Estimate for the Dichotomous Rasch Model: A Proof.

While several proofs exist that the number keyed (or number correct) score is a sufficient statistic to estimate person measure (or ability, beta) in the dichotomous Rasch model, there are few proofs about the direct mathematical link from beta to the number correct score. This manuscript proves that the estimation link going from score to beta is the test response function, which is the sum of the probabilities correct for all items given the difficulty (delta) values and beta.

scRNA-seq in medulloblastoma shows cellular heterogeneity and lineage expansion support resistance to SHH inhibitor therapy.

Targeting oncogenic pathways holds promise for brain tumor treatment, but inhibition of Sonic Hedgehog (SHH) signaling has failed in SHH-driven medulloblastoma. Cellular diversity within tumors and reduced lineage commitment can undermine targeted therapy by increasing the probability of treatment-resistant populations. Using single-cell RNA-seq and lineage tracing, we analyzed cellular diversity in medulloblastomas in transgenic, medulloblastoma-prone mice, and responses to the SHH-pathway inhibitor vismodegib.

Improved Survival with Immunotherapy but Lack of Synergistic Effect with Radiation for Stage IV Melanoma of the Head and Neck.

Prospective randomized studies have demonstrated a survival benefit of immunotherapy in stage IV cutaneous melanoma. Some retrospective studies have hypothesized a synergistic effect of radiation and immunotherapy. Our objective was to identify whether there is a survival benefit for patients treated with radiation and immunotherapy in stage IV cutaneous melanoma of the head and neck (CMHN).