PCCT: Progressive Class-Center Triplet Loss for Imbalanced Medical Image Classification.

Imbalanced training data in medical image diagnosis is a significant challenge for diagnosing rare diseases. For this purpose, we propose a novel two-stage Progressive Class-Center Triplet (PCCT) framework to overcome the class imbalance issue. In the first stage, PCCT designs a class-balanced triplet loss to coarsely separate distributions of different classes. Triplets are sampled equally for each class at each training iteration, which alleviates the imbalanced data issue and lays solid foundation for the successive stage. In the second stage, PCCT further designs a class-center involved triplet strategy to enable a more compact distribution for each class. The positive and negative samples in each triplet are replaced by their corresponding class centers, which prompts compact class representations and benefits training stability. The idea of class-center involved loss can be extended to the pair-wise ranking loss and the quadruplet loss, which demonstrates the generalization of the proposed framework. Extensive experiments support that the PCCT framework works effectively for medical image classification with imbalanced training images. On four challenging class-imbalanced datasets (two skin datasets Skin7 and Skin 198, one chest X-ray dataset ChestXray-COVID, and one eye dataset Kaggle EyePACs), the proposed approach respectively obtains the mean F1 score 86.20, 65.20, 91.32, and 87.18 over all classes and 81.40, 63.87, 82.62, and 79.09 for rare classes, achieving state-of-the-art performance and outperforming the widely used methods for the class imbalance issue.

Antibody-mediated cell entry of SARS-CoV-2 (preprint)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters host cells by first engaging its cellular receptor angiotensin converting enzyme 2 (ACE2) to induce conformational changes in the virus-encoded spike protein and fusion between the viral and target cell membranes. We report here that certain monoclonal neutralizing antibodies against distinct epitopic regions of the receptor-binding domain of the spike can replace ACE2 to serve as a receptor and efficiently support membrane fusion and viral infectivity. These receptor-like antibodies can function in the form of a complex of their soluble immunoglobulin G with Fc-gamma receptor I, a chimera of their antigen-binding fragment with the transmembrane domain of ACE2 or a membrane-bound B cell receptor, indicating that ACE2 and its specific interactions with the spike protein are dispensable for SARS-CoV-2 entry. These results suggest that antibody responses against SARS-CoV-2 may expand the viral tropism to otherwise nonpermissive cell types; they have important implications for viral transmission and pathogenesis.

Reciprocal Effect between Depressive Symptoms and Adolescent Non-suicidal self-injury before and after COVID-19: A Longitudinal Study (preprint)

Background Non-suicidal   self-injury (NSSI) is a common psychological and behavioral problem among   adolescents and has now become a major public health problem for adolescents.   Since the COVID-19 outbreak in 2019, it has caused various mental health   problems, such as anxiety, depression, and mental burnout, contributing to a   severe mental health crisis globally. Thus far, a few studies recorded the   temporal change in adolescents’ psychological status during the COVID-19   pandemic as well as that with the implementation of large-scale public health   intervention methods, and this study adds to the evidence. Methods Based on   the Chengdu Positive Child Development (CPCD) survey, the baseline dataset   was collected in December 2019, and the first follow-up of the CPCD was conducted   in July 2020. A total of 6,023 adolescents aged 10-19 were recruited from   five primary and middle schools. Two independent autoregressive cross-lagged   models were used to test the bidirectional relationship between NSSI and   depressive symptoms in adolescents; logistic regression analysis was used to   explore the predictors of NSSI implementation in adolescents with depressive   symptoms, which could provide an entry point for behavioral interventions to   NSSI. Results The   prevalence of depressive symptoms among our participants was 32.69% at   baseline, and 34.27% at follow-up. The occurrence rate of NSSI in adolescents   who may have depressive symptoms was 44.34%%, and that during the pandemic   was 53.44%. The difference was statistically significant (P <   0.05). The results of the binary logistic analysis showed that among   adolescents, gender, duration of the online class, depression mood, place of   residence, and self-perception of relationship with caregivers were the risk   factors for NSSI (or > 1, β> 0), and daily sleep hours positive mood   was the protective factor (or < 1, β< 0).  The lag effect of adolescent depression on   their NSSI behavior is significant, which means that based on controlling the   adolescent baseline NSSI, the deeper the adolescent depression degree, the   more frequent their NSSI behavior (β=0.26, P<0.01). At the same time,   adolescents' NSSI behavior also had a lagging effect on depressive symptoms,   and adolescents with self-injury behavior were more likely to be depressed (β=0.02, P<0.01). Depression and   NSSI are mutual(β=0.77,   P<0.05；β=0.27,   P<0.01). Conclusions The   increased depressive symptoms among adolescents exacerbated their NSSI   behaviors and hurt their mental health during COVID-19. Screening for   depression should be carried out early to serve as a warning sign in   preventing and reducing NSSI in adolescents.

Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane (preprint)

Entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into host cells depends on refolding of the virus-encoded spike protein from a prefusion conformation, metastable after cleavage, to a lower energy, stable postfusion conformation. This transition overcomes kinetic barriers for fusion of viral and target cell membranes. We report here a cryo-EM structure of the intact postfusion spike in a lipid bilayer that represents single-membrane product of the fusion reaction. The structure provides structural definition of the functionally critical membrane-interacting segments, including the fusion peptide and transmembrane anchor. The internal fusion peptide forms a hairpin-like wedge that spans almost the entire lipid bilayer and the transmembrane segment wraps around the fusion peptide at the last stage of membrane fusion. These results advance our understanding of the spike protein in a membrane environment and may guide development of intervention strategies.

Clinical predictors and RT-PCR profile of prolonged viral shedding in patients with SARS-CoV-2 Omicron variant in Shanghai: A retrospective observational study

Objective To evaluate determinants of prolonged viral RNA shedding in hospitalized patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant infection. Materials and methods Hospitalized patients tested SARS-CoV-2 positive by nasopharyngeal real-time reverse transcriptase-polymerase chain reaction (RT-PCR) were included in the single-center, retrospective study. Patients were divided into 2 groups according to the timing of viral clearance (≤ 8 days, “early clearance” and ≥15 days, “late clearance”). Results 4,084 patients were included in the study (1,023 late clearance, 3,061 early clearance), with median age of 50 years and a higher proportion (61.4%) of male. Univariate analyses showed that comorbidities (including hypertension, diabetes, and coronary heart disease), receiving vaccine, the number of vaccinations, cycle threshold (Ct) open reading frame 1ab (ORF 1ab), and nucleocapsid protein (N) gene values on admission were associated with late viral clearance. In the multivariable analysis, the number of vaccinations (P = 0.010) and Ct ORF 1ab gene (P < 0.001) values on admission were significantly associated with late viral clearance. Generalized Estimating Equations (GEE) analysis showed that the Ct value of ORF 1ab gene and N gene remained unchanged within 3 days, and showed progressively higher values with increasing days during late viral RNA clearance. Conclusion The number of vaccinations and Ct values of ORF 1ab gene were independently associated with a prolonged SARS-CoV-2 RNA shedding.

DAFLNet: Dual Asymmetric Feature Learning Network for COVID-19 Disease Diagnosis in X-Rays

COVID-19 has become the largest public health event worldwide since its outbreak, and early detection is a prerequisite for effective treatment. Chest X-ray images have become an important basis for screening and monitoring the disease, and deep learning has shown great potential for this task. Many studies have proposed deep learning methods for automated diagnosis of COVID-19. Although these methods have achieved excellent performance in terms of detection, most have been evaluated using limited datasets and typically use a single deep learning network to extract features. To this end, the dual asymmetric feature learning network (DAFLNet) is proposed, which is divided into two modules, DAFFM and WDFM. DAFFM mainly comprises the backbone networks EfficientNetV2 and DenseNet for feature fusion. WDFM is mainly for weighted decision-level fusion and features a new pretrained network selection algorithm (PNSA) for determination of the optimal weights. Experiments on a large dataset were conducted using two schemes, DAFLNet-1 and DAFLNet-2, and both schemes outperformed eight state-of-the-art classification techniques in terms of classification performance. DAFLNet-1 achieved an average accuracy of up to 98.56% for the triple classification of COVID-19, pneumonia, and healthy images.

A multispecific antibody confers pan-reactive SARS-CoV-2 neutralization and prevents immune escape (preprint)

Continued evolution of the SARS-CoV-2 spike poses a challenge to immune interventions. To develop antibodies that protect against evolving SARS-CoV-2 viruses, we combined antibodies that recognize different RBD sites to generate a trivalent antibody that potently neutralized all major variants, including the most recent Omicron lineages. Negative stain electron microscopy suggests that this multispecific achieves synergistic neutralization by engaging different epitopes in specific orientations that facilitate inter-spike binding. These interactions resulted in not only improved potency but also importantly prevented virus escape, a feature not seen with parental antibody cocktails or the most potent clinical mAb. Such multispecific antibodies simplify treatment, maximize coverage, decrease the likelihood of SARS-CoV-2 escape, and provide the basis for building universal SARS-CoV-2 antibody therapies that are more likely to maintain broad reactivity for future variants.

Convergent epitope specificities, V gene usage and public clones elicited by primary exposure to SARS-CoV-2 variants (preprint)

While humoral immune responses to infection or vaccination with ancestral SARS-CoV-2 have been well-characterized, responses elicited by infection with variants are less understood. Here we characterized the repertoire, epitope specificity, and cross-reactivity of antibodies elicited by Beta and Gamma variant infection compared to ancestral virus. We developed a high-throughput approach to obtain single-cell immunoglobulin sequences and isolate monoclonal antibodies for functional assessment. Spike-, RBD- and NTD-specific antibodies elicited by Beta- or Gamma-infection exhibited a remarkably similar hierarchy of epitope immunodominance for RBD and convergent V gene usage when compared to ancestral virus infection. Additionally, similar public B cell clones were elicited regardless of infecting variant. These convergent responses may account for the broad cross-reactivity and continued efficacy of vaccines based on a single ancestral variant.

Reliability and validity of the Pittsburgh Sleep Quality Index among frontline COVID-19 health care workers using classical test theory and item response theory.

STUDY OBJECTIVES: The applicability of sleep-related scales to frontline medical staff for the COVID-19 pandemic has not been fully proved, so sleep survey results lack credibility and accuracy, creating difficulties for the guidance and treatment of frontline medical staff with sleep disorders, which is not conducive to the prevention and control of COVID-19. This study sought to analyze the reliability and validity of the Pittsburgh Sleep Quality Index (PSQI) among frontline medical staff fighting the COVID-19 pandemic. METHODS: A network questionnaire survey was used to investigate the PSQI among frontline medical staff who fought COVID-19 in Wuhan, China from March 19 to April 15, 2020. Combined with classical test theory and item response theory, the content validity, internal consistency, construct validity, and other aspects of the PSQI were evaluated. RESULTS: According to classical test theory, content validity, criterion validity, and construct validity of the PSQI were good. But the internal consistency was better after the deletion of the "daytime dysfunction" subscale. With regard to item response theory, difficulty, the differential item function, and the Wright map performed well. CONCLUSIONS: The original PSQI showed acceptable applicability in frontline COVID-19 medical staff, and its characteristics moderately improved after the "daytime dysfunction" subscale was removed. CITATION: Wang L, Wu Y-X, Lin Y-Q, et al. Reliability and validity of the Pittsburgh Sleep Quality Index among frontline COVID-19 health care workers using classical test theory and item response theory. J Clin Sleep Med. 2022;18(2):541-551.

mRNA-1273 or mRNA-Omicron boost in vaccinated macaques elicits comparable B cell expansion, neutralizing antibodies and protection against Omicron (preprint)

SARS-CoV-2 Omicron is highly transmissible and has substantial resistance to antibody neutralization following immunization with ancestral spike-matched vaccines. It is unclear whether boosting with Omicron-specific vaccines would enhance immunity and protection. Here, nonhuman primates that received mRNA-1273 at weeks 0 and 4 were boosted at week 41 with mRNA-1273 or mRNA-Omicron. Neutralizing antibody titers against D614G were 4760 and 270 reciprocal ID50 at week 6 (peak) and week 41 (pre-boost), respectively, and 320 and 110 for Omicron. Two weeks after boost, titers against D614G and Omicron increased to 5360 and 2980, respectively, for mRNA-1273 and 2670 and 1930 for mRNA-Omicron. Following either boost, 70-80% of spike-specific B cells were cross-reactive against both WA1 and Omicron. Significant and equivalent control of virus replication in lower airways was observed following either boost. Therefore, an Omicron boost may not provide greater immunity or protection compared to a boost with the current mRNA-1273 vaccine.

Vaccine-elicited murine antibody WS6 neutralizes diverse beta-coronaviruses by recognizing a helical stem supersite of vulnerability (preprint)

Immunization with SARS-CoV-2 spike elicits diverse antibodies, but can any of these neutralize broadly? Here, we report the isolation and characterization of antibody WS6, from a mouse immunized with mRNA encoding the SARS-CoV-2 spike. WS6 bound diverse beta-coronavirus spikes and neutralized SARS-CoV-2 variants, SARS-CoV, and related sarbecoviruses. Epitope mapping revealed WS6 to target a region in the S2 subunit, which was conserved among SARS-CoV-2, MERS-CoV, and hCoV-OC43. The crystal structure at 2-angstrom resolution of WS6 with its S2 epitope revealed recognition to center on a conserved helix, which was occluded in both prefusion and post-fusion spike conformations. Structural and neutralization analyses indicated WS6 to neutralize by inhibiting fusion, post-viral attachment. Comparison of WS6 to other antibodies recently identified from convalescent donors or mice immunized with diverse spikes indicated a stem-helical supersite - centered on hydrophobic residues Phe1148, Leu1152, Tyr1155, and Phe1156 - to be a promising target for vaccine design.

The Mental Health Status and Associated Factors Among Medical Students Engaged in Online Learning at Home During the Pandemic: A Cross-Sectional Study From China

Background: The purpose of this study was to assess the mental health status of medical students engaged in online learning at home during the pandemic, and explore the potential risk factors of mental health. Methods: A cross-sectional study was conducted via an online survey among 5,100 medical students from Wannan Medical College in China. The Depression, Anxiety and Stress scale (DASS-21) was used to measure self-reported symptoms of depression, anxiety, and stress among medical students during online learning in the pandemic. Results: In total, 4,115 participants were included in the study. The prevalence symptoms of depression, anxiety, and stress were 31.9, 32.9, and 14.6%, respectively. Depression was associated with gender, grade, length of schooling, relationship with father, students' daily online learning time, and students' satisfaction with online learning effects. Anxiety was associated with gender, length of schooling, relationship with father, relationship between parents, students' daily online learning time, and students' satisfaction with online learning effects. Stress was associated with grade, relationship with father, relationship between parents, students' daily online learning time, and students' satisfaction with online learning effects. Conclusions: Nearly one-third of medical students survived with varying degrees of depression, anxiety, and stress symptoms during online learning of the COVID-19 pandemic. Gender, grade, length of schooling, family environment, and online learning environment play vital roles in medical students' mental health. Families and schools should provide targeted psychological counseling to high-risk students (male, second-year and third-year, four-year program). The findings of this study can provide reference for educators to cope with the psychological problems and formulate the mental health curriculum construction among medical students during online learning.

Structural basis for potent antibody neutralization of SARS-CoV-2 variants including B.1.1.529 (preprint)

With B.1.1.529 SARS-CoV-2 variant's rapid spread and substantially increased resistance to neutralization by vaccinee and convalescent sera, monoclonal antibodies with potent neutralization are eagerly sought. To provide insight into effective neutralization, we determined cryo-EM structures and evaluated potent receptor-binding domain (RBD) antibodies for their ability to bind and neutralize this new variant. B.1.1.529 RBD mutations altered 16% of the RBD surface, clustering on a ridge of this domain proximal to the ACE2-binding surface and reducing binding of most antibodies. Significant inhibitory activity was retained, however, by select monoclonal antibodies including A19-58.1, B1-182.1, COV2-2196, S2E12, A19-46.1, S309 and LY-CoV1404, which accommodated these changes and neutralized B.1.1.529 with IC50s between 5.1-281 ng/ml, and we identified combinations of antibodies with potent synergistic neutralization. Structure-function analyses delineated the impact of resistance mutations and revealed structural mechanisms for maintenance of potent neutralization against emerging variants.

Associations of stay-at-home order and face-masking recommendation with trends in daily new cases and deaths of laboratory-confirmed COVID-19 in the United States

BACKGROUND AND OBJECTIVES: Public health interventions were associated with reduction in coronavirus disease 2019 (COVID-19) transmission in China, but their impacts on COVID-19 epidemiology in other countries are unclear. We examined the associations of stay-at-home order (SAHO) and face-masking recommendation with epidemiology of laboratory-confirmed COVID-19 in the United States. METHODS: In this quasi-experimental study, we modeled the temporal trends in daily new cases and deaths of COVID-19, and COVID-19 time-varying reproduction numbers (Rt) in the United States between March 1 and April 20, 2020, and conducted simulation studies. RESULTS: The number and proportion of U.S. residents under SAHO increased between March 19 and April 7, and plateaued at 29,0829,980 and 88.6%, respectively. Trends in COVID-19 daily cases and Rt reduced after March 23 (P<0.001) and further reduced on April 3 (P<0.001), which was associated with implementation of SAHO by 10 states on March 23, and face-masking recommendation on April 3, respectively. The estimates of Rt eventually fell below/around 1.0 on April 13. Similar turning points were identified in the trends of daily deaths with a lag time. Early implementation and early-removal of SAHO would be associated with significantly reduced and increased daily new cases and deaths, respectively.

Protection against SARS-CoV-2 Beta variant in mRNA-1273 vaccine-boosted nonhuman primates.

Neutralizing antibody responses gradually wane against several variants of concern (VOCs) after vaccination with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine messenger RNA-1273 (mRNA-1273). We evaluated the immune responses in nonhuman primates that received a primary vaccination series of mRNA-1273 and were boosted about 6 months later with either homologous mRNA-1273 or heterologous mRNA-1273.ß, which encompasses the spike sequence of the B.1.351 Beta variant. After boost, animals had increased neutralizing antibody responses across all VOCs, which was sustained for at least 8 weeks after boost. Nine weeks after boost, animals were challenged with the SARS-CoV-2 Beta variant. Viral replication was low to undetectable in bronchoalveolar lavage and significantly reduced in nasal swabs in all boosted animals, suggesting that booster vaccinations may be required to sustain immunity and protection.

Protection from SARS-CoV-2 Delta one year after mRNA-1273 vaccination in nonhuman primates is coincident with an anamnestic antibody response in the lower airway (preprint)

mRNA-1273 vaccine efficacy against SARS-CoV-2 Delta wanes over time; however, there are limited data on the impact of durability of immune responses on protection. We immunized rhesus macaques at weeks 0 and 4 and assessed immune responses over one year in blood, upper and lower airways. Serum neutralizing titers to Delta were 280 and 34 reciprocal ID50 at weeks 6 (peak) and 48 (challenge), respectively. Antibody binding titers also decreased in bronchoalveolar lavage (BAL). Four days after challenge, virus was unculturable in BAL and subgenomic RNA declined ~3-log10 compared to control animals. In nasal swabs, sgRNA declined 1-log10 and virus remained culturable. Anamnestic antibody responses (590-fold increase) but not T cell responses were detected in BAL by day 4 post-challenge. mRNA-1273-mediated protection in the lungs is durable but delayed and potentially dependent on anamnestic antibody responses. Rapid and sustained protection in upper and lower airways may eventually require a boost.

Protection against SARS-CoV-2 Beta Variant in mRNA-1273 Boosted Nonhuman Primates (preprint)

Neutralizing antibody responses gradually wane after vaccination with mRNA-1273 against several variants of concern (VOC), and additional boost vaccinations may be required to sustain immunity and protection. Here, we evaluated the immune responses in nonhuman primates that received 100 {micro}g of mRNA-1273 vaccine at 0 and 4 weeks and were boosted at week 29 with mRNA-1273 (homologous) or mRNA-1273.{beta} (heterologous), which encompasses the spike sequence of the B.1.351 (beta or {beta}) variant. Reciprocal ID50 pseudovirus neutralizing antibody geometric mean titers (GMT) against live SARS-CoV-2 D614G and the {beta} variant, were 4700 and 765, respectively, at week 6, the peak of primary response, and 644 and 553, respectively, at a 5-month post-vaccination memory time point. Two weeks following homologous or heterologous boost {beta}-specific reciprocal ID50 GMT were 5000 and 3000, respectively. At week 38, animals were challenged in the upper and lower airway with the {beta} variant. Two days post-challenge, viral replication was low to undetectable in both BAL and nasal swabs in most of the boosted animals. These data show that boosting with the homologous mRNA-1273 vaccine six months after primary immunization provides up to a 20-fold increase in neutralizing antibody responses across all VOC, which may be required to sustain high-level protection against severe disease, especially for at-risk populations. One-sentence summarymRNA-1273 boosted nonhuman primates have increased immune responses and are protected against SARS-CoV-2 beta infection.

Associations of Stay-at-Home Order and Face-Masking Recommendation with Trends in Daily New Cases and Deaths of Laboratory-Confirmed COVID-19 in the United States.

BACKGROUND AND OBJECTIVES: Public health interventions have reduced coronavirus disease 2019 (COVID-19) transmission in several countries, but their impacts on COVID-19 epidemics in the USA are unclear. We examined associations of stay-at-home order (SAHO) and face-masking recommendation with COVID-19 epidemics in the USA. METHODS: In this quasi-experimental interrupted time-series study, we modeled temporal trends in daily new cases and deaths of laboratory-confirmed COVID-19 cases, and COVID-19 time-varying reproduction numbers in the USA between March 1 and April 20, 2020. In addition, we conducted simulation analyses. RESULTS: The number of residents under SAHO increased since March 19 and plateaued at 290,829,980 (88.6% of the U.S. population) on April 7. Trends in COVID-19 time-varying reproduction numbers peaked on March 23, further reduced on April 3, and fell below/around 1.0 on April 13. Early-implementation and early-lift of SAHO would reduce and increase COVID-19 epidemics, respectively. Multivariable piecewise log-linear regression revealed the states' neighboring relationship with New York was linked to COVID-19 daily new cases and deaths. There were two turning points in daily new-case trend, being March 28 (slope-changes = -0.09) and April 3 (slope-changes = -0.09), which appeared to be associated with implementation of SAHO on March 28 (affecting 48.5% of the US population in 22 states and District of Columbia), and face-masking recommendation on April 3, respectively. There were also two turning points in daily new-death trend, being April 9 (slope-changes = -0.06) and April 19 (slope-changes = -0.90). CONCLUSIONS: We identified two turning points of COVID-19 daily new cases or deaths in the USA, which seem to be linked to implementation of SAHO and the Center for Disease Control's face-masking recommendation.