Neighborhood-based inference and restricted Boltzmann machine for microbe and drug associations prediction.

Background: Efficient identification of microbe-drug associations is critical for drug development and solving problem of antimicrobial resistance. Traditional wet-lab method requires a lot of money and labor in identifying potential microbe-drug associations. With development of machine learning and publication of large amounts of biological data, computational methods become feasible. Methods: In this article, we proposed a computational model of neighborhood-based inference (NI) and restricted Boltzmann machine (RBM) to predict potential microbe-drug association (NIRBMMDA) by using integrated microbe similarity, integrated drug similarity and known microbe-drug associations. First, NI was used to obtain a score matrix of potential microbe-drug associations by using different thresholds to find similar neighbors for drug or microbe. Second, RBM was employed to obtain another score matrix of potential microbe-drug associations based on contrastive divergence algorithm and sigmoid function. Because generalization ability of individual method is poor, we used an ensemble learning to integrate two score matrices for predicting potential microbe-drug associations more accurately. In particular, NI can fully utilize similar (neighbor) information of drug or microbe and RBM can learn potential probability distribution hid in known microbe-drug associations. Moreover, ensemble learning was used to integrate individual predictor for obtaining a stronger predictor. Results: In global leave-one-out cross validation (LOOCV), NIRBMMDA gained the area under the receiver operating characteristics curve (AUC) of 0.8666, 0.9413 and 0.9557 for datasets of DrugVirus, MDAD and aBiofilm, respectively. In local LOOCV, AUCs of 0.8512, 0.9204 and 0.9414 were obtained for NIRBMMDA based on datasets of DrugVirus, MDAD and aBiofilm, respectively. For five-fold cross validation, NIRBMMDA acquired AUC and standard deviation of 0.8569 ± -0.0027, 0.9248 ± -0.0014 and 0.9369 ± -0.0020 on the basis of datasets of DrugVirus, MDAD and aBiofilm, respectively. Moreover, case study for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) showed that 13 out of the top 20 predicted drugs were verified by searching literature. The other two case studies indicated that 17 and 17 out of the top 20 predicted microbes for the drug of ciprofloxacin and minocycline were confirmed by identifying published literature, respectively.

Beijing Pinggu Childhood Eye Study: The Baseline Refractive Characteristics in 6- to 12-Year-Old Chinese Primary School Students.

Purpose: To report the design and baseline data of a 3-year cohort study in Beijing Pinggu District primary school students in China after COVID-19. Methods: Noncycloplegic and cycloplegic spherical equivalent refraction (SER) were measured, ocular biometry, including the axial length (AL), anterior chamber depth (ACD) and corneal power (CP), were collected before cycloplegia. Corneal radius (CR), AL-to-CR ratio, and lens power (LP) were calculated. Results: Among the 4,806 (89.1%) eligible students (51.5% male), the prevalence of emmetropia, myopia, mild hyperopia, and mild-to-high hyperopia was 12.8, 30.8, 53.0, and 3.3% after cycloplegia, respectively. Myopia increased from 2.5% in 6- to 71.6% in 12-year-old students, with 9- and 10-year-olds showing the most prominent increases. The median of cycloplegic SER was 0.50 (IQR = 1.63), and the noncycloplegic SER was -0.38 D (IQR = 1.50), which is more negative than the cycloplegic refraction. The mean AL increased with age, from 22.46 ± 0.70 mm to 24.26 ± 1.07 mm. The ACD increased from 3.38 ± 0.28 mm to 3.70 ± 0.30 mm, and the AL-to-CR ratio increased from 2.91 ± 0.08 to 3.12 ± 0.13 between 6- and 12-year-old students. AL, CR and LP explained the SER variance with R2 of 86.4% after adjusting the age and gender. Conclusions and Relevance: The myopia prevalence since emergence of COVID-19 rapidly increased from 6- to 12-year primary school Chinese children, especially after 7 years of age. The non-cycloplegia SER overestimated the prevalence of myopia, and the cycloplegic SER is a more accurate and reliable method to assess the prevalence of refractive status.

Effects of baffle and intraocular pressure on aerosols generated in the noncontact tonometer measurement during COVID-19.

AIM: To investigate the effects of baffle and intraocular pressure (IOP) on the aerosols generated in the noncontact tonometer (NCT) measurement and provide recommendations for the standardized use of the NCT during coronavirus disease 2019 (COVID-19). METHODS: This clinical trial included 252 subjects (312 eyes) in The Eye Hospital, Wenzhou Medical University from March 7, 2020, to March 28, 2020. Sixty subjects (120 eyes) with normal IOP were divided into two groups. One group used an NCT without a baffle, another group used an NCT with a baffle. Another 192 subjects (192 eyes) were divided into four groups: Group A1 (without a baffle+normal IOP), Group A2 (without a baffle+high IOP), Group B1 (with a baffle+normal IOP) and Group B2 (with a baffle+high IOP). Particulate matter (PM) 2.5 and PM10 generated by all subjects were quantified during the NCT measurement. The IOP values were recorded simultaneously. Effects of baffle and IOP on aerosols generated during the NCT measurement were analyzed. RESULTS: In the normal eye group with a baffle, the aerosol density decreased in a wave-like shape near the NCT with the increase in the number of people measured for IOP, demonstrating no cumulative effect. However, in the normal eye group without a baffle, there was a cumulative effect. PM2.5 and PM10 in Group A2 were higher than Group A1 (both P<0.001). The PM2.5 and PM10 in Group B2 were higher than Group B1 (P<0.01, P<0.001 respectively). The PM10 of Group B1 was lower than Group A1 (P<0.01). PM2.5 in Group B2 were lower than Group A2 (P<0.01). The median of per capita PM2.5 and PM10 in the combined Group A1+A2 were 0.80 and 1.10 µg/m3 respectively, which were higher than 0.20 and 0.60 µg/m3 in the combined Group B1+B2 (both P<0.01). The median of per capita PM2.5 and PM10 in the combined Group A1+B1 were 0.10 and 0.20 µg/m3 respectively, which were lower than 1.30 and 1.70 µg/m3 in the combined Group A2+B2 (both P<0.001). CONCLUSION: More aerosols could be generated in patients with high IOP. After the NCT is equipped with a baffle, per capita aerosol density generated decreased significantly near the NCT; And with the increase in the number of people measured for IOP, the aerosols gradually dissipated near the NCT, demonstrating no cumulative effect. Therefore, it is suggested that the NCT should be equipped with a baffle, especially for patients with high IOP.

Integrating single-cell sequencing data with GWAS summary statistics reveals CD16+monocytes and memory CD8+T cells involved in severe COVID-19.

BACKGROUND: Understanding the host genetic architecture and viral immunity contributes to the development of effective vaccines and therapeutics for controlling the COVID-19 pandemic. Alterations of immune responses in peripheral blood mononuclear cells play a crucial role in the detrimental progression of COVID-19. However, the effects of host genetic factors on immune responses for severe COVID-19 remain largely unknown. METHODS: We constructed a computational framework to characterize the host genetics that influence immune cell subpopulations for severe COVID-19 by integrating GWAS summary statistics (N = 969,689 samples) with four independent scRNA-seq datasets containing healthy controls and patients with mild, moderate, and severe symptom (N = 606,534 cells). We collected 10 predefined gene sets including inflammatory and cytokine genes to calculate cell state score for evaluating the immunological features of individual immune cells. RESULTS: We found that 34 risk genes were significantly associated with severe COVID-19, and the number of highly expressed genes increased with the severity of COVID-19. Three cell subtypes that are CD16+monocytes, megakaryocytes, and memory CD8+T cells were significantly enriched by COVID-19-related genetic association signals. Notably, three causal risk genes of CCR1, CXCR6, and ABO were highly expressed in these three cell types, respectively. CCR1+CD16+monocytes and ABO+ megakaryocytes with significantly up-regulated genes, including S100A12, S100A8, S100A9, and IFITM1, confer higher risk to the dysregulated immune response among severe patients. CXCR6+ memory CD8+ T cells exhibit a notable polyfunctionality including elevation of proliferation, migration, and chemotaxis. Moreover, we observed an increase in cell-cell interactions of both CCR1+ CD16+monocytes and CXCR6+ memory CD8+T cells in severe patients compared to normal controls among both PBMCs and lung tissues. The enhanced interactions of CXCR6+ memory CD8+T cells with epithelial cells facilitate the recruitment of this specific population of T cells to airways, promoting CD8+T cell-mediated immunity against COVID-19 infection. CONCLUSIONS: We uncover a major genetics-modulated immunological shift between mild and severe infection, including an elevated expression of genetics-risk genes, increase in inflammatory cytokines, and of functional immune cell subsets aggravating disease severity, which provides novel insights into parsing the host genetic determinants that influence peripheral immune cells in severe COVID-19.

Innovative FO-SPR Label-free Strategy for Detecting Anti-RBD Antibodies in COVID-19 Patient Serum and Whole Blood.

The ongoing COVID-19 pandemic has emphasized the urgent need for rapid, accurate, and large-scale diagnostic tools. Next to this, the significance of serological tests (i.e., detection of SARS-CoV-2 antibodies) also became apparent for studying patients' immune status and past viral infection. In this work, we present a novel approach for not only measuring antibody levels but also profiling of binding kinetics of the complete polyclonal antibody response against the receptor binding domain (RBD) of SARS-CoV-2 spike protein, an aspect not possible to achieve with traditional serological tests. This fiber optic surface plasmon resonance (FO-SPR)-based label-free method was successfully accomplished in COVID-19 patient serum and, for the first time, directly in undiluted whole blood, omitting the need for any sample preparation. Notably, this bioassay (1) was on par with FO-SPR sandwich bioassays (traditionally regarded as more sensitive) in distinguishing COVID-19 from control samples, irrespective of the type of sample matrix, and (2) had a significantly shorter time-to-result of only 30 min compared to >1 or 4 h for the FO-SPR sandwich bioassay and the conventional ELISA, respectively. Finally, the label-free approach revealed that no direct correlation was present between antibody levels and their kinetic profiling in different COVID-19 patients, as another evidence to support previous hypothesis that antibody-binding kinetics against the antigen in patient blood might play a role in the COVID-19 severity. Taking all this into account, the presented work positions the FO-SPR technology at the forefront of other COVID-19 serological tests, with a huge potential toward other applications in need for quantification and kinetic profiling of antibodies.

Novel Regeneration Approach for Creating Reusable FO-SPR Probes with NTA Surface Chemistry.

To date, surface plasmon resonance (SPR) biosensors have been exploited in numerous different contexts while continuously pushing boundaries in terms of improved sensitivity, specificity, portability and reusability. The latter has attracted attention as a viable alternative to disposable biosensors, also offering prospects for rapid screening of biomolecules or biomolecular interactions. In this context here, we developed an approach to successfully regenerate a fiber-optic (FO)-SPR surface when utilizing cobalt (II)-nitrilotriacetic acid (NTA) surface chemistry. To achieve this, we tested multiple regeneration conditions that can disrupt the NTA chelate on a surface fully saturated with His6-tagged antibody fragments (scFv-33H1F7) over ten regeneration cycles. The best surface regeneration was obtained when combining 100 mM EDTA, 500 mM imidazole and 0.5% SDS at pH 8.0 for 1 min with shaking at 150 rpm followed by washing with 0.5 M NaOH for 3 min. The true versatility of the established approach was proven by regenerating the NTA surface for ten cycles with three other model system bioreceptors, different in their size and structure: His6-tagged SARS-CoV-2 spike fragment (receptor binding domain, RBD), a red fluorescent protein (RFP) and protein origami carrying 4 RFPs (Tet12SN-RRRR). Enabling the removal of His6-tagged bioreceptors from NTA surfaces in a fast and cost-effective manner can have broad applications, spanning from the development of biosensors and various biopharmaceutical analyses to the synthesis of novel biomaterials.

Identification of the RNase-binding site of SARS-CoV-2 RNA for anchor primer-PCR detection of viral loading in 306 COVID-19 patients.

The pandemic of coronavirus disease 2019 (COVID-19) urgently calls for more sensitive molecular diagnosis to improve sensitivity of current viral nuclear acid detection. We have developed an anchor primer (AP)-based assay to improve viral RNA stability by bioinformatics identification of RNase-binding site of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and implementing AP dually targeting the N gene of SARS-CoV-2 RNA and RNase 1, 3, 6. The arbitrarily primed polymerase chain reaction (AP-PCR) improvement of viral RNA integrity was supported by (a) the AP increased resistance of the targeted gene (N gene) of SARS-CoV-2 RNA to RNase treatment; (b) the detection of SARS-CoV-2 RNA by AP-PCR with lower cycle threshold values (-2.7 cycles) compared to two commercially available assays; (c) improvement of the viral RNA stability of the ORF gene upon targeting of the N gene and RNase. Furthermore, the improved sensitivity by AP-PCR was demonstrated by detection of SARS-CoV-2 RNA in 70-80% of sputum, nasal, pharyngeal swabs and feces and 36% (4/11) of urine of the confirmed cases (n = 252), 7% convalescent cases (n = 54) and none of 300 negative cases. Lastly, AP-PCR analysis of 306 confirmed and convalescent cases revealed prolonged presence of viral loading for >20 days after the first positive diagnosis. Thus, the AP dually targeting SARS-CoV-2 RNA and RNase improves molecular detection by preserving SARS-CoV-2 RNA integrity and reveals the prolonged viral loading associated with older age and male gender in COVID-19 patients.

Machine learning algorithm improves accuracy of ortho-K lens fitting in vision shaping treatment.

PURPOSE: To construct a machine learning (ML)-based model for estimating the alignment curve (AC) curvature in orthokeratology lens fitting for vision shaping treatment (VST), which can minimize the number of lens trials, improving efficiency while maintaining accuracy, with regards to its improvement over a previous calculation method. METHODS: Data were retrospectively collected from the clinical case files of 1271 myopic subjects (1271 right eyes). The AC curvatures calculated with a previously published algorithm were used as the target data sets. Four kinds of machine learning algorithms were implemented in the experimental analyses to predict the targeted AC curvatures: robust linear regression models, support vector machine (SVM) regression models with linear kernel functions, bagging decision trees, and Gaussian processes. The previously published calculation method and the novel machine learning method were then compared to assess the final parameters of ordered lenses. RESULTS: The linear SVM and Gaussian process machine learning models achieved the best performance. The input variables included sex, age, horizontal visible iris diameter (HVID), spherical refraction (SER), cylindrical refraction, eccentricity value (e value), flat K (K1) and steep K (K2) readings, anterior chamber depth (ACD), and axial length (AL). The R-squared values for the output AC1K1, AC1K2 and AC2K1 values were 0.91, 0.84, and 0.73, respectively. The previous calculation method and machine learning methods displayed excellent consistency, and the proposed methods performed best based on flat K reading and e values. CONCLUSIONS: The ML model can provide practitioners with an efficient method for estimating the AC curvatures of VST lenses and reducing the probability of cross-infection originating from trial lenses, which is especially useful during pandemics, such as that for COVID-19.

EyeDiseases: an integrated resource for dedicating to genetic variants, gene expression and epigenetic factors of human eye diseases.

Eye diseases are remarkably common and encompass a large and diverse range of morbidities that affect different components of the visual system and visual function. With advances in omics technology of eye disorders, genome-scale datasets have been rapidly accumulated in genetics and epigenetics field. However, the efficient collection and comprehensive analysis of different kinds of omics data are lacking. Herein, we developed EyeDiseases (https://eyediseases.bio-data.cn/), the first database for multi-omics data integration and interpretation of human eyes diseases. It contains 1344 disease-associated genes with genetic variation, 1774 transcription files of bulk cell expression and single-cell RNA-seq, 105 epigenomics data across 185 kinds of human eye diseases. Using EyeDiseases, we investigated SARS-CoV-2 potential tropism in eye infection and found that the SARS-CoV-2 entry factors, ACE2 and TMPRSS2 are highly correlated with cornea and keratoconus, suggest that ocular surface cells are susceptible to infection by SARS-CoV-2. Additionally, integrating analysis of Age-related macular degeneration (AMD) GWAS loci and co-expression data revealed 9 associated genes involved in HIF-1 signaling pathway and voltage-gate potassium channel complex. The EyeDiseases provides a valuable resource for accelerating the discovery and validation of candidate loci and genes contributed to the molecular diagnosis and therapeutic vulnerabilities with various eyes diseases.

Integrative genomics analysis reveals a 21q22.11 locus contributing risk to COVID-19.

The systematic identification of host genetic risk factors is essential for the understanding and treatment of coronavirus disease 2019 (COVID-19). By performing a meta-analysis of two independent genome-wide association summary datasets (N = 680 128), a novel locus at 21q22.11 was identified to be associated with COVID-19 infection (rs9976829 in IFNAR2-IL10RB, odds ratio = 1.16, 95% confidence interval = 1.09-1.23, P = 2.57 × 10-6). The rs9976829 represents a strong splicing quantitative trait locus for both IFNAR2 and IL10RB genes, especially in lung tissue (P = 1.8 × 10-24). Integrative genomics analysis of combining genome-wide association study with expression quantitative trait locus data showed the expression variations of IFNAR2 and IL10RB have prominent effects on COVID-19 in various types of tissues, especially in lung tissue. The majority of IFNAR2-expressing cells were dendritic cells (40%) and plasmacytoid dendritic cells (38.5%), and IL10RB-expressing cells were mainly nonclassical monocytes (29.6%). IFNAR2 and IL10RB are targeted by several interferons-related drugs. Together, our results uncover 21q22.11 as a novel susceptibility locus for COVID-19, in which individuals with G alleles of rs9976829 have a higher probability of COVID-19 susceptibility than those with non-G alleles.

Effect of Intraocular Pressure on Aerosol Density Generated by Noncontact Tonometer Measurement.

PRECIS: Aerosols generated by a noncontact tonometer (NCT) were quantified. There was a positive correlation between aerosols and intraocular pressure (IOP), and the concentration of aerosols beside the air jet port was the highest. PURPOSE: To investigate the effects of IOP on the aerosol density generated during the use of an NCT and provide references and suggestions for daily protection of ophthalmic medical staff during the coronavirus disease-19 (COVID-19) outbreak. OBJECTIVE AND METHODS: This cross-sectional clinical trial included 214 eyes of 140 patients from a hospital in Wenzhou city, Zhejiang Province. All subjects' IOPs were measured by an NCT (39 eyes with low IOP, 90 eyes with normal IOP, 37 eyes with moderately high IOP, and 48 eyes with very high IOP) between March 7 and June 17, 2020. The density of particulate matter (PM) 2.5 and PM10 generated during the process of IOP measurement with an NCT was analyzed. IOP values were recorded simultaneously. The aerosols generated during different IOP measurements were plotted in scatter plots. RESULTS: PM2.5 was generated more at the air jet port of the tonometer during the process of IOP measurement (H=2.731, P=0.019). Larger quantities of PM2.5 and PM10 were generated when the IOP was higher, and these differences were statistically significant (PM2.5: H=119.476, P<0.001; PM10: H=160.801, P<0.001). Linear correlation analysis with one variable demonstrated that IOP had significantly positive correlations with PM2.5 (r=0.756, P<0.001) and PM10 (r=0.864, P<0.001). CONCLUSIONS: Aerosols can be generated while using an NCT to measure IOP, and aerosols and IOP are positively correlated. Patients with moderately high IOP or very high IOP tend to generate more aerosols during the IOP measurement. The concentration of aerosols beside the air jet port was the highest.

Co-Expression of Mitochondrial Genes and ACE2 in Cornea Involved in COVID-19.

Purpose: The coronavirus disease 2019 (COVID-19) pandemic severely challenges public health and necessitates the need for increasing our understanding of COVID-19 pathogenesis, especially host factors facilitating virus infection and propagation. The aim of this study was to investigate key factors for cellular susceptibility to severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection in the ocular surface cells. Methods: We combined co-expression and SARS-CoV-2 interactome network to predict key genes at COVID-19 in ocular infection based on the premise that genes underlying a disease are often functionally related and functionally related genes are often co-expressed. Results: The co-expression network was constructed by mapping the well-known angiotensin converting enzyme (ACE2), TMPRSS2, and host susceptibility genes implicated in COVID-19 genomewide association study (GWAS) onto a cornea, retinal pigment epithelium, and lung. We found a significant co-expression module of these genes in the cornea, revealing that cornea is potential extra-respiratory entry portal of SARS-CoV-2. Strikingly, both co-expression and interaction networks show a significant enrichment in mitochondrial function, which are the hub of cellular oxidative homeostasis, inflammation, and innate immune response. We identified a corneal mitochondrial susceptibility module (CMSM) of 14 mitochondrial genes by integrating ACE2 co-expression cluster and SARS-CoV-2 interactome. The gene ECSIT, as a cytosolic adaptor protein involved in inflammatory responses, exhibits the strongest correlation with ACE2 in CMSM, which has shown to be an important risk factor for SARS-CoV-2 infection and prognosis. Conclusions: Our co-expression and protein interaction network analysis uncover that the mitochondrial function related genes in cornea contribute to the dissection of COVID-19 susceptibility and potential therapeutic interventions.

A Comprehensive Strategy for Laser Corneal Refractive Surgery during the COVID-19 Epidemic in a Tertiary Teaching Hospital in Wenzhou, China.

The novel coronavirus pneumonia COVID-19 is caused by the novel coronavirus SARS-CoV-2, which is highly contagious, has a long incubation period, and can be detected in patients' tears and conjunctival secretions. In this study, we describe our experience regarding the necessary protective measures that need to be taken during ophthalmic examination and treatment. The authors reviewed the clinical work arrangements during the epidemic situation at the Eye Hospital of Wenzhou Medical University in China and analyzed the prevention and control measures that were applied during the laser corneal refractive surgery process. The comprehensive protection protocol, which was established throughout the entire process, included both horizontal (medical staff-patient, medical staff-medical staff, and patient-patient) and vertical (preoperative, intraoperative, and postoperative transmission assessment) approach and was mainly focused on strengthening the protection against potential aerosol transmission that may occur during intraocular pressure measurements and laser ablation. The described and proposed protocol, along with the further guidelines followed by the medical personnel, proved to be efficacious and contributed significantly to the control of the COVID-19 outbreak and the protection of both the patients and the medical staff.

Aerosol formation during non-contact 'air-puff' tonometry and its significance for prevention of COVID-19

Objective To evaluate the aerosol concentration(PM2.5,PM10.0 and aerosol particle number) formation in non-contact 'air-puff' tonometry and provide suggestions for medical workers to take appropriate daily protection during the prevalence of 2019-nCoV. Methods A cross-sectional study was carried out in this study. Thirty healthy subjects were enrolled on February 22, 2020 at Eye Hospital of Wenzhou Medical University. The intraocular pressure (IOP) was measured by non-contact 'air-puff' tonometer in the ophthalmic consulting room and the hall with or without masks. PM2.5, PM10.0 and aerosol particles were recorded by air quality detector. The cumulative effects of IOP measurement, PM2.5, PM10.0 and aerosol particle number were analyzed, and the aerosol density of subjects with and without masks was compared. Results The PM2.5, PM10.0 and aerosol particles produced by the non-contact 'air-puff' tonometry and increased with the increase of spray times. The IOP curves of 60 eyes of 30 subjects were measured respectively in two environments of medical consulting room and medical institution hall. It was found that PM2.5, pm10.0 and particle number fluctuated and increased with the increase of IOP measurement person times, showing cumulative effect, and the accumulation speed of aerosol density in hall was faster than that in consulting room. The density of PM2.5 and PM10.0 produced without gauze mask were (53.417±2.306) and (85.350±3.488) μg/m 3 , which were higher than those of (50.567±0.862) and (80.617±1.463) μg/m 3 with gauze mask. The differences were statistically significant ( P =0.028, 0.019). Conclusions Aerosol can be produced by non-contact 'air-puff' tonometer spraying, and it fluctuates with the increase of spraying times, showing a cumulative effect. The aerosol accumulation is higher in the hall with insufficient air circulation. And more aerosol can be produced without gauze mask.