Machine learning-augmented surface-enhanced spectroscopy toward next-generation molecular diagnostics† † Electronic supplementary information (ESI) available. See DOI: https://doi.org/10.1039/d2na00608a

The world today is witnessing the significant role and huge demand for molecular detection and screening in healthcare and medical diagnosis, especially during the outbreak of COVID-19. Surface-enhanced spectroscopy techniques, including Surface-Enhanced Raman Scattering (SERS) and Infrared Absorption (SEIRA), provide lattice and molecular vibrational fingerprint information which is directly linked to the molecular constituents, chemical bonds, and configuration. These properties make them an unambiguous, nondestructive, and label-free toolkit for molecular diagnostics and screening. However, new issues in molecular diagnostics, such as increasing molecular species, faster spread of viruses, and higher requirements for detection accuracy and sensitivity, have brought great challenges to detection technology. Advancements in artificial intelligence and machine learning (ML) techniques show promising potential in empowering SERS and SEIRA with rapid analysis and automatic data processing to jointly tackle the challenge. This review introduces the combination of ML and SERS/SEIRA by investigating how ML algorithms can be beneficial to SERS/SEIRA, discussing the general process of combining ML and SEIRA/SERS, highlighting the molecular diagnostics and screening applications based on ML-combined SEIRA/SERS, and providing perspectives on the future development of ML-integrated SEIRA/SERS. In general, this review offers comprehensive knowledge about the recent advances and the future outlook regarding ML-integrated SEIRA/SERS for molecular diagnostics and screening. This review summarizes the integration of machine learning with surface-enhanced Raman scattering and infrared absorption in terms of concepts, processes, and applications, and provides an outlook on the future development of this technology.

Machine learning-augmented surface-enhanced spectroscopy toward next-generation molecular diagnostics.

The world today is witnessing the significant role and huge demand for molecular detection and screening in healthcare and medical diagnosis, especially during the outbreak of COVID-19. Surface-enhanced spectroscopy techniques, including Surface-Enhanced Raman Scattering (SERS) and Infrared Absorption (SEIRA), provide lattice and molecular vibrational fingerprint information which is directly linked to the molecular constituents, chemical bonds, and configuration. These properties make them an unambiguous, nondestructive, and label-free toolkit for molecular diagnostics and screening. However, new issues in molecular diagnostics, such as increasing molecular species, faster spread of viruses, and higher requirements for detection accuracy and sensitivity, have brought great challenges to detection technology. Advancements in artificial intelligence and machine learning (ML) techniques show promising potential in empowering SERS and SEIRA with rapid analysis and automatic data processing to jointly tackle the challenge. This review introduces the combination of ML and SERS/SEIRA by investigating how ML algorithms can be beneficial to SERS/SEIRA, discussing the general process of combining ML and SEIRA/SERS, highlighting the molecular diagnostics and screening applications based on ML-combined SEIRA/SERS, and providing perspectives on the future development of ML-integrated SEIRA/SERS. In general, this review offers comprehensive knowledge about the recent advances and the future outlook regarding ML-integrated SEIRA/SERS for molecular diagnostics and screening.

Innate immune imprints in SARS-CoV-2 Omicron variant infection convalescents.

SARS-CoV-2 Omicron variant infection generally gives rise to asymptomatic to moderate COVID-19 in vaccinated people. The immune cells can be reprogrammed or "imprinted" by vaccination and infections to generate protective immunity against subsequent challenges. Considering the immune imprint in Omicron infection is unclear, here we delineate the innate immune landscape of human Omicron infection via single-cell RNA sequencing, surface proteome profiling, and plasma cytokine quantification. We found that monocyte responses predominated in immune imprints of Omicron convalescents, with IL-1ß-associated and interferon (IFN)-responsive signatures with mild and moderate symptoms, respectively. Low-density neutrophils increased and exhibited IL-1ß-associated and IFN-responsive signatures similarly. Mild convalescents had increased blood IL-1ß, CCL4, IL-9 levels and PI3+ neutrophils, indicating a bias to IL-1ß responsiveness, while moderate convalescents had increased blood CXCL10 and IFN-responsive monocytes, suggesting durative IFN responses. Therefore, IL-1ß- or IFN-responsiveness of myeloid cells may indicate the disease severity of Omicron infection and mediate post-COVID conditions.

ROS-responsive polymer nanoparticles with enhanced loading of dexamethasone effectively modulate the lung injury microenvironment.

The acute lung injury (ALI) is an inflammatory disorder associated with cytokine storm, which activates various reactive oxygen species (ROS) signaling pathways and causes severe complications in patients as currently seen in coronavirus disease 2019 (COVID-19). There is an urgent need for medication of the inflammatory lung environment and effective delivery of drugs to lung to reduce the burden of high doses of medications and attenuate inflammatory cells and pathways. Herein, we prepared dexamethasone-loaded ROS-responsive polymer nanoparticles (PFTU@DEX NPs) by a modified emulsion approach, which achieved high loading content of DEX (11.61 %). DEX was released faster from the PFTU@DEX NPs in a ROS environment, which could scavenge excessive ROS efficiently both in vitro and in vivo. The PFTU NPs and PFTU@DEX NPs showed no hemolysis and cytotoxicity. Free DEX, PFTU NPs and PFTU@DEX NPs shifted M1 macrophages to M2 macrophages in RAW264.7 cells, and showed anti-inflammatory modulation to A549 cells in vitro. The PFTU@DEX NPs treatment significantly reduced the increased total protein concentration in BALF of ALI mice. The delivery of PFTU@DEX NPs decreased the proportion of neutrophils significantly, mitigated the cell apoptosis remarkably compared to the other groups, reduced M1 macrophages and increased M2 macrophages in vivo. Moreover, the PFTU@DEX NPs had the strongest ability to suppress the expression of NLRP3, Caspase1, and IL-1ß. Therefore, the PFTU@DEX NPs could efficiently suppress inflammatory cells, ROS signaling pathways, and cell apoptosis to ameliorate LPS-induced ALI. STATEMENT OF SIGNIFICANCE: The acute lung injury (ALI) is an inflammatory disorder associated with cytokine storm, which activates various reactive oxygen species (ROS) signaling pathways and causes severe complications in patients. There is an urgent need for medication of the inflammatory lung environment and effective delivery of drugs to modulate the inflammatory disorder and suppress the expression of ROS and inflammatory cytokines. The inhaled PFTU@DEX NPs prepared through a modified nanoemulsification method suppressed the activation of NLRP3, induced the polarization of macrophage phenotype from M1 to M2, and thereby reduced the neutrophil infiltration, inhibited the release of proteins and inflammatory mediators, and thus decreased the acute lung injury in vivo.

Mesenchymal stem cell treatment improves outcome of COVID-19 patients via multiple immunomodulatory mechanisms.

The infusion of coronavirus disease 2019 (COVID-19) patients with mesenchymal stem cells (MSCs) potentially improves clinical symptoms, but the underlying mechanism remains unclear. We conducted a randomized, single-blind, placebo-controlled (29 patients/group) phase II clinical trial to validate previous findings and explore the potential mechanisms. Patients treated with umbilical cord-derived MSCs exhibited a shorter hospital stay (P = 0.0198) and less time required for symptoms remission (P = 0.0194) than those who received placebo. Based on chest images, both severe and critical patients treated with MSCs showed improvement by day 7 (P = 0.0099) and day 21 (P = 0.0084). MSC-treated patients had fewer adverse events. MSC infusion reduced the levels of C-reactive protein, proinflammatory cytokines, and neutrophil extracellular traps (NETs) and promoted the maintenance of SARS-CoV-2-specific antibodies. To explore how MSCs modulate the immune system, we employed single-cell RNA sequencing analysis on peripheral blood. Our analysis identified a novel subpopulation of VNN2+ hematopoietic stem/progenitor-like (HSPC-like) cells expressing CSF3R and PTPRE that were mobilized following MSC infusion. Genes encoding chemotaxis factors - CX3CR1 and L-selectin - were upregulated in various immune cells. MSC treatment also regulated B cell subsets and increased the expression of costimulatory CD28 in T cells in vivo and in vitro. In addition, an in vivo mouse study confirmed that MSCs suppressed NET release and reduced venous thrombosis by upregulating kindlin-3 signaling. Together, our results underscore the role of MSCs in improving COVID-19 patient outcomes via maintenance of immune homeostasis.

Coronavirus Disease 2019 Exposure in Surgeons and Anesthesiologists at a New York City Specialty Hospital: A Cross-Sectional Study of Symptoms and SARS-CoV-2 Antibody Status.

OBJECTIVE: We measured the seroprevalence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) immunoglobulin G (IgG) antibodies among surgeons and anesthesiologists and associated antibody status with coronavirus disease 2019 (COVID-19) clinical illness. METHODS: A cross-sectional study of SARS-CoV-2 IgG seroprevalence with a survey assessing demographics, SARS-CoV-2 exposure risk, and COVID-19 illness. The primary outcome was the period prevalence of SARS-CoV-2 IgG antibodies associated with COVID-19 illness. RESULTS: One hundred forty three surgeons and anesthesiologists completed both serology and survey testing. We found no significant relationships between antibody status and clinical role (anesthesiologist, surgeon), mode of commuting to work, other practice settings, or place of residence. SARS-CoV-2 IgG seroprevalence was 9.8%. Positive IgG status was highly correlated with presence of symptoms of COVID-19 illness. CONCLUSIONS: These results suggest the relative safety of surgeons and anesthesiologists where personal protective equipment (PPE) is available and infection control protocols are implemented.

Revealing the therapeutic targets and molecular mechanisms of emodin-treated coronavirus disease 2019 via a systematic study of network pharmacology.

Emodin has shown pharmacological effects in the treatment of infection with severe acute respiratory syndrome coronavirus-2, which leads to coronavirus disease 2019 (COVID-19). Thus, we speculated that emodin may possess anti-COVID-19 activity. In this study, using bioinformatics databases, we screened and harvested the candidate genes or targets of emodin and COVID-19 prior to the determination of pharmacological targets and molecular mechanisms of emodin against COVID-19. We discovered core targets for the treatment of COVID-19, including mitogen-activated protein kinase 1 (MAPK1), tumor protein (TP53), tumor necrosis factor (TNF), caspase-3 (CASP3), epidermal growth factor receptor (EGFR), vascular endothelial growth factor A (VEGFA), interleukin 1B (IL1B), mitogen-activated protein kinase 14 (MAPK14), prostaglandin-endoperoxide synthase 2 (PTGS2), B-cell lymphoma-2-like protein 1 (BCL2L1), interleukin-8 (CXCL8), myeloid cell leukemia-1 (MCL1), and colony stimulating factor 2 (CSF2). The GO analysis of emodin against COVID-19 mainly included cytokine-mediated signaling pathway, response to lipopolysaccharide, response to molecule of bacterial origin, developmental process involved in reproduction, and reproductive structure development. The KEGG results exhibited that the molecular pathways mainly included IL-17 signaling pathway, AGE-RAGE signaling pathway in diabetic complications, TNF signaling pathway, pertussis, proteoglycans in cancer, pathways in cancer, MAPK signaling pathway, NOD-like receptor signaling pathway, NF-kappa B signaling pathway, etc. Also, molecular docking results revealed the docking capability between emodin and COVID-19 and the potential pharmacological activity of emodin against COVID-19. Taken together, these findings uncovered the targets and pharmacological mechanisms of emodin for treating COVID-19 and suggested that the vital targets might be used as biomarkers against COVID-19.

Immune-Inflammatory Parameters in COVID-19 Cases: A Systematic Review and Meta-Analysis.

Background: The recent outbreak of coronavirus disease 2019 (COVID-19) has been rapidly spreading on a global scale and poses a great threat to human health. Acute respiratory distress syndrome, characterized by a rapid onset of generalized inflammation, is the leading cause of mortality in patients with COVID-19. We thus aimed to explore the effect of risk factors on the severity of the disease, focusing on immune-inflammatory parameters, which represent the immune status of patients. Methods: A comprehensive systematic search for relevant studies published up to April 2020 was performed by using the PubMed, Web of Science, EMBASE, and China National Knowledge Internet (CNKI) databases. After extracting all available data of immune-inflammatory indicators, we statistically analyzed the risk factors of severe and non-severe COVID-19 patients with a meta-analysis. Results: A total of 4,911 patients from 29 studies were included in the final meta-analysis. The results demonstrated that severe patients tend to present with increased white blood cell (WBC) and neutrophil counts, neutrophil-lymphocyte ratio (NLR), procalcitonin (PCT), C-reaction protein (CRP), erythrocyte sedimentation rate (ESR), and Interleukin-6 (IL-6) and a decreased number of total lymphocyte and lymphocyte subtypes, such as CD4+ T lymphocyte and CD8+ T lymphocyte, compared to the non-severe patients. In addition, the WBC count>10 × 109/L, lymphocyte count<1 × 109/L, PCT>0.5 ng/mL, and CRP>10 mg/L were risk factors for disease progression in patients with COVID-19 (WBC count>10 × 109/L: OR = 2.92, 95% CI: 1.96-4.35; lymphocyte count<1 × 109/L: OR = 4.97, 95% CI: 3.53-6.99; PCT>0.5 ng/mL: OR = 6.33, 95% CI: 3.97-10.10; CRP>10 mg/L: OR = 3.51, 95% CI: 2.38-5.16). Furthermore, we found that NLR, as a novel marker of systemic inflammatory response, can also help predict clinical severity in patients with COVID-19 (OR = 2.50, 95% CI: 2.04-3.06). Conclusions: Immune-inflammatory parameters, such as WBC, lymphocyte, PCT, CRP, and NLR, could imply the progression of COVID-19. NLR has taken both the levels of neutrophil and lymphocyte into account, indicating a more complete, accurate, and reliable inspection efficiency; surveillance of NLR may help clinicians identify high-risk COVID-19 patients at an early stage.

Immune Characteristics of Patients with Coronavirus Disease 2019 (COVID-19).

Up to now, little is known about the detailed immune profiles of COVID-19 patients from admission to discharge. In this study we retrospectively reviewed the clinical and laboratory characteristics of 18 COVID-19 patients from January 30, 2020 to February 21, 2020. These patients were divided into two groups; group 1 had a severe acute respiratory syndrome coronavirus 2 nucleic acid-positive duration for more than 15 days (n = 6) and group 2 had a nucleic acid-positive duration for less than 15 days (n = 12). Group 1 patients had lower level of peripheral blood lymphocytes (0.40 vs. 0.78 ×109/L, p = 0.024) and serum potassium (3.36 vs. 3.79 mmol/L, p = 0.043) on admission but longer hospitalization days (23.17 vs. 15.75 days, p < 0.001) compared to Group 2 patients. Moreover, baseline level of lymphocytes (r = -0.62, p = 0.006) was negatively correlated with the nucleic acid-positive duration. Additionally, lymphocytes (420.83 vs. 1100.56 /µL), T cells (232.50 vs. 706.78 /µL), CD4+ T cells (114.67 vs. 410.44 /µL), and CD8+ T cells (94.83 vs. 257.44 /µL) in the peripheral blood analyzed by flow cytometry were significantly different between Group 1and Group 2. Furthermore, there was also a negative correlation between lymphocytes (r = -0.54, p = 0.038) or T cells (r = -0.55, p = 0.034) at diagnosis and the nucleic acid-positive duration, separately. In conclusion, the patients with nucleic acid-positive ≥ 15 days had significantly decreased lymphocytes, T cell and its subsets compared to those who remained positive for less than 15 days.