ARTICLE | doi:10.20944/preprints202002.0381.v2
Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: SARS-CoV2; corona virus; glycopeptide; N-linked glycans; mass spectrometry; antibody; cryo-EM structure; crystal structures; epitope prediction
Online: 13 April 2020 (11:09:29 CEST)
Corona viruses hijack human enzymes to assembly sugar coat on Spike glycoproteins. The mechanism that human antibodies may uncover the antigenic viral peptide epitopes hidden by sugar coat are unknown. In this study, we analyzed recombinant SARS-CoV-2 Spike protein secreted from BTI-Tn-5B1-4 cells, by trypsin and chymotrypsin digestion followed by mass spectrometry analysis. We acquired MS/MS spectrums for glycopeptides of all 22 predicted N-glycosylated sites. We further analyzed the surface accessibility of Spike proteins according to Cryo-EM and homolog-modeled structures, and available antibodies that bind to SARS-CoV-1. The results showed that all 22 N-glycosylated sites of SARS-CoV-2 are modified by high-mannose type of N-glycans. MS/MS fragmentation clearly established the glycopeptide identities. Electron densities of glycans cover most of the Spike receptor binding domain of SARS-CoV-2, except YQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQ, similar to a region FSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQ in SARS-CoV-1. Other surface-exposed domains included those located on Central Helix, between amino acids 967 and 1016 of SARS-CoV-1, and 985 to 1034 of SARS-CoV-2 Spike protein. As the majority of antibody paratopes bind to peptide portion with or without sugar modification, we propose a snake-catcher model that a minimal length of peptide is first clamped by a paratope, and the binding is either strengthened by sugars close to peptide, or not interfered by sugar modification.
REVIEW | doi:10.20944/preprints202306.0508.v1
Subject: Public Health And Healthcare, Public Health And Health Services Keywords: SARS-CoV-2; Hematology; COVID-19; Biomarkers
Online: 7 June 2023 (08:05:43 CEST)
The SARS coronavirus 2 (SARS-CoV-2) is the causative agent of the 2019 coronavirus disease (COVID-19) pandemic that has executed 6.9 million people and infected over 765 million. It’s become a major worldwide health alarm and is also known to cause abnormalities in various systems, including the hematologic system. COVID-19 infection primarily affects the lower res-piratory tract and can lead to a cascade of events, including a cytokine storm, intravascular thrombosis, and subsequent complications such as arterial and venous thromboses. COVID-19 can cause thrombocytopenia, lymphopenia, and neutrophilia, which are associated with worse out-comes. Prophylactic anticoagulation is essential to prevent complication and death rate associated with the virus's effect on the coagulation system. It is crucial to recognize these complications early and promptly start therapeutic anticoagulation to improve patient outcomes. While rare, COVID-19-induced disseminated intravascular coagulation exhibits some similarities to DIC induced by sepsis. LDH, D-dimer, ferritin, and CRP biomarker are often increase in serious COVID-19 cases and poor prognosis. Understanding the pathophysiology of the disease and identifying risk factors for adverse outcomes is critical for effective management of COVID-19.
ARTICLE | doi:10.20944/preprints202111.0506.v1
Subject: Medicine And Pharmacology, Obstetrics And Gynaecology Keywords: endometrial cancer; fertility-sparing management; molecular classification; reproductive age; pregnancy
Online: 26 November 2021 (12:42:15 CET)
Conclusions: Molecular classification could provide reliable supplementary information for evaluating prognostic and contribute to treatment option decision-making in EEC patients. Fertility-sparing treatment is not recommended for EEC patients with CNH and MSI-H. Furthermore, fertility-sparing treatment can be attempted in EEC patients with CHL, but regular follow-up should be carried out to early detection of EC relapse and prevention of disease progression.
ARTICLE | doi:10.20944/preprints202212.0316.v1
Subject: Environmental And Earth Sciences, Oceanography Keywords: sea surface salinity; ocean reanalysis; moored buoy; in situ measurements; validation
Online: 19 December 2022 (03:45:59 CET)
Sea surface salinity (SSS) is one of the Essential Climate Variables (ECVs) as defined by the Global Climate Observing System (GCOS). Acquiring high-quality SSS datasets with high spatial-temporal resolution is cruicial for research on the hydrological cycle and earth climate. This study assessed the quality of SSS data provided by four high-resolution ocean reanalysis products, including the Hybrid Coordinate Ocean Model (HYCOM) 1/12° global reanalysis, the The Copernicus Global 1/12° Oceanic and Sea Ice GLORYS12 Reanal-ysis, the Simple Ocean Data Assimilation (SODA) reanalysis, the ECMWF Oceanic Reanalysis System 5 (ORAS5) product and the Estimating the Circulation and Climate of the Ocean Phase II (ECCO2) reanalysis. Regional comparison in the Mediterranean Sea shows that reanalysis largely depicts the accurate spatial SSS structure away from river mouths and coastal areas but slightly underestimates the mean SSS values. Better SSS reanalysis performance is found in the Levantine Sea while larger SSS uncertainties are found in the Adriatic Sea and the Aegean Sea. The global comparison with CMEMS level-4 (L4) SSS show generally con-sistent large-scale structures. The mean ΔSSS between monthly gridded reanalysis data and in situ analyzed data is -0.1 PSU in the open seas between 40°S and 40°N with the mean Root Mean Square Deviation (RMSD) generally smaller than 0.3 PSU and the majority of correlation coefficients higher than 0.5. Comparison with collocated buoy salinity shows that reanalysis products well captures the SSS variations at the locations of tropical moored buoy arrays at weekly scale. Among all the four products, the data quality of HYCOM re-analysis SSS is highest in marginal sea, GLORYS12 has the best performance in the global ocean especially in tropical regions. Comparatively, ECCO2 has the overall worst performance to reproduce SSS states and variations by showing the largest discrepancies with CMEMS L4 SSS.
ARTICLE | doi:10.20944/preprints202305.1953.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: micro-nano bioglass; 3D printing; osteogenesis; angiogenesis; immunomodulation
Online: 29 May 2023 (03:30:12 CEST)
Magnesium ions play an important immune-regulatory role during bone repair. For this study, we prepared micro-nano bioactive glass containing magnesium, which can release magnesium, silicon, and calcium ions and has a positive impact on osteogenic differentiation and vascular regeneration. In this study, MgMNBG was compounded and combined with PLGA and PCL for 3D printing. Afterwards, the physicochemical properties and bone repair performance of the scaffolds were evaluated through in vitro and in vivo experiments. We also investigated the effects of MgMNBG on osteogenic differentiation, immune regulation, and vascular regeneration. The results showed that MgMNBG can inhibit inflammation and promote osteogenesis and angiogenesis by regulating macrophages. PLGA/PCL/MgMNBG scaffolds have good osteogenic and angiogenic effects, and the composite scaffolds have excellent bone repair performance and potential application value.
REVIEW | doi:10.20944/preprints202305.0684.v1
Subject: Physical Sciences, Optics And Photonics Keywords: fiber-optic sensor; tapered optical fiber structure; physical sensors; chemical sensors; gas sensors; novel tapered optical fiber; humanoid tapered fiber structure
Online: 10 May 2023 (04:33:10 CEST)
Optical fiber sensors based on tapered optical fiber (TOF) structure have attracted a considerable amount of attention from researchers due to the advantages of simple fabrication, high stability, diverse structures, and have great potential for applications in many fields such as physics, chemistry and biology. Compared with ordinary optical fibers, TOF with their unique structural characteristics significantly improve the sensitivity and response speed of fiber-optic sensors and broaden the application range. This review presents an overview of the latest research status and characteristics of fiber-optic sensors and TOF sensors. Then the working principle of TOF sensors, fabrication schemes of TOF structures, novel TOF structures in recent years, and the growing emerging application areas are described. Finally, the development trends and challenges of TOF sensors are prospected. The objective of this review is to convey novel perspectives and strategies for the performance optimization and design of TOF sensors based on fiber-optic sensing technologies.
ARTICLE | doi:10.20944/preprints201911.0147.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: endometriosis; microbiome; 16s-rrna sequencing; atopobium
Online: 13 November 2019 (11:42:32 CET)
Abstract Objective: Endometriosis is a chronic disease characterized by the growth of endometrial cells outside the uterine cavity. The dysfunction of the immune system is strongly associated with the progression of endometriosis, and is also correlated to the diversity of microbiota in the genital tract. According to previous studies, the microbiota significantly contributes to multi-systemic function, but the evidence of endometriosis and adenomyosis remains insufficient. Thus, the present study attempted to identify the characteristics of microbiota in endometriosis patients, and the connection between microbiota and immunological dysfunction. Methods: In order to compare and explore the potential microbiota correlated to endometriosis and adenomyosis in the genital tract, 134 samples obtained from the cervical canal, posterior fornix and uterine cavity were analyzed by 16s-rRNA sequencing. The raw data was filtered, analyzed and visualized, and bio-information methods were used to identify the different and distinctive characteristics of microbiota. Results: Two different locations near the cervix, cervical canal and posterior fornix, exhibited no differences in alpha diversity. Among the different disease groups, five microbiota were distinctive in the genus level, and Atopobium presented with the greatest significance in adenomyoisis-endometriosis patients. The LEfSe analysis failed to identify the special biomarkers, while several characteristic functions were identified through PICRUSt. Conclusion: Lactobacillus is dominant in the female lower genital tract, and Atopobium is distinctively higher in patients with endometriosis combined with adenomyosis. Several different functions of microbiota were explored, and these are found to be associated with endometriosis and adenomyosis. These findings may provide a new concept of microbiota/immune system/endometriosis system. There is an urgent need to investigate the potential microbial biomarkers of endometriosis in the future.
ARTICLE | doi:10.20944/preprints202112.0359.v1
Subject: Chemistry And Materials Science, Surfaces, Coatings And Films Keywords: 6H-SiC; the first principles; copper matrix composites; electronic properties
Online: 22 December 2021 (12:06:53 CET)
The interfacial mechanics and electrical properties of the SiC reinforced copper matrix composites were studied via the first principles method. The work of adhesion (Wad) and the interfacial energies were calculated to evaluate the stabilities of the SiC/Cu interfacial models. The carbon terminated (CT)-SiC/Cu interfaces were predicted more stable than those of the silicon terminated (ST)-SiC/Cu from the results of the Wad and interfacial energies. The interfacial electron properties of SiC/Cu were studied via the charge density distribution, charge density difference, electron localized functions and partial density of the state. The covalent C-Cu bonds were formed based on the results of the electron properties, which further explained the fact that the interfaces of the CT-SiC/Cu are stable than those of the ST-SiC/Cu. The interfacial mechanics of the SiC/Cu were investigated via the interfacial fracture toughness and ultimate tensile stress, and the results indicate that both CT- and ST-SiC/Cu interfaces are hard to fracture. The ultimate tensile stress of the CT-SiC/Cu is nearly 23GPa, which is smaller than those of the ST-SiC/Cu of 25 GPa. The strains corresponding to their ultimate tensile stresses of the CT- and ST-SiC/Cu are about 0.28 and 0.26, respectively. The higher strains of CT-SiC/Cu indicate their stronger plastic properties on the interfaces of the composites.
ARTICLE | doi:10.20944/preprints202003.0286.v1
Subject: Medicine And Pharmacology, Pharmacy Keywords: COVID-2019; SARS-CoV-2; repurposing; network bioinformatics
Online: 18 March 2020 (08:50:10 CET)
The COVID-2019 disease caused by the SARS-CoV-2 virus (aka 2019-nCoV) has raised significant health concerns in China and worldwide. While novel drug discovery and vaccine studies are long, repurposing old drugs against the COVID-2019 epidemic can help identify treatments, with known preclinical, pharmacokinetic, pharmacodynamic, and toxicity profiles, which can rapidly enter Phase 3 or 4 or can be used directly in clinical settings. In this study, we presented a novel network based drug repurposing platform to identify potential drugs for the treatment of COVID-2019. We first analysed the genome sequence of SARS-CoV-2 and identified SARS as the closest disease, based on genome similarity between both causal viruses, followed by MERS and other human coronavirus diseases. Using our AutoSeed pipeline (text mining and database searches), we obtained 34 COVID-2019-related genes. Taking those genes as seeds, we automatically built a molecular network for which our module detection and drug prioritization algorithms identified 24 disease-related human pathways, five modules and finally suggested 78 drugs to repurpose. Following manual filtering based on clinical knowledge, we re-prioritized 30 potential repurposable drugs against COVID-2019 (including pseudoephedrine, andrographolide, chloroquine, abacavir, and thalidomide) . We hope that this data can provide critical insights into SARS-CoV-2 biology and help design rapid clinical trials of treatments against COVID-2019.
ARTICLE | doi:10.20944/preprints201703.0181.v1
Subject: Chemistry And Materials Science, Food Chemistry Keywords: total aflatoxin; quantum dot nanobead; test strip; on-site; peanut and rice; agro-food safety
Online: 24 March 2017 (03:59:06 CET)
An on-site, ultra-sensitive, and quantitative sensing method was developed based on quantum dot nanobeads (QDNBs) and test strip for the determination of total aflatoxins (AFTs) in rice and peanut. The monoclonal antibody against AFT (mAbAFT) was home-made and labeled with QDNB. After the pre-coating of the AFT antigen on the test line (T line), the competitive immunoreactions were conducted between AFT and AFT antigen on the T line with QDNBs-mAbAFT. Under optimal conditions, this approach allowed a rapid response towards AFT with a considerable sensitivity of 1.4 pg/mL and 2.9 pg/mL in rice and peanut matrices, respectively. The put-in and put-out duration were within 10 min. The recoveries for AFT in rice and peanut samples matrices were recorded from 86.25–118.0% with the relative deviations (RSD) below 12%. The assay was further validated via the comparison between this QDNB strip and the conventional HPLC method using spiked samples. Thus, the design provided a potential alternative for on-site, ultra-sensitive, and quantitative sensing of AFT that could also be expanded to other chemical contaminants for food safety.
ARTICLE | doi:10.20944/preprints202309.1163.v1
Subject: Biology And Life Sciences, Virology Keywords: viral metagenomics; black-necked crane; genomic structure; phylogenetic analysis
Online: 18 September 2023 (11:52:56 CEST)
The black-necked crane is the only species that lives in the plateau. At present, there is little re-search on viral diseases of the black-necked crane. In this study, a virus metagenomics approach was employed to investigate the viral composition of black-necked cranes in Saga County, Shi-gatse City, Tibet, China. The identified virus families carried by black-necked cranes mainly in-clude Genomoviridae, Parvoviridae, and Picornaviridae. Among them, one picornavirus genome is characterized as a novel species in the genus Grusopivirus of the family Picornaviridae, four new parvoviruses genome were obtained and classified into four different novel species within the genus Chaphamaparvovirus of the subfamily Hamaparvovirinae, and four novel genomoviruses ge-nome were also acquired and identified as members of three different species including Ge-mykroznavirus haeme1, Gemycircularvirus ptero6, and Gemycircularvirus ptero10. All of these viruses were firstly detected in fecal samples of black-necked cranes. This study provides valuable in-formation for understanding the viral community composition in the digestive tract of black-necked cranes in Tibet and for monitoring, preventing, and treating black-necked cranes viral diseases.