IEAtlas: an atlas of HLA-presented immune epitopes derived from non-coding regions.

Cancer-related epitopes can engage the immune system against tumor cells, thus exploring epitopes derived from non-coding regions is emerging as a fascinating field in cancer immunotherapies. Here, we described a database, IEAtlas (http://bio-bigdata.hrbmu.edu.cn/IEAtlas), which aims to provide and visualize the comprehensive atlas of human leukocyte antigen (HLA)-presented immunogenic epitopes derived from non-coding regions. IEAtlas reanalyzed publicly available mass spectrometry-based HLA immunopeptidome datasets against our integrated benchmarked non-canonical open reading frame information. The current IEAtlas identified 245 870 non-canonical epitopes binding to HLA-I/II allotypes across 15 cancer types and 30 non-cancerous tissues, greatly expanding the cancer immunopeptidome. IEAtlas further evaluates the immunogenicity via several commonly used immunogenic features, including HLA binding affinity, stability and T-cell receptor recognition. In addition, IEAtlas provides the biochemical properties of epitopes as well as the clinical relevance of corresponding genes across major cancer types and normal tissues. Several flexible tools were also developed to aid retrieval and to analyze the epitopes derived from non-coding regions. Overall, IEAtlas will serve as a valuable resource for investigating the immunogenic capacity of non-canonical epitopes and the potential as therapeutic cancer vaccines.

Pressure-Driven Polymorphic Transition, Emergent Insulator-To-Metal Transition, and Photoconductivity Switching in Violet Phosphorus.

Polymorphic phase transition is an essential phenomenon in condensed matter that the physical properties of materials may undergo significant changes due to the structural transformation. Phase transition has thus become an important means and dimension for regulating material properties. Herein, this study demonstrates the pressure-induced multi-transition of both structure and physical properties in violet phosphorus, a novel phosphorus allotrope. Under compression, violet phosphorus undergoes sequential polymorphic phase transitions. Concomitant with the first phase transition, violet phosphorus exhibits emergent insulator-metal transition, superconductivity, and dramatic switching from positive to negative photoconductivity. Remarkably, the resistance of violet phosphorus shows a sudden drop of around 107 along with the phase transition. In addition, piezochromism from translucent red to opaque black and suppression of photoluminescence are observed upon compression. Of particular interest is that the sample irreversibly transforms into black phosphorus with a pronounced discrepancy in physical properties from the pristine violet phosphorus after decompression. The abundant polymorphic transitions and property changes in violet phosphorus have significant implications for designing novel pressure-responsive electronic/optoelectronic devices and exploring concealed polymorphic transition materials.

The profile of HIV-1 drug resistance in Shanghai, China: a retrospective study from 2017 to 2021.

BACKGROUND: HIV-1 drug resistance is a huge challenge in the era of ART. OBJECTIVES: To investigate the prevalence and characteristics of acquired HIV-1 drug resistance (ADR) in Shanghai, China. METHODS: An epidemiological study was performed among people living with human immunodeficiency virus (PLWH) receiving ART in Shanghai from January 2017 to December 2021. A total of 8669 PLWH were tested for drug resistance by genotypic resistance testing. Drug resistance mutations (DRMs) were identified using the Stanford University HIV Drug Resistance Database program. RESULTS: Ten HIV-1 subtypes/circulating recombinant forms (CRFs) were identified, mainly including CRF01_AE (46.8%), CRF07_BC (35.7%), B (6.4%), CRF55_01B (2.8%) and CRF08_BC (2.4%). The prevalence of ADR was 48% (389/811). Three NRTI-associated mutations (M184V/I/L, S68G/N/R and K65R/N) and four NNRTI-associated mutations (V179D/E/T/L, K103N/R/S/T, V106M/I/A and G190A/S/T/C/D/E/Q) were the most common DRMs. These DRMs caused high-level resistance to lamivudine, emtricitabine, efavirenz and nevirapine. The DRM profiles appeared to be significantly different among different subtypes. CONCLUSIONS: We revealed HIV-1 subtype characteristics and the DRM profile in Shanghai, which provide crucial guidance for clinical treatment and management of PLWH.

Proposals for gas-detection improvement of the FeMPc monolayer towards ethylene and formaldehyde by using bimetallic synergy.

Development and fabrication of a novel gas sensor with superb performance are crucial for enabling real-time monitoring of ethylene (C2H4) and formaldehyde (H2CO) emissions from industrial manufacture. Herein, first-principles calculations and AIMD simulations were carried out to investigate the effect of the Fe-M dimer on the adsorption of C2H4 and H2CO on metal dimer phthalocyanine (FeMPc, M = Ti-Zn) monolayers, and the electronic structures and sensing properties of the above adsorption systems were systematically discussed. The results show that the FeMPc (M = Ti, V, Cr, Mn) monolayers interact with C2H4 and H2CO by chemisorption except for the FeMnPc/H2CO system, while the other adsorption systems are all characterized by physisorption. Interestingly, the adsorption strength of C2H4 and H2CO can be effectively regulated by the bimetallic synergy of the Fe-M dimer. Moreover, the FeCrPc and FeMnPc monolayers exhibit excellent sensitivity towards C2H4 and H2CO, and have short recovery time (4.69 ms-2.31 s) for these gases at room temperature due to the effective surface diffusion at 300 K. Consequently, the FeCrPc and FeMnPc materials can be utilized as high-performance, reusable gas sensors for detecting C2H4 and H2CO, and have promising applications in monitoring the release of ethylene and formaldehyde from industrial processes.

Design, synthesis, and anti-oomycete activity of 3-acyloxymaltol/ethyl maltol derivatives.

Twenty 3-acyloxymaltol/ethyl maltol derivatives (7a-j and 8a-j) were synthesized and evaluated in vitro for their anti-oomycete activity against Phytophthora capsici, respectively. Among all of twenty derivatives, more than half of the compounds 7f, 7h, 8a-h and 8j had anti-oomycete activity higher than the positive control zoxamide (EC50 = 22.23 mg/L), and the EC50 values of 18.66, 20.32, 12.80, 16.18, 10.59, 14.98, 16.80, 10.36, 15.32, 12.64, and 13.59 mg/L, respectively. Especially, compounds 8c and 8f exhibited the best anti-oomycete activity against P. capsici with EC50 values of 10.59 and 10.36 mg/L, respectively. Overall, hydroxyl group of maltol/ethyl maltol is important active modification site.

Novel Circovirus in Blood from Intravenous Drug Users, Yunnan, China.

We identified a novel circovirus (human-associated circovirus 2 [HuCV2]) from the blood of 2 intravenous drug users in China who were infected with HIV-1, hepatitis C virus, or both. HuCV2 is most closely related to porcine circovirus 3. Our findings underscore the risk for HuCV2 and other emerging viruses among this population.

Poor pretransplantation minimal residual disease clearance as an independent prognostic risk factor for survival in myelodysplastic syndrome with excess blasts: A multicenter, retrospective cohort study.

BACKGROUND: Minimal residual disease (MRD) is an important prognostic factor for survival in adults with acute leukemia. The role of pretransplantation MRD status in myelodysplastic syndrome with excess blasts (MDS-EB) is unknown. This study retrospectively analyzed the relationship between pretransplantation MRD status and long-term survival. MATERIALS AND METHODS: Patients with MDS-EB who underwent allogeneic hematopoietic stem cell transplantation (allo-HSCT) from March 5, 2005, to November 8, 2020, were included. The relationship between pretransplantation MRD status and long-term survival was analyzed using univariate and multivariate logistic regression models. RESULTS: Of 220 patients with MDS-EB who underwent allo-HSCT, 198 were eligible for inclusion in this multicenter, retrospective cohort study. Complete remission was attained in 121 (61.1%) patients, and 103 patients underwent detection of MRD pretransplantation, with 67 patients being MRD-positive and 36 patients being MRD-negative. The median follow-up time was 16 months, the median age was 41 years (6-65 years), and 58% of the patients were men. The 3-year disease-free survival (DFS) and overall survival (OS) probabilities for all patients were 70.1% and 72.9%, respectively. For patients in complete remission, the 3-year DFS and OS probabilities were 72.2% and 74.8%, respectively. Further analysis found that the 3-year DFS rates of MRD-negative and MRD-positive patients were 85.6% and 66.5% (p = .045), respectively, whereas the 3-year OS rates were 91.3% and 66.4% (p = .035), respectively. Univariate and multivariate analyses showed that poor pretransplantation MRD clearance was an independent prognostic risk factor for DFS and OS. CONCLUSION: Poor pretransplantation MRD clearance is an independent prognostic risk factor for long-term survival after allo-HSCT for patients with MDS-EB. PLAIN LANGUAGE SUMMARY: Poor minimal residual disease clearance pretransplanation is an independent prognostic risk factor for long-term survival after allogeneic hematopoietic stem cell transplantation for patients with myelodysplastic syndrome with excess blasts.

Augmentation of 3ß-hydroxysteroid-Δ24 Reductase (DHCR24) Expression Induced by Bovine Viral Diarrhea Virus Infection Facilitates Viral Replication via Promoting Cholesterol Synthesis.

Bovine viral diarrhea virus (BVDV) is the etiologic agent of bovine viral diarrhea-mucosal disease, one of the most important viral diseases of cattle, leading to numerous losses to the cattle rearing industry worldwide. The pathogenicity of BVDV is extremely complex, and many underlying mechanisms involved in BVDV-host interactions are poorly understood, especially how BVDV utilizes host metabolism pathway for efficient viral replication and spread. In our previous study, using an integrative analysis of transcriptomics and proteomics, we found that DHCR24 (3ß-hydroxysteroid-Δ24 reductase), a key enzyme in regulating cholesterol synthesis, was significantly upregulated at both gene and protein levels in the BVDV-infected bovine cells, indicating that cholesterol is important for BVDV replication. In the present study, the effects of DHCR24-mediated cholesterol synthesis on BVDV replication was explored. Our results showed that overexpression of the DHCR24 effectively promoted cholesterol synthesis, as well as BVDV replication, while acute cholesterol depletion in the bovine cells by treating cells with methyl-ß-cyclodextrin (MßCD) obviously inhibited BVDV replication. In addition, knockdown of DHCR24 (gene silencing with siRNA targeting DHCR24, siDHCR24) or chemical inhibition (treating bovine cells with U18666A, an inhibitor of DHCR24 activity and cholesterol synthesis) significantly suppressed BVDV replication, whereas supplementation with exogenous cholesterol to the siDHCR24-transfected or U18666A-treated bovine cells remarkably restored viral replication. We further confirmed that BVDV nonstructural protein NS5A contributed to the augmentation of DHCR24 expression. Conclusively, augmentation of the DHCR24 induced by BVDV infection plays an important role in BVDV replication via promoting cholesterol production. IMPORTANCE Bovine viral diarrhea virus (BVDV), an important pathogen of cattle, is the causative agent of bovine viral diarrhea-mucosal disease, which causes extensive economic losses in both cow- and beef-rearing industry worldwide. The molecular interactions between BVDV and its host are extremely complex. In our previous study, we found that an essential host factor 3ß-hydroxysteroid-δ24 reductase (DHCR24), a key enzyme involved in cholesterol synthesis, was significantly upregulated at both gene and protein levels in BVDV-infected bovine cells. Here, we experimentally explored the function of the DHCR24-mediated cholesterol synthesis in regulating BVDV replication. We elucidated that the augmentation of the DHCR24 induced by BVDV infection played a significant role in viral replication via promoting cholesterol synthesis. Our data provide evidence that BVDV utilizes a host metabolism pathway to facilitate its replication and spread.

Evaluation of Commercially Available Machine Interpretation Applications for Simple Clinical Communication.

BACKGROUND: Accessing professional medical interpreters for brief, low risk exchanges can be challenging. Machine translation (MT) for verbal communication has the potential to be a useful clinical tool, but few evaluations exist. OBJECTIVE: We evaluated the quality of three MT applications for English-Spanish and English-Mandarin two-way interpretation of low complexity brief clinical communication compared with human interpretation. DESIGN: Audio-taped phrases were interpreted via human and 3 MT applications. Bilingual assessors evaluated the quality of MT interpretation on four assessment categories (accuracy, fluency, meaning, and clinical risk) using 5-point Likert scales. We used a non-inferiority design with 15% inferiority margin to evaluate the quality of three MT applications with professional medical interpreters serving as gold standards. MAIN MEASURES: Proportion of interpretation exchanges deemed acceptable, defined as a composite score of 16 or greater out of 20 based on the four assessment categories. KEY RESULTS: For English to Spanish, the proportion of MT-interpreted phrases scored as acceptable ranged from 0.68 to 0.84, while for English to Mandarin, the range was from 0.62 to 0.76. Both Spanish/Mandarin to English MT interpretation had low acceptable scores (range 0.36 to 0.41). No MT interpretation met the non-inferiority threshold. CONCLUSION: While MT interpretation was better for English to Spanish or Mandarin than the reverse, the overall quality of MT interpretation was poor for two-way clinical communication. Clinicians should advocate for easier access to professional interpretation in all clinical spaces and defer use of MT until these applications improve.

Proinflammatory Polarization of Macrophages Causes Intestinal Inflammation in Low-Birth-Weight Piglets and Mice.

BACKGROUND: Low-birth-weight (LBW) animals suffer from intestinal damage and inflammation in their early life. OBJECTIVES: The aim of this study was to investigate the role of macrophages in intestinal inflammation in LBW piglets and mice. METHODS: Major genes involved in intestinal barrier function such as claudin-1, zonula occludens-1 (ZO-1), occludin, and mucin 2 and inflammatory cytokines such as IL-1ß, TNF-α, IL-10, and IL-13 were evaluated in 21-day-old, normal-birth-weight (NBW) and LBW piglets and mice. Macrophage markers such as CD16/32, CD163, and CD206 were also assessed by immunofluorescence and flow cytometry. Polarized and unpolarized macrophages were further transferred into NBW and LBW mice, followed by an evaluation of intestinal permeability and inflammation. RESULTS: Claudin-1 mRNA in LBW piglets as well as claudin-1, occludin, ZO-1, and mucin 2 mRNAs in LBW mice, was significantly downregulated. IL-1ß and TNF-α were significantly upregulated in LBW piglets (P < 0.05). LBW mice showed a reduced expression of IL-10 and IL-13 (P < 0.05), with a heightened IL-6 level (P < 0.01) in the jejunum. CD16, a marker for M1 macrophages, was significantly elevated in the jejunum of LBW piglets, whereas CD163, a marker for M2 macrophages, was significantly decreased (P < 0.05). Similarly, LBW mice had more CD11b+CD16/32+ M1 macrophages (P < 0.05) and fewer CD206+ M2 macrophages (P < 0.01) than NBW mice. Moreover, the transfer of M1 macrophages exacerbated intestinal inflammation in LBW mice. Furthermore, 2 major glycolysis-associated genes, hexokinase 2 (HK2) and lactate dehydrogenase A (LDHA), were significantly upregulated in LBW piglets and mice (P < 0.05). CONCLUSIONS: This study revealed for the first time that the intestinal macrophages are polarized toward a proinflammatory phenotype in LBW piglets and mice, contributing to intestinal inflammation. The findings of this study provide new options for the management of intestinal inflammation in LBW animals.

Novel third-generation tyrosine kinase inhibitor for newly diagnosed Philadelphia chromosome-positive acute lymphoblastic leukemia: a case study.

Although Philadelphia chromosome-positive acute leukemia (Ph + -ALL) has been revolutionized with tyrosine kinase inhibitors (TKIs), resistance and mutation are universal events during treatment with first-generation and second-generation TKIs. The present third-generation TKI has a dose-dependent, increased risk of serious cardiovascular events and the sensitivity is poor for patients with ≥2 mutations accompanied by the T315I mutation. Thus, novel and well-tolerated TKIs should be explored. This study analyzes the efficacy and advert effects of olverembatinib, a novel third TKI, in the treatment of newly diagnosed adult Ph + -ALL in induction therapy. Four adult patients with newly diagnosed Ph + -ALL were treated with olverembatinib as the first-line treatment. For induction therapy, these patients received 40 mg of oral olverembatinib quaque omni die for 28 days, 1 mg/kg/d of prednisone for 14 days, then tapered and stopped at 28 days and vindesine 4 mg/d at days 1, 8 and 15. After induction therapy, these patients received median or high-dose of cytarabine and methotrexate combined with oral olverembatinib as consolidation therapy. Then the allogeneic hematopoietic stem cell transplantation (allo-HSCT) was performed. All patients reached complete remission with a complete cytogenetic response after induction therapy. Two patients reached major molecular remission and one with complete molecular remission. Before allo-HSCT, all the patients achieved complete molecular remission. All the patients have survived disease-free for 3-6 months. No severe advert effects were observed. It is well-tolerated and effective for olverembatinib in the treatment of newly diagnosed adult patients with Ph + -ALL. A prospective study should be performed to further testify the role.

Application of spectroscopic techniques combined with chemometrics to the authenticity and quality attributes of rice.

Rice is a staple food for two-thirds of the world's population and is grown in over a hundred countries around the world. Due to its large scale, it is vulnerable to adulteration. In addition, the quality attribute of rice is an important factor affecting the circulation and price, which is also paid more and more attention. The combination of spectroscopy and chemometrics enables rapid detection of authenticity and quality attributes in rice. This article described the application of seven spectroscopic techniques combined with chemometrics to the rice industry. For a long time, near-infrared spectroscopy and linear chemometric methods (e.g., PLSR and PLS-DA) have been widely used in the rice industry. Although some studies have achieved good accuracy, with models in many studies having greater than 90% accuracy. However, higher accuracy and stability were more likely to be obtained using multiple spectroscopic techniques, nonlinear chemometric methods, and key wavelength selection algorithms. Future research should develop larger rice databases to include more rice varieties and larger amounts of rice depending on the type of rice, and then combine various spectroscopic techniques, nonlinear chemometric methods, and key wavelength selection algorithms. This article provided a reference for a more efficient and accurate determination of rice quality and authenticity.

Accelerated Design for High-Entropy Alloys Based on Machine Learning and Multiobjective Optimization.

High-entropy alloys (HEAs) with high hardness and high ductility can be considered as candidates for wear-resistant applications. However, designing novel HEAs with multiple desired properties using traditional alloy design methods remains challenging due to the enormous composition space. In this work, we proposed a machine-learning-based framework to design HEAs with high Vickers hardness (H) and high compressive fracture strain (D). Initially, we constructed data sets containing 172,467 data with 161 features for D and H, respectively. Four-step feature selection was performed, with the selection of 12 and 8 features for the D and H prediction models based on the optimal algorithms of the support vector machine (SVR) and light gradient boosting machine (LightGBM), respectively. The R2 of the well-trained models reached 0.76 and 0.90 for the 10-fold cross validation. Nondominated sorting genetic algorithm version II (NSGA-II) and virtual screening were employed to search for the optimal alloying compositions, and four recommended candidates were synthesized to validate our methods. Notably, the D of three candidates have shown significant improvements compared to the samples with similar H in the original data sets, with increases of 135.8, 282.4, and 194.1% respectively. Analyzing the candidates, we have recommended suitable atomic percentage ranges for elements such as Al (2-14.8 at %), Nb (4-25 at %), and Mo (3-9.9 at %) in order to design HEAs with high hardness and ductility.

Short-term exposure to ambient fine particulate pollution aggravates ventilator-associated pneumonia in pediatric intensive care patients undergoing cardiovascular surgeries.

BACKGROUND: Ambient air pollutants can be hazardous to human health, especially for vulnerable children. The impact of ambient air pollutant exposure before and during intensive care unit (ICU) stays on the development of ventilator-associated pneumonia (VAP) in critically ill children has not been established. We aimed to determine the correlations between short-term exposures to ambient fine particulate matter (PM2.5) and VAP in pediatric cardiac surgery patients in the ICU, and explore the effect of delayed exposure. METHODS: The medical record of 1755 child patients requiring artificial ventilation in the ICU between December 2013 to December 2020, were analyzed. The daily average concentrations of particulate matters (PM2.5 and PM10), sulfur dioxide (SO2), and ozone (O3) were calculated from public data. Interactions between these pollutants and VAP were simulated with the distributed lag non-linear model. RESULTS: Three hundred forty-eight cases (19.829%) of VAP were identified in this study, while the average concentrations of PM2.5, PM10, O3 and SO2 were 58, 118, 98 and 26 µg/m3, respectively. Exposure to increased levels of PM2.5 two days prior (lag 2-day) to VAP diagnosis is significantly correlated with an enhanced risk for VAP development. Even a slight increase of 10 µg/m3 in PM2.5 can translate to a 5.4% increase in VAP incidence (95% CI: 1.4%-9.5%) while the VAP incidence increased to 11.1% (95%CI: 4.5-19.5%) when PM2.5 concentration is well below the National Ambient Air Quality standard (NAAQS) of 50 µg/m3. The association was more pronounced in those aged below 3-months, with low body mass index or suffered from pulmonary arterial hypertension. CONCLUSION: Short-term PM2.5 exposure is a significant risk for development of VAP in pediatric patients. This risk is present even with PM2.5 levels below the NAAQS. Ambient PM2.5 may represent a previously unrecognized risk factor for pneumonia and the current environmental pollution standards need to be reevaluated to consider susceptible populations. TRIAL REGISTRATION: The trial was registered with the National Clinical Trial Center: The correlation between ambient air pollution and the complications in ICU underwent cardiac surgery. TRIAL REGISTRATION NUMBER: ChiCTR2000030507. Date of registration: March 5, 2020. URL of trial registry record: http://www.chictr.org.cn/index.aspx .

Tumor microenvironment-responsive spherical nucleic acid nanoparticles for enhanced chemo-immunotherapy.

Certain chemotherapeutics can induce tumor cells' immunogenic cell death (ICD), release tumor antigens, and thereby trigger personalized antitumor immune responses. Co-delivery of adjuvants using nanocarriers could amplify the ICD-induced tumor-specific immunity achieving a synergistic chemo-immunotherapeutic effect. However, complicated preparation, low drug loading efficiency, and potential carrier-associated toxicity are the major challenges that limited its clinical applications. Herein, a carrier-free core-shell nanoparticle (MPLA-CpG-sMMP9-DOX, MCMD NPs) was constructed by facile self-assembly of spherical nucleic acids (SNA) with two adjuvants of CpG ODN and monophosphoryl lipid A (MPLA) as a core and doxorubicin (DOX) radially around the dual-adjuvants SNA as a shell. The results demonstrated that MCMD NPs could enhance drugs accumulation in tumors, and release DOX upon enzymatic degradation of matrix metalloproteinase-9 (MMP-9) peptide in the tumor microenvironment (TME), which enhanced the direct-killing effect of DOX on tumor cells. The core of MPLA-CpG SNA efficiently boosted the ICD-induced antitumor immune response to further attack tumor cells. Thus, MCMD NPs achieved a synergistic therapeutic effect of chemo-immunotherapy with reduced off-target toxicity. This study provided an efficient strategy for the development of a carrier-free nano-delivery system for enhanced cancer chemo-immunotherapy.

Diagnostic value of high-risk HPV E6/E7 mRNA in patients with ASCUS.

OBJECTIVE: To investigate the infection status of high-risk human papillomavirus (HR-HPV) E6/E7 mRNA in patients with a cytological diagnosis of "atypical squamous cells of undetermined significance" (ASCUS) and to analyze the pathogenic rate of different high-risk HPV subtypes combined with biopsy pathological results to provide a more accurate basis for managing ASCUS patients. METHODS: A total of 1387 patients with ASCUS and HPV E6/E7 mRNA positivity who were referred for colposcopy were retrospectively analyzed. They were divided into HPV16+, 18/45 + and other HR-HPV + groups premenopausal and postmenopausal groups. The pathological results of the biopsy were divided into the LSIL- group (including normal and low-grade squamous intraepithelial lesions) and the HSIL + group (including high-grade squamous intraepithelial lesions and higher lesions). SPSS was used for the analysis. RESULTS: The age group 31-40 years had the highest level of HPV16+, and HPV18/45 + was the highest in the 41-50 years group. The detection rates of HSIL + in the HPV16+, HPV18/45+, HPV 16/18/45 + and Other HR-HPV + groups were 48.4%, 18.8%, 43.9% and 15.0%, respectively. The infection rates of HPV16/18/45 in postmenopausal and premenopausal women were 42.4% and 34.3%, respectively. In the HPV18/45 group, the incidence of HSIL + was 30.0% in postmenopausal women and 15.0% in premenopausal women (P < 0.01). In the HPV 16 + and Other HR-HPV + groups, the incidence of HSIL + in postmenopausal patients was not significantly different from that in premenopausal patients. The incidence of cervical cancer in postmenopausal patients is significantly higher than that in premenopausal patients. CONCLUSIONS: Colposcopy referral or further biopsy is recommended for all ASCUS patients with HPV16/18/45E6/E7 mRNA positivity and postmenopausal patients with HR-HPVE6/E7 mRNA positivity. For premenopausal ASCUS patients with other HR-HPV E6/E7 mRNA positivity, colposcopy should be performed if possible, depending on the specific situation, to achieve early detection and diagnosis.

Measuring the worldwide spread of COVID-19 using a comprehensive modeling method.

BACKGROUND: With the global spread of COVID-19, detecting high-risk countries/regions timely and dynamically is essential; therefore, we sought to develop automatic, quantitative and scalable analysis methods to observe and estimate COVID-19 spread worldwide and further generate reliable and timely decision-making support for public health management using a comprehensive modeling method based on multiple mathematical models. METHODS: We collected global COVID-19 epidemic data reported from January 23 to September 30, 2020, to observe and estimate its possible spread trends. Countries were divided into three outbreak levels: high, middle, and low. Trends analysis was performed by calculating the growth rate, and then country grouping was implemented using group-based trajectory modeling on the three levels. Individual countries from each group were also chosen to further disclose the outbreak situations using two predicting models: the logistic growth model and the SEIR model. RESULTS: All 187 observed countries' trajectory subgroups were identified using two grouping strategies: with and without population consideration. By measuring epidemic trends and predicting the epidemic size and peak of individual countries, our study found that the logistic growth model generally estimated a smaller epidemic size than the SEIR model. According to SEIR modeling, confirmed cases in each country would take an average of 9-12 months to reach the outbreak peak from the day the first case occurred. Additionally, the average number of cases at the peak time will reach approximately 10-20% of the countries' populations, and the countries with high trends and a high predicted size must pay special attention and implement public health interventions in a timely manner. CONCLUSIONS: We demonstrated comprehensive observations and predictions of the COVID-19 outbreak in 187 countries using a comprehensive modeling method. The methods proposed in this study can measure COVID-19 development from multiple perspectives and are generalizable to other epidemic diseases. Furthermore, the methods also provide reliable and timely decision-making support for public health management.

Functionalized Fullerene Potentially Inhibits SARS-CoV-2 Infection by Modulating Spike Protein Conformational Changes.

The disease of SARS-CoV-2 has caused considerable morbidity and mortality globally. Spike proteins on the surface of SARS-CoV-2 allow it to bind with human cells, leading to infection. Fullerenes and their derivatives are promising SARS-CoV-2 inhibitors and drug-delivery vehicles. In this study, Gaussian accelerated molecular dynamics simulations and the Markov state model were employed to delve into the inhibitory mechanism of Fullerene-linear-polyglycerol-b-amine sulfate (F-LGPS) on spike proteins. During the study, it was discovered that fullerene derivatives can operate at the interface of the receptor-binding domain (RBD) and the N-terminal domain (NTD), keeping structural domains in a downward conformation. It was also observed that F-LGPS demonstrated superior inhibitory effects on the XBB variant in comparison to the wild-type variant. This study yielded invaluable insights for the potential development of efficient therapeutics targeting the spike protein of SARS-CoV-2.

Probing the Mechanisms of Inhibitors Binding to Presenilin Homologue Using Molecular Dynamics Simulations.

γ-secretase is an intramembrane proteolytic enzyme that is mainly involved in the cleavage and hydrolysis of the amyloid precursor (APP). The catalytic subunit presenilin 1 (PS1) is the catalytic subunit of γ-secretase. Since it was found that PS1 is responsible for Aß-producing proteolytic activity, which is involved in Alzheimer's disease, it is believed that reducing the activity of PS1 and preventing or delaying the production of Aß could help treat Alzheimer's disease. Consequently, in recent years, researchers have begun investigating the potential clinical efficacy of PS1 inhibitors. Currently, most PS1 inhibitors are only used as a tool to study the structure and function of PS1, and a few inhibitors with a high selectivity have been tested in clinics. Less-selective PS1 inhibitors were found to not only inhibit Aß production but also inhibit Notch cleavage, which led to serious adverse events. The archaeal presenilin homologue (PSH) is a surrogate protease of presenilin that is useful for agent screening. In this study, we performed 200 ns molecular dynamics simulations (MD) of four systems to explore the conformational changes of different ligands binding to PSH. Our results indicated that the PSH-L679 system formed 3-10 helices in TM4, loosening up TM4 and allowing substrates to enter the catalytic pocket, thereby making it less inhibitory. Additionally, we found that III-31-C can bring TM4 and TM6 closer, resulting in the contraction of the PSH active pocket. Altogether, these results provide the basis for the potential design of newer PS1 inhibitors.

Exploration of the Product Specificity of chitosanase CsnMY002 and Mutants Using Molecular Dynamics Simulations.

Chitosanase CsnMY002 is a new type of enzyme isolated from Bacillus subtilis that is used to prepare chitosan oligosaccharide. Although mutants G21R and G21K could increase Chitosan yield and thus increase the commercial value of the final product, the mechanism by which this happens is not known. Herein, we used molecular dynamics simulations to explore the conformational changes in CsnMY002 wild type and mutants when they bind substrates. The binding of substrate changed the conformation of protein, stretching and deforming the active and catalytic region. Additionally, the mutants caused different binding modes and catalysis, resulting in different degrees of polymerization of the final Chitooligosaccharide degradation product. Finally, Arg37, Ile145 ~ Gly148 and Trp204 are important catalytic residues of CsnMY002. Our study provides a basis for the engineering of chitosanases.